Starting phenix.real_space_refine on Sun May 11 14:59:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wv4_37864/05_2025/8wv4_37864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wv4_37864/05_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_37864/05_2025/8wv4_37864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wv4_37864/05_2025/8wv4_37864.map" model { file = "/net/cci-nas-00/data/ceres_data/8wv4_37864/05_2025/8wv4_37864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wv4_37864/05_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-5687/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: 3.47, per 1000 atoms: 0.42 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: 2.02 Conformation dependent library (CDL) restraints added in 1.2 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: 1.24 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: 2.21 Time building geometry restraints manager: 2.37 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: 2.390 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.170 Process input model: 20.120 Find NCS groups from input model: 0.160 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:2.580 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.440 ------------------------------------------------------------------------------- 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 : 0.923 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: 0.1914 time to fit residues: 63.4932 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 : 0.903 ------------------------------------------------------------------------------- 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 = 0.079408 restraints weight = 12604.380| |-----------------------------------------------------------------------------| r_work (start): 0.2718 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: 0.8608 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 0.60890 (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 : 0.923 Fit side-chains REVERT: A 101 GLU cc_start: 0.8899 (tt0) cc_final: 0.8504 (tt0) REVERT: A 172 ASN cc_start: 0.8684 (t0) cc_final: 0.8470 (t0) REVERT: A 175 TYR cc_start: 0.9031 (t80) cc_final: 0.8715 (t80) REVERT: A 190 LEU cc_start: 0.9173 (tp) cc_final: 0.8814 (mp) REVERT: B 59 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7906 (tp-100) REVERT: B 137 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8387 (mm-40) REVERT: C 190 LEU cc_start: 0.9197 (tp) cc_final: 0.8844 (mp) REVERT: D 62 GLU cc_start: 0.8946 (tp30) cc_final: 0.8640 (tp30) REVERT: D 125 TYR cc_start: 0.8903 (t80) cc_final: 0.8024 (t80) REVERT: D 137 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8408 (mm-40) REVERT: D 193 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: E 49 TYR cc_start: 0.9227 (p90) cc_final: 0.8971 (p90) REVERT: E 163 ASP cc_start: 0.8441 (p0) cc_final: 0.8196 (p0) outliers start: 16 outliers final: 10 residues processed: 168 average time/residue: 0.2052 time to fit residues: 46.5454 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 : 0.908 ------------------------------------------------------------------------------- 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: 0.0980 chunk 2 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 chunk 4 optimal weight: 0.8980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.3154 r_free = 0.3154 target = 0.102607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.083321 restraints weight = 12775.093| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.82 r_work: 0.2687 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2566 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= 0.096 Angle : 0.497 4.142 11415 Z= 0.276 Chirality : 0.048 0.164 1235 Planarity : 0.003 0.029 1450 Dihedral : 4.003 17.559 1100 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: -1.40 (0.25), residues: 1020 helix: 2.97 (0.69), residues: 55 sheet: -0.74 (0.32), residues: 280 loop : -1.40 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 162 HIS 0.003 0.001 HIS E 38 PHE 0.010 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 0.04223 ( 290) hydrogen bonds : angle 5.37636 ( 735) SS BOND : bond 0.00018 ( 5) SS BOND : angle 0.58115 ( 10) covalent geometry : bond 0.00224 ( 8390) covalent geometry : angle 0.49646 (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 172 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 1.005 Fit side-chains REVERT: A 101 GLU cc_start: 0.8615 (tt0) cc_final: 0.8245 (tt0) REVERT: A 175 TYR cc_start: 0.8919 (t80) cc_final: 0.8649 (t80) REVERT: A 190 LEU cc_start: 0.9197 (tp) cc_final: 0.8872 (mp) REVERT: B 137 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8007 (mm-40) REVERT: C 16 ASP cc_start: 0.8618 (p0) cc_final: 0.8413 (p0) REVERT: C 62 GLU cc_start: 0.8766 (tp30) cc_final: 0.8553 (tp30) REVERT: C 186 ASN cc_start: 0.8933 (t0) cc_final: 0.8374 (t0) REVERT: C 190 LEU cc_start: 0.9165 (tp) cc_final: 0.8904 (mp) REVERT: D 16 ASP cc_start: 0.8491 (p0) cc_final: 0.8225 (p0) REVERT: D 62 GLU cc_start: 0.8635 (tp30) cc_final: 0.8121 (tp30) REVERT: D 125 TYR cc_start: 0.8825 (t80) cc_final: 0.7899 (t80) REVERT: E 163 ASP cc_start: 0.8165 (p0) cc_final: 0.7940 (p0) REVERT: E 180 PHE cc_start: 0.8317 (p90) cc_final: 0.7937 (p90) outliers start: 8 outliers final: 4 residues processed: 170 average time/residue: 0.2117 time to fit residues: 48.6591 Evaluate side-chains 152 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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: 0.8980 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3121 r_free = 0.3121 target = 0.100413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.081404 restraints weight = 12657.864| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.77 r_work: 0.2663 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2772 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= 0.161 Angle : 0.511 4.158 11415 Z= 0.285 Chirality : 0.049 0.212 1235 Planarity : 0.003 0.029 1450 Dihedral : 4.064 19.363 1100 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.67 % Allowed : 10.67 % Favored : 87.67 % 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: 2.99 (0.68), residues: 55 sheet: -0.67 (0.32), residues: 280 loop : -1.17 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 162 HIS 0.003 0.001 HIS D 38 PHE 0.008 0.002 PHE D 180 TYR 0.017 0.002 TYR B 54 ARG 0.003 0.000 ARG E 6 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 290) hydrogen bonds : angle 5.25165 ( 735) SS BOND : bond 0.00273 ( 5) SS BOND : angle 0.72560 ( 10) covalent geometry : bond 0.00391 ( 8390) covalent geometry : angle 0.51085 (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 167 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 1.017 Fit side-chains REVERT: A 101 GLU cc_start: 0.8639 (tt0) cc_final: 0.8202 (tt0) REVERT: A 175 TYR cc_start: 0.8948 (t80) cc_final: 0.8602 (t80) REVERT: A 190 LEU cc_start: 0.9223 (tp) cc_final: 0.8830 (mp) REVERT: B 137 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8064 (mm-40) REVERT: B 190 LEU cc_start: 0.9177 (tp) cc_final: 0.8911 (mp) REVERT: C 186 ASN cc_start: 0.8951 (t0) cc_final: 0.8409 (t0) REVERT: C 190 LEU cc_start: 0.9206 (tp) cc_final: 0.8887 (mp) REVERT: D 16 ASP cc_start: 0.8481 (p0) cc_final: 0.8261 (p0) REVERT: D 62 GLU cc_start: 0.8770 (tp30) cc_final: 0.8186 (tp30) REVERT: D 125 TYR cc_start: 0.8834 (t80) cc_final: 0.7972 (t80) REVERT: E 163 ASP cc_start: 0.8208 (p0) cc_final: 0.7975 (p0) outliers start: 15 outliers final: 14 residues processed: 163 average time/residue: 0.2058 time to fit residues: 45.2749 Evaluate side-chains 162 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain E residue 198 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 79 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 195 GLN D 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.100750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.081759 restraints weight = 12629.922| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.76 r_work: 0.2706 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2846 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= 0.140 Angle : 0.495 4.173 11415 Z= 0.277 Chirality : 0.048 0.172 1235 Planarity : 0.004 0.050 1450 Dihedral : 4.026 19.332 1100 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.00 % Allowed : 11.44 % Favored : 86.56 % 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: -1.00 (0.26), residues: 1020 helix: 3.08 (0.68), residues: 55 sheet: -0.66 (0.32), residues: 280 loop : -1.01 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 162 HIS 0.003 0.001 HIS E 38 PHE 0.009 0.001 PHE D 180 TYR 0.018 0.001 TYR B 54 ARG 0.003 0.000 ARG E 6 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 290) hydrogen bonds : angle 5.18006 ( 735) SS BOND : bond 0.00231 ( 5) SS BOND : angle 0.92015 ( 10) covalent geometry : bond 0.00337 ( 8390) covalent geometry : angle 0.49484 (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 174 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.916 Fit side-chains REVERT: A 101 GLU cc_start: 0.8604 (tt0) cc_final: 0.8143 (tt0) REVERT: A 175 TYR cc_start: 0.8944 (t80) cc_final: 0.8606 (t80) REVERT: A 190 LEU cc_start: 0.9230 (tp) cc_final: 0.8853 (mp) REVERT: B 137 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8052 (mm-40) REVERT: B 190 LEU cc_start: 0.9217 (tp) cc_final: 0.8921 (mp) REVERT: C 16 ASP cc_start: 0.8614 (p0) cc_final: 0.8386 (p0) REVERT: C 62 GLU cc_start: 0.8837 (tp30) cc_final: 0.8637 (tp30) REVERT: C 186 ASN cc_start: 0.8954 (t0) cc_final: 0.8442 (t0) REVERT: C 190 LEU cc_start: 0.9188 (tp) cc_final: 0.8828 (mp) REVERT: D 16 ASP cc_start: 0.8450 (p0) cc_final: 0.8232 (p0) REVERT: D 62 GLU cc_start: 0.8855 (tp30) cc_final: 0.8291 (tp30) REVERT: D 125 TYR cc_start: 0.8834 (t80) cc_final: 0.7955 (t80) REVERT: D 190 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8784 (mp) REVERT: E 85 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8536 (mp0) REVERT: E 163 ASP cc_start: 0.8214 (p0) cc_final: 0.7974 (p0) REVERT: E 186 ASN cc_start: 0.8953 (t0) cc_final: 0.8629 (t0) outliers start: 18 outliers final: 16 residues processed: 168 average time/residue: 0.2101 time to fit residues: 47.8041 Evaluate side-chains 169 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 D residue 190 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 198 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 52 optimal weight: 0.0050 chunk 66 optimal weight: 6.9990 chunk 82 optimal weight: 0.2980 chunk 97 optimal weight: 0.3980 overall best weight: 1.9398 ------------------------------------------------------------------------------- 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 = 0.3091 r_free = 0.3091 target = 0.098552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.079582 restraints weight = 12683.997| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.76 r_work: 0.2659 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3037 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= 0.208 Angle : 0.537 4.471 11415 Z= 0.300 Chirality : 0.049 0.186 1235 Planarity : 0.004 0.049 1450 Dihedral : 4.297 21.122 1100 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.01 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: -1.21 (0.26), residues: 1020 helix: 3.16 (0.68), residues: 55 sheet: -0.98 (0.26), residues: 395 loop : -1.02 (0.25), residues: 570 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 0.010 0.002 PHE C 39 TYR 0.018 0.002 TYR B 54 ARG 0.002 0.000 ARG E 6 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 290) hydrogen bonds : angle 5.22932 ( 735) SS BOND : bond 0.00424 ( 5) SS BOND : angle 1.13571 ( 10) covalent geometry : bond 0.00501 ( 8390) covalent geometry : angle 0.53651 (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 167 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.931 Fit side-chains REVERT: A 101 GLU cc_start: 0.8601 (tt0) cc_final: 0.8329 (tt0) REVERT: A 175 TYR cc_start: 0.8969 (t80) cc_final: 0.8654 (t80) REVERT: A 190 LEU cc_start: 0.9241 (tp) cc_final: 0.8810 (mp) REVERT: B 137 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8160 (mm-40) REVERT: B 190 LEU cc_start: 0.9231 (tp) cc_final: 0.8877 (mp) REVERT: C 190 LEU cc_start: 0.9290 (tp) cc_final: 0.8900 (mp) REVERT: D 16 ASP cc_start: 0.8464 (p0) cc_final: 0.8261 (p0) REVERT: D 62 GLU cc_start: 0.8947 (tp30) cc_final: 0.8455 (tp30) REVERT: D 125 TYR cc_start: 0.8842 (t80) cc_final: 0.8024 (t80) REVERT: E 163 ASP cc_start: 0.8246 (p0) cc_final: 0.8009 (p0) outliers start: 18 outliers final: 15 residues processed: 162 average time/residue: 0.2097 time to fit residues: 45.6941 Evaluate side-chains 156 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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 198 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 0.0970 chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 overall best weight: 2.1182 ------------------------------------------------------------------------------- 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 = 0.3084 r_free = 0.3084 target = 0.098151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.079114 restraints weight = 12765.869| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.77 r_work: 0.2641 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3117 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= 0.223 Angle : 0.548 4.488 11415 Z= 0.305 Chirality : 0.050 0.181 1235 Planarity : 0.004 0.036 1450 Dihedral : 4.402 21.705 1100 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.44 % Allowed : 12.00 % 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: -1.21 (0.26), residues: 1020 helix: 3.13 (0.67), residues: 55 sheet: -0.98 (0.26), residues: 395 loop : -1.03 (0.25), residues: 570 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 0.021 0.002 TYR B 54 ARG 0.002 0.000 ARG C 118 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 290) hydrogen bonds : angle 5.22801 ( 735) SS BOND : bond 0.00394 ( 5) SS BOND : angle 1.23284 ( 10) covalent geometry : bond 0.00536 ( 8390) covalent geometry : angle 0.54737 (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 163 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.890 Fit side-chains REVERT: A 101 GLU cc_start: 0.8597 (tt0) cc_final: 0.8292 (tt0) REVERT: A 175 TYR cc_start: 0.9000 (t80) cc_final: 0.8728 (t80) REVERT: A 190 LEU cc_start: 0.9256 (tp) cc_final: 0.8835 (mp) REVERT: B 137 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8186 (mm-40) REVERT: B 190 LEU cc_start: 0.9239 (tp) cc_final: 0.8891 (mp) REVERT: D 62 GLU cc_start: 0.8966 (tp30) cc_final: 0.8488 (tp30) REVERT: D 125 TYR cc_start: 0.8844 (t80) cc_final: 0.7996 (t80) REVERT: E 163 ASP cc_start: 0.8232 (p0) cc_final: 0.7990 (p0) outliers start: 22 outliers final: 20 residues processed: 158 average time/residue: 0.2053 time to fit residues: 43.9657 Evaluate side-chains 161 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain E residue 198 VAL 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: 2.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 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 = 0.3091 r_free = 0.3091 target = 0.098634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.080264 restraints weight = 12874.889| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.72 r_work: 0.2678 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3138 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= 0.178 Angle : 0.535 4.466 11415 Z= 0.298 Chirality : 0.049 0.180 1235 Planarity : 0.004 0.031 1450 Dihedral : 4.294 20.449 1100 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.33 % Allowed : 12.56 % Favored : 85.11 % 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: -1.18 (0.26), residues: 1020 helix: 3.18 (0.67), residues: 55 sheet: -0.98 (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 B 162 HIS 0.003 0.001 HIS D 38 PHE 0.009 0.001 PHE E 52 TYR 0.020 0.002 TYR B 54 ARG 0.003 0.000 ARG C 6 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 290) hydrogen bonds : angle 5.20872 ( 735) SS BOND : bond 0.00382 ( 5) SS BOND : angle 1.23867 ( 10) covalent geometry : bond 0.00429 ( 8390) covalent geometry : angle 0.53385 (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 164 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.978 Fit side-chains REVERT: A 101 GLU cc_start: 0.8716 (tt0) cc_final: 0.8279 (tt0) REVERT: A 175 TYR cc_start: 0.9000 (t80) cc_final: 0.8749 (t80) REVERT: B 137 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8275 (mm-40) REVERT: B 190 LEU cc_start: 0.9275 (tp) cc_final: 0.8894 (mp) REVERT: D 62 GLU cc_start: 0.9073 (tp30) cc_final: 0.8635 (tp30) REVERT: D 125 TYR cc_start: 0.8897 (t80) cc_final: 0.8018 (t80) REVERT: E 83 LEU cc_start: 0.9320 (mm) cc_final: 0.9069 (mm) REVERT: E 163 ASP cc_start: 0.8344 (p0) cc_final: 0.8076 (p0) outliers start: 21 outliers final: 20 residues processed: 159 average time/residue: 0.2111 time to fit residues: 45.3796 Evaluate side-chains 162 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.0040 chunk 88 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 2 optimal weight: 0.0010 chunk 45 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 ** 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 = 0.3151 r_free = 0.3151 target = 0.102534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.083514 restraints weight = 12891.532| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.80 r_work: 0.2674 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3146 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= 0.102 Angle : 0.503 4.973 11415 Z= 0.280 Chirality : 0.048 0.179 1235 Planarity : 0.003 0.030 1450 Dihedral : 3.900 15.087 1100 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.67 % Allowed : 13.67 % Favored : 84.67 % 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: -0.98 (0.26), residues: 1020 helix: 3.18 (0.68), residues: 55 sheet: -1.17 (0.28), residues: 335 loop : -0.65 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 162 HIS 0.004 0.001 HIS E 38 PHE 0.011 0.001 PHE A 33 TYR 0.021 0.001 TYR B 54 ARG 0.004 0.000 ARG C 6 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 290) hydrogen bonds : angle 5.09848 ( 735) SS BOND : bond 0.00308 ( 5) SS BOND : angle 1.10198 ( 10) covalent geometry : bond 0.00245 ( 8390) covalent geometry : angle 0.50235 (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 181 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8541 (tt0) cc_final: 0.8259 (tt0) REVERT: A 175 TYR cc_start: 0.8896 (t80) cc_final: 0.8631 (t80) REVERT: B 137 GLN cc_start: 0.8469 (mm-40) cc_final: 0.7990 (mm-40) REVERT: B 190 LEU cc_start: 0.9235 (tp) cc_final: 0.8926 (mp) REVERT: C 175 TYR cc_start: 0.8906 (t80) cc_final: 0.8621 (t80) REVERT: D 62 GLU cc_start: 0.8826 (tp30) cc_final: 0.8347 (tp30) REVERT: D 125 TYR cc_start: 0.8807 (t80) cc_final: 0.7853 (t80) REVERT: E 83 LEU cc_start: 0.9262 (mm) cc_final: 0.8924 (mm) REVERT: E 163 ASP cc_start: 0.8170 (p0) cc_final: 0.7921 (p0) outliers start: 15 outliers final: 14 residues processed: 176 average time/residue: 0.2039 time to fit residues: 48.4316 Evaluate side-chains 160 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.9990 chunk 4 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 82 optimal weight: 0.0570 chunk 45 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.098842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.080661 restraints weight = 12695.084| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.67 r_work: 0.2607 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 8395 Z= 0.234 Angle : 0.579 5.750 11415 Z= 0.322 Chirality : 0.051 0.185 1235 Planarity : 0.004 0.031 1450 Dihedral : 4.343 18.959 1100 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.78 % Allowed : 13.67 % 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: -1.12 (0.27), residues: 1020 helix: 3.21 (0.66), residues: 55 sheet: -0.95 (0.27), residues: 395 loop : -0.94 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 162 HIS 0.005 0.002 HIS D 38 PHE 0.010 0.002 PHE E 52 TYR 0.025 0.002 TYR B 54 ARG 0.003 0.001 ARG E 6 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 290) hydrogen bonds : angle 5.21616 ( 735) SS BOND : bond 0.00497 ( 5) SS BOND : angle 1.46457 ( 10) covalent geometry : bond 0.00565 ( 8390) covalent geometry : angle 0.57768 (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 158 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.015 Fit side-chains REVERT: A 101 GLU cc_start: 0.8731 (tt0) cc_final: 0.8280 (tt0) REVERT: A 175 TYR cc_start: 0.8996 (t80) cc_final: 0.8711 (t80) REVERT: A 190 LEU cc_start: 0.9280 (tp) cc_final: 0.8843 (mp) REVERT: B 38 HIS cc_start: 0.8773 (OUTLIER) cc_final: 0.8270 (t-170) REVERT: B 137 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8275 (mm-40) REVERT: C 71 ILE cc_start: 0.8954 (mt) cc_final: 0.8732 (mt) REVERT: D 62 GLU cc_start: 0.9069 (tp30) cc_final: 0.8610 (tp30) REVERT: D 125 TYR cc_start: 0.8889 (t80) cc_final: 0.8052 (t80) REVERT: E 163 ASP cc_start: 0.8353 (p0) cc_final: 0.8104 (p0) outliers start: 16 outliers final: 15 residues processed: 153 average time/residue: 0.2151 time to fit residues: 44.1996 Evaluate side-chains 158 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 39 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 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 = 0.3133 r_free = 0.3133 target = 0.101442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.083137 restraints weight = 12738.451| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.72 r_work: 0.2632 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3220 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= 0.131 Angle : 0.528 5.701 11415 Z= 0.294 Chirality : 0.049 0.182 1235 Planarity : 0.003 0.031 1450 Dihedral : 4.099 16.763 1100 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.78 % Allowed : 13.89 % Favored : 84.33 % 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: -1.08 (0.27), residues: 1020 helix: 3.25 (0.67), residues: 55 sheet: -0.95 (0.27), residues: 395 loop : -0.89 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 162 HIS 0.003 0.001 HIS E 38 PHE 0.009 0.001 PHE A 33 TYR 0.022 0.001 TYR B 54 ARG 0.004 0.000 ARG E 6 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 290) hydrogen bonds : angle 5.13724 ( 735) SS BOND : bond 0.00346 ( 5) SS BOND : angle 1.26089 ( 10) covalent geometry : bond 0.00315 ( 8390) covalent geometry : angle 0.52728 (11405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3546.63 seconds wall clock time: 62 minutes 18.40 seconds (3738.40 seconds total)