Starting phenix.real_space_refine on Thu Feb 5 09:31:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jny_61631/02_2026/9jny_61631.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jny_61631/02_2026/9jny_61631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jny_61631/02_2026/9jny_61631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jny_61631/02_2026/9jny_61631.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jny_61631/02_2026/9jny_61631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jny_61631/02_2026/9jny_61631.map" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 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 S 20 5.16 5 C 5290 2.51 5 N 1305 2.21 5 O 1545 1.98 5 H 7960 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16120 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Restraints were copied for chains: A, B, C, D Time building chain proxies: 2.14, per 1000 atoms: 0.13 Number of scatterers: 16120 At special positions: 0 Unit cell: (116.28, 114.57, 53.01, 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) S 20 16.00 O 1545 8.00 N 1305 7.00 C 5290 6.00 H 7960 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.31 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 97 " distance=2.31 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.31 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 97 " distance=2.31 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 97 " distance=2.31 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: 1.40 Conformation dependent library (CDL) restraints added in 475.2 milliseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 20 sheets defined 9.7% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.919A pdb=" N SER E 45 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 176 Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.918A pdb=" N SER A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 176 Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.919A pdb=" N SER B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 176 Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.918A pdb=" N SER C 45 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 176 Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.919A pdb=" N SER D 45 " --> pdb=" O GLU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 176 Processing sheet with id=AA1, first strand: chain 'E' and resid 114 through 115 removed outlier: 3.574A pdb=" N LYS E 119 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 114 through 115 removed outlier: 3.992A pdb=" N ILE E 106 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N HIS E 38 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASN E 158 " --> pdb=" O HIS E 38 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR E 40 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE E 156 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASN E 158 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N LYS E 7 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 80 through 81 Processing sheet with id=AA4, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.475A pdb=" N ASN E 61 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA E 55 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE E 63 " --> pdb=" O SER E 53 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 53 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE E 65 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 20 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.574A pdb=" N LYS A 119 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.992A pdb=" N ILE A 106 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N HIS A 38 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASN A 158 " --> pdb=" O HIS A 38 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR A 40 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE A 156 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN A 158 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N LYS A 7 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA8, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.474A pdb=" N ASN A 61 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA A 55 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 63 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER A 53 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 65 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 20 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 115 removed outlier: 3.573A pdb=" N LYS B 119 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 115 removed outlier: 3.992A pdb=" N ILE B 106 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N HIS B 38 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASN B 158 " --> pdb=" O HIS B 38 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N TYR B 40 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE B 156 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASN B 158 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 9.811A pdb=" N LYS B 7 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.474A pdb=" N ASN B 61 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA B 55 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 63 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER B 53 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 65 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 20 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 115 removed outlier: 3.574A pdb=" N LYS C 119 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 115 removed outlier: 3.993A pdb=" N ILE C 106 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N HIS C 38 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASN C 158 " --> pdb=" O HIS C 38 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR C 40 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE C 156 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN C 158 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N LYS C 7 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AB7, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.475A pdb=" N ASN C 61 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA C 55 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE C 63 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER C 53 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 65 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 20 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 114 through 115 removed outlier: 3.573A pdb=" N LYS D 119 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 115 removed outlier: 3.992A pdb=" N ILE D 106 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N HIS D 38 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASN D 158 " --> pdb=" O HIS D 38 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N TYR D 40 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE D 156 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN D 158 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N LYS D 7 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AC2, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.474A pdb=" N ASN D 61 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA D 55 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE D 63 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER D 53 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE D 65 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 20 " --> pdb=" O LEU D 135 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 720 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: 3.40 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 7960 1.02 - 1.21: 5 1.21 - 1.41: 3530 1.41 - 1.61: 4825 1.61 - 1.80: 30 Bond restraints: 16350 Sorted by residual: bond pdb=" C ASN C 160 " pdb=" N MET C 161 " ideal model delta sigma weight residual 1.331 1.417 -0.086 1.55e-02 4.16e+03 3.08e+01 bond pdb=" C ASN D 160 " pdb=" N MET D 161 " ideal model delta sigma weight residual 1.331 1.417 -0.086 1.55e-02 4.16e+03 3.06e+01 bond pdb=" C ASN E 160 " pdb=" N MET E 161 " ideal model delta sigma weight residual 1.331 1.417 -0.086 1.55e-02 4.16e+03 3.05e+01 bond pdb=" C ASN A 160 " pdb=" N MET A 161 " ideal model delta sigma weight residual 1.331 1.416 -0.085 1.55e-02 4.16e+03 3.04e+01 bond pdb=" C ASN B 160 " pdb=" N MET B 161 " ideal model delta sigma weight residual 1.331 1.416 -0.085 1.55e-02 4.16e+03 3.04e+01 ... (remaining 16345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 26507 1.18 - 2.35: 2528 2.35 - 3.53: 355 3.53 - 4.70: 95 4.70 - 5.88: 45 Bond angle restraints: 29530 Sorted by residual: angle pdb=" O ASN D 160 " pdb=" C ASN D 160 " pdb=" N MET D 161 " ideal model delta sigma weight residual 123.33 128.86 -5.53 1.21e+00 6.83e-01 2.09e+01 angle pdb=" O ASN E 160 " pdb=" C ASN E 160 " pdb=" N MET E 161 " ideal model delta sigma weight residual 123.33 128.85 -5.52 1.21e+00 6.83e-01 2.08e+01 angle pdb=" O ASN A 160 " pdb=" C ASN A 160 " pdb=" N MET A 161 " ideal model delta sigma weight residual 123.33 128.85 -5.52 1.21e+00 6.83e-01 2.08e+01 angle pdb=" O ASN C 160 " pdb=" C ASN C 160 " pdb=" N MET C 161 " ideal model delta sigma weight residual 123.33 128.84 -5.51 1.21e+00 6.83e-01 2.07e+01 angle pdb=" O ASN B 160 " pdb=" C ASN B 160 " pdb=" N MET B 161 " ideal model delta sigma weight residual 123.33 128.83 -5.50 1.21e+00 6.83e-01 2.07e+01 ... (remaining 29525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6780 17.76 - 35.53: 720 35.53 - 53.29: 205 53.29 - 71.05: 45 71.05 - 88.82: 25 Dihedral angle restraints: 7775 sinusoidal: 4100 harmonic: 3675 Sorted by residual: dihedral pdb=" CB CYS D 36 " pdb=" SG CYS D 36 " pdb=" SG CYS D 97 " pdb=" CB CYS D 97 " ideal model delta sinusoidal sigma weight residual 93.00 128.54 -35.54 1 1.00e+01 1.00e-02 1.79e+01 dihedral pdb=" CB CYS B 36 " pdb=" SG CYS B 36 " pdb=" SG CYS B 97 " pdb=" CB CYS B 97 " ideal model delta sinusoidal sigma weight residual 93.00 128.53 -35.53 1 1.00e+01 1.00e-02 1.79e+01 dihedral pdb=" CB CYS C 36 " pdb=" SG CYS C 36 " pdb=" SG CYS C 97 " pdb=" CB CYS C 97 " ideal model delta sinusoidal sigma weight residual 93.00 128.53 -35.53 1 1.00e+01 1.00e-02 1.79e+01 ... (remaining 7772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 863 0.050 - 0.100: 292 0.100 - 0.150: 60 0.150 - 0.200: 15 0.200 - 0.250: 5 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CB ILE C 156 " pdb=" CA ILE C 156 " pdb=" CG1 ILE C 156 " pdb=" CG2 ILE C 156 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE E 156 " pdb=" CA ILE E 156 " pdb=" CG1 ILE E 156 " pdb=" CG2 ILE E 156 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE A 156 " pdb=" CA ILE A 156 " pdb=" CG1 ILE A 156 " pdb=" CG2 ILE A 156 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1232 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 33 " 0.015 2.00e-02 2.50e+03 2.84e-02 8.07e+00 pdb=" N THR A 34 " -0.049 2.00e-02 2.50e+03 pdb=" CA THR A 34 " 0.012 2.00e-02 2.50e+03 pdb=" H THR A 34 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 33 " -0.015 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" N THR C 34 " 0.049 2.00e-02 2.50e+03 pdb=" CA THR C 34 " -0.012 2.00e-02 2.50e+03 pdb=" H THR C 34 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 33 " 0.015 2.00e-02 2.50e+03 2.82e-02 7.96e+00 pdb=" N THR E 34 " -0.049 2.00e-02 2.50e+03 pdb=" CA THR E 34 " 0.012 2.00e-02 2.50e+03 pdb=" H THR E 34 " 0.022 2.00e-02 2.50e+03 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1517 2.22 - 2.81: 34028 2.81 - 3.41: 41640 3.41 - 4.00: 58408 4.00 - 4.60: 86269 Nonbonded interactions: 221862 Sorted by model distance: nonbonded pdb=" OE1 GLU B 85 " pdb=" H GLU B 85 " model vdw 1.623 2.450 nonbonded pdb=" OE1 GLU C 85 " pdb=" H GLU C 85 " model vdw 1.623 2.450 nonbonded pdb=" OE1 GLU A 85 " pdb=" H GLU A 85 " model vdw 1.624 2.450 nonbonded pdb=" OE1 GLU D 85 " pdb=" H GLU D 85 " model vdw 1.624 2.450 nonbonded pdb=" OE1 GLU E 85 " pdb=" H GLU E 85 " model vdw 1.624 2.450 ... (remaining 221857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'A' selection = chain 'B' selection = chain 'C' 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 group one per residue 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.640 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 : 0.009 0.276 8395 Z= 0.484 Angle : 0.918 9.607 11415 Z= 0.534 Chirality : 0.054 0.250 1235 Planarity : 0.008 0.093 1450 Dihedral : 13.440 79.526 2990 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.24), residues: 1020 helix: 0.42 (0.58), residues: 55 sheet: -0.35 (0.23), residues: 430 loop : -1.44 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 58 TYR 0.016 0.003 TYR D 54 PHE 0.012 0.002 PHE C 199 TRP 0.014 0.002 TRP B 162 HIS 0.003 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 8390) covalent geometry : angle 0.89468 (11405) SS BOND : bond 0.27596 ( 5) SS BOND : angle 7.02342 ( 10) hydrogen bonds : bond 0.26346 ( 290) hydrogen bonds : angle 9.26997 ( 720) *********************** 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 101 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.9252 (pt0) cc_final: 0.9048 (pm20) REVERT: B 81 GLU cc_start: 0.9266 (pt0) cc_final: 0.9046 (pm20) REVERT: C 81 GLU cc_start: 0.9278 (pt0) cc_final: 0.9050 (pm20) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2813 time to fit residues: 35.9388 Evaluate side-chains 79 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 HIS ** D 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 = 0.2729 r_free = 0.2729 target = 0.048354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.038766 restraints weight = 94664.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.041512 restraints weight = 36717.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.043405 restraints weight = 19436.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.044696 restraints weight = 11785.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.045540 restraints weight = 7815.470| |-----------------------------------------------------------------------------| r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 8395 Z= 0.166 Angle : 0.602 4.939 11415 Z= 0.321 Chirality : 0.046 0.149 1235 Planarity : 0.004 0.029 1450 Dihedral : 5.192 16.318 1100 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.56 % Allowed : 12.00 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.26), residues: 1020 helix: 2.00 (0.69), residues: 55 sheet: 0.02 (0.30), residues: 315 loop : -1.05 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 118 TYR 0.014 0.002 TYR B 40 PHE 0.009 0.001 PHE D 52 TRP 0.007 0.001 TRP E 162 HIS 0.002 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8390) covalent geometry : angle 0.60111 (11405) SS BOND : bond 0.00074 ( 5) SS BOND : angle 1.08525 ( 10) hydrogen bonds : bond 0.05144 ( 290) hydrogen bonds : angle 6.53814 ( 720) *********************** 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 85 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 80 average time/residue: 0.2370 time to fit residues: 24.2402 Evaluate side-chains 74 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 155 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 HIS ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 HIS A 139 GLN B 95 HIS ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 HIS C 139 GLN D 139 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.043620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2314 r_free = 0.2314 target = 0.033852 restraints weight = 96697.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.036385 restraints weight = 36911.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.038173 restraints weight = 19752.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.039454 restraints weight = 12323.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.040324 restraints weight = 8391.483| |-----------------------------------------------------------------------------| r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 8395 Z= 0.225 Angle : 0.600 4.828 11415 Z= 0.324 Chirality : 0.044 0.137 1235 Planarity : 0.004 0.030 1450 Dihedral : 5.075 17.421 1100 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.67 % Allowed : 9.89 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.26), residues: 1020 helix: -0.63 (0.58), residues: 85 sheet: -0.54 (0.26), residues: 405 loop : -0.98 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 58 TYR 0.013 0.001 TYR E 54 PHE 0.014 0.001 PHE D 52 TRP 0.008 0.001 TRP C 162 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00505 ( 8390) covalent geometry : angle 0.59926 (11405) SS BOND : bond 0.00375 ( 5) SS BOND : angle 1.18890 ( 10) hydrogen bonds : bond 0.04522 ( 290) hydrogen bonds : angle 5.74415 ( 720) *********************** 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 84 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.9003 (mmm) cc_final: 0.8779 (mmm) REVERT: B 4 MET cc_start: 0.9082 (mmm) cc_final: 0.8790 (mmm) REVERT: C 4 MET cc_start: 0.9006 (mmm) cc_final: 0.8787 (mmm) outliers start: 15 outliers final: 8 residues processed: 78 average time/residue: 0.2248 time to fit residues: 23.0667 Evaluate side-chains 74 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 70 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.043614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2316 r_free = 0.2316 target = 0.033808 restraints weight = 96085.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.036346 restraints weight = 36444.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.038141 restraints weight = 19555.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.039396 restraints weight = 12242.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.040294 restraints weight = 8385.312| |-----------------------------------------------------------------------------| r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 8395 Z= 0.162 Angle : 0.565 4.914 11415 Z= 0.299 Chirality : 0.045 0.133 1235 Planarity : 0.004 0.031 1450 Dihedral : 4.881 16.520 1100 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.11 % Allowed : 10.44 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.26), residues: 1020 helix: -0.32 (0.60), residues: 85 sheet: -0.59 (0.26), residues: 405 loop : -0.92 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 58 TYR 0.009 0.001 TYR E 54 PHE 0.010 0.001 PHE D 52 TRP 0.005 0.001 TRP C 162 HIS 0.002 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8390) covalent geometry : angle 0.56434 (11405) SS BOND : bond 0.00328 ( 5) SS BOND : angle 0.76744 ( 10) hydrogen bonds : bond 0.03775 ( 290) hydrogen bonds : angle 5.57627 ( 720) *********************** 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 81 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.9077 (mmm) cc_final: 0.8803 (mmm) REVERT: B 4 MET cc_start: 0.9124 (mmm) cc_final: 0.8755 (mmm) REVERT: C 4 MET cc_start: 0.8975 (mmm) cc_final: 0.8728 (mmm) outliers start: 10 outliers final: 8 residues processed: 76 average time/residue: 0.2694 time to fit residues: 26.6437 Evaluate side-chains 78 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 70 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 0.0570 chunk 32 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.3300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.043723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.034362 restraints weight = 94409.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.036925 restraints weight = 35846.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.038568 restraints weight = 18991.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.039859 restraints weight = 12196.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.040778 restraints weight = 8232.016| |-----------------------------------------------------------------------------| r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8395 Z= 0.111 Angle : 0.545 5.388 11415 Z= 0.285 Chirality : 0.045 0.133 1235 Planarity : 0.003 0.029 1450 Dihedral : 4.676 14.961 1100 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.11 % Allowed : 11.33 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.27), residues: 1020 helix: -0.06 (0.62), residues: 85 sheet: -0.56 (0.26), residues: 405 loop : -0.72 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 58 TYR 0.008 0.001 TYR D 73 PHE 0.009 0.001 PHE C 52 TRP 0.005 0.001 TRP C 110 HIS 0.002 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8390) covalent geometry : angle 0.54486 (11405) SS BOND : bond 0.00252 ( 5) SS BOND : angle 0.62698 ( 10) hydrogen bonds : bond 0.03280 ( 290) hydrogen bonds : angle 5.30246 ( 720) *********************** 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 73 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9074 (mmm) cc_final: 0.8686 (mmm) REVERT: A 4 MET cc_start: 0.9060 (mmm) cc_final: 0.8794 (mmm) REVERT: B 4 MET cc_start: 0.9072 (mmm) cc_final: 0.8688 (mmm) REVERT: C 4 MET cc_start: 0.8979 (mmm) cc_final: 0.8738 (mmm) outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.2544 time to fit residues: 24.2212 Evaluate side-chains 73 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 HIS ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.041902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2290 r_free = 0.2290 target = 0.032598 restraints weight = 96075.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.035061 restraints weight = 37211.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.036817 restraints weight = 20090.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.038040 restraints weight = 12647.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.038942 restraints weight = 8723.974| |-----------------------------------------------------------------------------| r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 8395 Z= 0.201 Angle : 0.574 5.832 11415 Z= 0.305 Chirality : 0.044 0.127 1235 Planarity : 0.004 0.030 1450 Dihedral : 4.729 15.091 1100 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.22 % Allowed : 10.22 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.26), residues: 1020 helix: -0.40 (0.58), residues: 85 sheet: -0.77 (0.26), residues: 405 loop : -0.86 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 58 TYR 0.011 0.001 TYR E 54 PHE 0.009 0.001 PHE C 52 TRP 0.005 0.001 TRP E 67 HIS 0.002 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 8390) covalent geometry : angle 0.57396 (11405) SS BOND : bond 0.00416 ( 5) SS BOND : angle 0.93683 ( 10) hydrogen bonds : bond 0.03866 ( 290) hydrogen bonds : angle 5.35285 ( 720) *********************** 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 76 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9176 (mmm) cc_final: 0.8802 (mmm) REVERT: A 4 MET cc_start: 0.9163 (mmm) cc_final: 0.8877 (mmm) REVERT: C 4 MET cc_start: 0.9090 (mmm) cc_final: 0.8797 (mmm) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.2587 time to fit residues: 22.5347 Evaluate side-chains 74 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 81 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 HIS B 38 HIS ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.042768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2318 r_free = 0.2318 target = 0.033421 restraints weight = 95425.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.035937 restraints weight = 36654.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.037714 restraints weight = 19612.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.038963 restraints weight = 12228.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.039852 restraints weight = 8380.836| |-----------------------------------------------------------------------------| r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8395 Z= 0.124 Angle : 0.543 5.794 11415 Z= 0.285 Chirality : 0.045 0.132 1235 Planarity : 0.003 0.033 1450 Dihedral : 4.565 14.252 1100 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.22 % Allowed : 11.00 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.27), residues: 1020 helix: -0.18 (0.60), residues: 85 sheet: -0.73 (0.26), residues: 405 loop : -0.74 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 58 TYR 0.007 0.001 TYR E 54 PHE 0.008 0.001 PHE A 52 TRP 0.004 0.001 TRP C 110 HIS 0.005 0.001 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8390) covalent geometry : angle 0.54302 (11405) SS BOND : bond 0.00276 ( 5) SS BOND : angle 0.58809 ( 10) hydrogen bonds : bond 0.03269 ( 290) hydrogen bonds : angle 5.12059 ( 720) *********************** 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 72 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9124 (mmm) cc_final: 0.8749 (mmm) REVERT: A 4 MET cc_start: 0.9122 (mmm) cc_final: 0.8833 (mmm) REVERT: B 4 MET cc_start: 0.9167 (mmm) cc_final: 0.8794 (mmm) REVERT: C 4 MET cc_start: 0.9059 (mmm) cc_final: 0.8768 (mmm) outliers start: 2 outliers final: 2 residues processed: 72 average time/residue: 0.2903 time to fit residues: 26.9051 Evaluate side-chains 72 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain B residue 34 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.043294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2336 r_free = 0.2336 target = 0.033949 restraints weight = 95188.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.036477 restraints weight = 36486.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.038262 restraints weight = 19446.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.039513 restraints weight = 12122.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.040422 restraints weight = 8232.823| |-----------------------------------------------------------------------------| r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8395 Z= 0.108 Angle : 0.536 6.231 11415 Z= 0.280 Chirality : 0.045 0.133 1235 Planarity : 0.003 0.034 1450 Dihedral : 4.412 13.067 1100 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.22 % Allowed : 10.67 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.27), residues: 1020 helix: -0.00 (0.60), residues: 85 sheet: -0.63 (0.26), residues: 405 loop : -0.70 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 58 TYR 0.008 0.001 TYR E 54 PHE 0.007 0.001 PHE B 39 TRP 0.004 0.001 TRP C 110 HIS 0.005 0.002 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8390) covalent geometry : angle 0.53575 (11405) SS BOND : bond 0.00248 ( 5) SS BOND : angle 0.58661 ( 10) hydrogen bonds : bond 0.03046 ( 290) hydrogen bonds : angle 4.91370 ( 720) *********************** 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 72 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9119 (mmm) cc_final: 0.8772 (mmm) REVERT: A 4 MET cc_start: 0.9106 (mmm) cc_final: 0.8809 (mmm) REVERT: B 4 MET cc_start: 0.9164 (mmm) cc_final: 0.8793 (mmm) REVERT: C 4 MET cc_start: 0.9046 (mmm) cc_final: 0.8752 (mmm) outliers start: 2 outliers final: 2 residues processed: 72 average time/residue: 0.2825 time to fit residues: 26.2065 Evaluate side-chains 70 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain C residue 34 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 79 optimal weight: 0.0670 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.042647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2315 r_free = 0.2315 target = 0.033258 restraints weight = 95358.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2392 r_free = 0.2392 target = 0.035774 restraints weight = 36699.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.037555 restraints weight = 19606.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.038809 restraints weight = 12231.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.039711 restraints weight = 8339.885| |-----------------------------------------------------------------------------| r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8395 Z= 0.141 Angle : 0.550 6.316 11415 Z= 0.288 Chirality : 0.044 0.128 1235 Planarity : 0.003 0.026 1450 Dihedral : 4.407 13.195 1100 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.78 % Allowed : 10.33 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.27), residues: 1020 helix: -0.04 (0.59), residues: 85 sheet: -0.64 (0.26), residues: 405 loop : -0.78 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 58 TYR 0.009 0.001 TYR E 54 PHE 0.007 0.001 PHE D 52 TRP 0.005 0.001 TRP D 67 HIS 0.004 0.001 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8390) covalent geometry : angle 0.55009 (11405) SS BOND : bond 0.00317 ( 5) SS BOND : angle 0.71095 ( 10) hydrogen bonds : bond 0.03293 ( 290) hydrogen bonds : angle 4.90734 ( 720) *********************** 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 77 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9140 (mmm) cc_final: 0.8767 (mmm) REVERT: A 4 MET cc_start: 0.9117 (mmm) cc_final: 0.8821 (mmm) REVERT: C 4 MET cc_start: 0.9072 (mmm) cc_final: 0.8774 (mmm) outliers start: 7 outliers final: 7 residues processed: 73 average time/residue: 0.2703 time to fit residues: 25.6103 Evaluate side-chains 77 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 70 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.042285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2307 r_free = 0.2307 target = 0.032913 restraints weight = 95208.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.035408 restraints weight = 36687.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.037177 restraints weight = 19675.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.038410 restraints weight = 12278.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.039300 restraints weight = 8440.776| |-----------------------------------------------------------------------------| r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8395 Z= 0.146 Angle : 0.550 5.829 11415 Z= 0.289 Chirality : 0.044 0.130 1235 Planarity : 0.004 0.044 1450 Dihedral : 4.417 12.470 1100 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.89 % Allowed : 10.11 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.27), residues: 1020 helix: -0.02 (0.58), residues: 85 sheet: -0.68 (0.26), residues: 405 loop : -0.86 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 58 TYR 0.008 0.001 TYR E 54 PHE 0.008 0.001 PHE A 52 TRP 0.005 0.001 TRP D 67 HIS 0.004 0.001 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8390) covalent geometry : angle 0.54989 (11405) SS BOND : bond 0.00335 ( 5) SS BOND : angle 0.72218 ( 10) hydrogen bonds : bond 0.03325 ( 290) hydrogen bonds : angle 4.87304 ( 720) ********************** 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 78 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.9171 (mmm) cc_final: 0.8799 (mmm) REVERT: A 4 MET cc_start: 0.9147 (mmm) cc_final: 0.8848 (mmm) REVERT: C 4 MET cc_start: 0.9083 (mmm) cc_final: 0.8785 (mmm) REVERT: D 4 MET cc_start: 0.9155 (mmm) cc_final: 0.8826 (mmm) outliers start: 8 outliers final: 8 residues processed: 73 average time/residue: 0.2828 time to fit residues: 26.6673 Evaluate side-chains 77 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 70 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 = 0.2648 r_free = 0.2648 target = 0.044147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2346 r_free = 0.2346 target = 0.034146 restraints weight = 93608.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.036755 restraints weight = 37094.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.038622 restraints weight = 20168.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.039927 restraints weight = 12766.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.040872 restraints weight = 8827.646| |-----------------------------------------------------------------------------| r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8395 Z= 0.097 Angle : 0.544 6.594 11415 Z= 0.282 Chirality : 0.045 0.134 1235 Planarity : 0.003 0.022 1450 Dihedral : 4.282 11.739 1100 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.33 % Allowed : 10.78 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.27), residues: 1020 helix: 0.29 (0.61), residues: 85 sheet: -0.71 (0.26), residues: 415 loop : -0.72 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 58 TYR 0.008 0.001 TYR C 54 PHE 0.007 0.001 PHE E 39 TRP 0.005 0.001 TRP E 110 HIS 0.005 0.002 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8390) covalent geometry : angle 0.54358 (11405) SS BOND : bond 0.00248 ( 5) SS BOND : angle 0.51355 ( 10) hydrogen bonds : bond 0.02916 ( 290) hydrogen bonds : angle 4.69641 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2212.79 seconds wall clock time: 38 minutes 29.37 seconds (2309.37 seconds total)