Starting phenix.real_space_refine on Fri Aug 22 12:39:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qlu_53234/08_2025/9qlu_53234_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qlu_53234/08_2025/9qlu_53234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qlu_53234/08_2025/9qlu_53234_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qlu_53234/08_2025/9qlu_53234_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qlu_53234/08_2025/9qlu_53234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qlu_53234/08_2025/9qlu_53234.map" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 1440 2.51 5 N 430 2.21 5 O 450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2360 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 472 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "B" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 472 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "C" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 472 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "D" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 472 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "E" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 472 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Time building chain proxies: 0.86, per 1000 atoms: 0.36 Number of scatterers: 2360 At special positions: 0 Unit cell: (78, 61.1, 49.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 450 8.00 N 430 7.00 C 1440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.21 Conformation dependent library (CDL) restraints added in 98.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 570 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 57.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 106 removed outlier: 6.825A pdb=" N VAL B 103 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A 104 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR B 105 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU A 106 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 103 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 104 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 105 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU B 106 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL D 103 " --> pdb=" O GLY C 102 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C 104 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR D 105 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU C 106 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL E 103 " --> pdb=" O GLY D 102 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL D 104 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR E 105 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU D 106 " --> pdb=" O THR E 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 117 removed outlier: 9.192A pdb=" N ARG A 110 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 10.377A pdb=" N GLY B 113 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ALA A 112 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE B 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N MET A 114 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLN B 117 " --> pdb=" O MET A 114 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER A 116 " --> pdb=" O GLN B 117 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N ARG B 110 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N GLY C 113 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA B 112 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE C 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N MET B 114 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLN C 117 " --> pdb=" O MET B 114 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER B 116 " --> pdb=" O GLN C 117 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N ARG C 110 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N GLY D 113 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA C 112 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE D 115 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N MET C 114 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLN D 117 " --> pdb=" O MET C 114 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER C 116 " --> pdb=" O GLN D 117 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N ARG D 110 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 10.394A pdb=" N GLY E 113 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA D 112 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE E 115 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET D 114 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLN E 117 " --> pdb=" O MET D 114 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER D 116 " --> pdb=" O GLN E 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 131 removed outlier: 6.838A pdb=" N MET B 131 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N MET C 131 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET D 131 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET E 131 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 138 Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 149 removed outlier: 6.333A pdb=" N CYS A 141 " --> pdb=" O ASN B 142 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN B 144 " --> pdb=" O CYS A 141 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU A 143 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N THR B 146 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N HIS A 145 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE B 148 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLY A 147 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N CYS B 141 " --> pdb=" O ASN C 142 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLN C 144 " --> pdb=" O CYS B 141 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU B 143 " --> pdb=" O GLN C 144 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR C 146 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N HIS B 145 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE C 148 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLY B 147 " --> pdb=" O PHE C 148 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N CYS C 141 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLN D 144 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU C 143 " --> pdb=" O GLN D 144 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N THR D 146 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS C 145 " --> pdb=" O THR D 146 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE D 148 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY C 147 " --> pdb=" O PHE D 148 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N CYS D 141 " --> pdb=" O ASN E 142 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLN E 144 " --> pdb=" O CYS D 141 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU D 143 " --> pdb=" O GLN E 144 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N THR E 146 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N HIS D 145 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N PHE E 148 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLY D 147 " --> pdb=" O PHE E 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 72 hydrogen bonds defined for protein. 216 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: 0.32 Time building geometry restraints manager: 0.26 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: 835 1.34 - 1.46: 498 1.46 - 1.58: 1007 1.58 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 2395 Sorted by residual: bond pdb=" CG LEU D 135 " pdb=" CD2 LEU D 135 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.61e-01 bond pdb=" CG LEU C 96 " pdb=" CD1 LEU C 96 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.86e-01 bond pdb=" CG LEU D 96 " pdb=" CD1 LEU D 96 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.76e-01 bond pdb=" CG LEU E 96 " pdb=" CD1 LEU E 96 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.57e-01 bond pdb=" CG LEU A 135 " pdb=" CD2 LEU A 135 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.56e-01 ... (remaining 2390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 2876 1.04 - 2.07: 300 2.07 - 3.11: 37 3.11 - 4.15: 7 4.15 - 5.18: 10 Bond angle restraints: 3230 Sorted by residual: angle pdb=" CA ARG E 110 " pdb=" CB ARG E 110 " pdb=" CG ARG E 110 " ideal model delta sigma weight residual 114.10 117.18 -3.08 2.00e+00 2.50e-01 2.38e+00 angle pdb=" CA ARG C 110 " pdb=" CB ARG C 110 " pdb=" CG ARG C 110 " ideal model delta sigma weight residual 114.10 117.18 -3.08 2.00e+00 2.50e-01 2.36e+00 angle pdb=" CA ARG D 110 " pdb=" CB ARG D 110 " pdb=" CG ARG D 110 " ideal model delta sigma weight residual 114.10 117.07 -2.97 2.00e+00 2.50e-01 2.21e+00 angle pdb=" CA LEU A 143 " pdb=" CB LEU A 143 " pdb=" CG LEU A 143 " ideal model delta sigma weight residual 116.30 121.48 -5.18 3.50e+00 8.16e-02 2.19e+00 angle pdb=" CA LEU B 143 " pdb=" CB LEU B 143 " pdb=" CG LEU B 143 " ideal model delta sigma weight residual 116.30 121.46 -5.16 3.50e+00 8.16e-02 2.17e+00 ... (remaining 3225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.97: 1232 11.97 - 23.94: 124 23.94 - 35.90: 29 35.90 - 47.87: 6 47.87 - 59.84: 14 Dihedral angle restraints: 1405 sinusoidal: 505 harmonic: 900 Sorted by residual: dihedral pdb=" CA ALA A 126 " pdb=" C ALA A 126 " pdb=" N THR A 127 " pdb=" CA THR A 127 " ideal model delta harmonic sigma weight residual 180.00 162.66 17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ALA E 132 " pdb=" C ALA E 132 " pdb=" N SER E 133 " pdb=" CA SER E 133 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ALA E 126 " pdb=" C ALA E 126 " pdb=" N THR E 127 " pdb=" CA THR E 127 " ideal model delta harmonic sigma weight residual 180.00 162.98 17.02 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 1402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 206 0.027 - 0.053: 102 0.053 - 0.080: 17 0.080 - 0.106: 18 0.106 - 0.133: 17 Chirality restraints: 360 Sorted by residual: chirality pdb=" CA VAL A 111 " pdb=" N VAL A 111 " pdb=" C VAL A 111 " pdb=" CB VAL A 111 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA VAL E 111 " pdb=" N VAL E 111 " pdb=" C VAL E 111 " pdb=" CB VAL E 111 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA VAL B 111 " pdb=" N VAL B 111 " pdb=" C VAL B 111 " pdb=" CB VAL B 111 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 357 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 138 " -0.008 2.00e-02 2.50e+03 7.73e-03 1.19e+00 pdb=" CG TYR B 138 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR B 138 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 138 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 138 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 138 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 138 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 138 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 92 " -0.087 9.50e-02 1.11e+02 3.92e-02 1.12e+00 pdb=" NE ARG A 92 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 92 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 92 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 92 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 138 " -0.008 2.00e-02 2.50e+03 7.20e-03 1.04e+00 pdb=" CG TYR E 138 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR E 138 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR E 138 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 138 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 138 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 138 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 138 " -0.003 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 820 2.87 - 3.38: 1857 3.38 - 3.89: 4122 3.89 - 4.39: 4345 4.39 - 4.90: 8760 Nonbonded interactions: 19904 Sorted by model distance: nonbonded pdb=" NH2 ARG C 101 " pdb=" OE1 GLN E 144 " model vdw 2.367 3.120 nonbonded pdb=" NH2 ARG B 101 " pdb=" OE1 GLN D 144 " model vdw 2.390 3.120 nonbonded pdb=" NH2 ARG A 101 " pdb=" OE1 GLN C 144 " model vdw 2.412 3.120 nonbonded pdb=" OG SER B 133 " pdb=" O SER C 133 " model vdw 2.439 3.040 nonbonded pdb=" OG SER D 133 " pdb=" O SER E 133 " model vdw 2.459 3.040 ... (remaining 19899 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.740 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.580 Find NCS groups from input model: 0.020 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:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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 : 0.004 0.032 2395 Z= 0.143 Angle : 0.676 5.181 3230 Z= 0.350 Chirality : 0.043 0.133 360 Planarity : 0.005 0.039 435 Dihedral : 12.317 59.841 835 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % 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 aren not related in a simple way. whole: -1.75 (0.37), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 110 TYR 0.017 0.006 TYR B 138 PHE 0.004 0.001 PHE A 149 HIS 0.003 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 2395) covalent geometry : angle 0.67559 ( 3230) hydrogen bonds : bond 0.10610 ( 72) hydrogen bonds : angle 7.58083 ( 216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 131 MET cc_start: 0.8575 (ttm) cc_final: 0.8374 (ttp) REVERT: B 131 MET cc_start: 0.8543 (ttm) cc_final: 0.8342 (ttp) REVERT: E 101 ARG cc_start: 0.8349 (ttm170) cc_final: 0.6541 (tpt170) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.8115 time to fit residues: 49.4253 Evaluate side-chains 38 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0370 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.0870 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 0.0030 chunk 25 optimal weight: 3.9990 overall best weight: 1.0248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.113375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.094016 restraints weight = 2302.232| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.90 r_work: 0.3381 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2395 Z= 0.126 Angle : 0.579 5.735 3230 Z= 0.285 Chirality : 0.045 0.126 360 Planarity : 0.003 0.016 435 Dihedral : 4.883 12.481 350 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.08 % Allowed : 14.17 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.36), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 110 TYR 0.013 0.003 TYR B 138 PHE 0.004 0.001 PHE C 148 HIS 0.001 0.000 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 2395) covalent geometry : angle 0.57861 ( 3230) hydrogen bonds : bond 0.03389 ( 72) hydrogen bonds : angle 5.82988 ( 216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.102 Fit side-chains REVERT: E 101 ARG cc_start: 0.8318 (ttm170) cc_final: 0.6369 (tpt170) REVERT: E 136 THR cc_start: 0.8569 (m) cc_final: 0.8317 (t) outliers start: 5 outliers final: 0 residues processed: 39 average time/residue: 0.7482 time to fit residues: 29.7001 Evaluate side-chains 37 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 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 = 0.3682 r_free = 0.3682 target = 0.105047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.085370 restraints weight = 2470.252| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.99 r_work: 0.3256 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2395 Z= 0.233 Angle : 0.628 5.009 3230 Z= 0.320 Chirality : 0.047 0.127 360 Planarity : 0.004 0.036 435 Dihedral : 4.958 12.669 350 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.75 % Allowed : 12.50 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.37), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 110 TYR 0.013 0.003 TYR B 138 PHE 0.006 0.001 PHE E 154 HIS 0.002 0.001 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 2395) covalent geometry : angle 0.62760 ( 3230) hydrogen bonds : bond 0.04047 ( 72) hydrogen bonds : angle 5.46436 ( 216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.056 Fit side-chains REVERT: D 117 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7810 (tp40) REVERT: E 101 ARG cc_start: 0.8349 (ttm170) cc_final: 0.6324 (tpt170) REVERT: E 117 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7953 (tt0) outliers start: 9 outliers final: 1 residues processed: 36 average time/residue: 0.7364 time to fit residues: 26.9720 Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain E residue 117 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 117 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.104985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.085489 restraints weight = 2438.352| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.97 r_work: 0.3263 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2395 Z= 0.235 Angle : 0.609 4.641 3230 Z= 0.312 Chirality : 0.047 0.125 360 Planarity : 0.004 0.036 435 Dihedral : 4.875 12.677 350 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.17 % Allowed : 12.92 % Favored : 82.92 % 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 aren not related in a simple way. whole: -1.82 (0.37), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 110 TYR 0.012 0.003 TYR B 138 PHE 0.005 0.001 PHE E 154 HIS 0.002 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 2395) covalent geometry : angle 0.60922 ( 3230) hydrogen bonds : bond 0.03909 ( 72) hydrogen bonds : angle 5.29197 ( 216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.087 Fit side-chains REVERT: D 117 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7768 (tp40) REVERT: E 101 ARG cc_start: 0.8340 (ttm170) cc_final: 0.6383 (tpt170) REVERT: E 106 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7545 (mt-10) REVERT: E 117 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7921 (tt0) outliers start: 10 outliers final: 1 residues processed: 43 average time/residue: 0.7026 time to fit residues: 30.7473 Evaluate side-chains 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain E residue 117 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 20 optimal weight: 0.0060 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 117 GLN ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.111279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.091902 restraints weight = 2355.845| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.93 r_work: 0.3376 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2395 Z= 0.105 Angle : 0.480 3.859 3230 Z= 0.248 Chirality : 0.044 0.125 360 Planarity : 0.002 0.021 435 Dihedral : 4.191 11.231 350 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.33 % Allowed : 13.33 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.37), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 110 TYR 0.008 0.002 TYR C 138 PHE 0.003 0.001 PHE D 154 HIS 0.002 0.000 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 2395) covalent geometry : angle 0.48042 ( 3230) hydrogen bonds : bond 0.02819 ( 72) hydrogen bonds : angle 5.02008 ( 216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.090 Fit side-chains REVERT: E 101 ARG cc_start: 0.8294 (ttm170) cc_final: 0.6416 (tpt170) REVERT: E 106 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7374 (mt-10) REVERT: E 110 ARG cc_start: 0.8694 (mmt-90) cc_final: 0.8176 (mpt-90) REVERT: E 117 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: E 136 THR cc_start: 0.8539 (m) cc_final: 0.8309 (t) REVERT: E 143 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8472 (tt) outliers start: 8 outliers final: 1 residues processed: 42 average time/residue: 0.7393 time to fit residues: 31.6303 Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 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 = 0.3648 r_free = 0.3648 target = 0.102490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083352 restraints weight = 2455.282| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.93 r_work: 0.3226 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 2395 Z= 0.385 Angle : 0.708 5.090 3230 Z= 0.366 Chirality : 0.051 0.126 360 Planarity : 0.005 0.052 435 Dihedral : 5.168 13.357 350 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 5.00 % Allowed : 13.75 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.38), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 110 TYR 0.013 0.003 TYR B 138 PHE 0.008 0.002 PHE A 154 HIS 0.004 0.002 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00823 ( 2395) covalent geometry : angle 0.70818 ( 3230) hydrogen bonds : bond 0.04528 ( 72) hydrogen bonds : angle 5.44007 ( 216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.097 Fit side-chains REVERT: A 117 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7624 (tp-100) REVERT: C 143 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8115 (tt) REVERT: D 110 ARG cc_start: 0.8521 (mmt-90) cc_final: 0.8289 (mpt-90) REVERT: E 101 ARG cc_start: 0.8407 (ttm170) cc_final: 0.6306 (tpt170) REVERT: E 117 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: E 143 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8617 (tt) outliers start: 12 outliers final: 0 residues processed: 43 average time/residue: 0.7766 time to fit residues: 33.9439 Evaluate side-chains 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.0000 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 117 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.110789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.091914 restraints weight = 2364.552| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.89 r_work: 0.3386 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2395 Z= 0.105 Angle : 0.484 3.619 3230 Z= 0.250 Chirality : 0.044 0.123 360 Planarity : 0.002 0.015 435 Dihedral : 4.229 11.677 350 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.33 % Allowed : 13.33 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.38), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 110 TYR 0.008 0.002 TYR E 138 PHE 0.003 0.001 PHE D 154 HIS 0.002 0.000 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 2395) covalent geometry : angle 0.48393 ( 3230) hydrogen bonds : bond 0.02816 ( 72) hydrogen bonds : angle 5.04695 ( 216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.081 Fit side-chains REVERT: E 101 ARG cc_start: 0.8329 (ttm170) cc_final: 0.6357 (tpt170) REVERT: E 117 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: E 136 THR cc_start: 0.8536 (m) cc_final: 0.8327 (t) outliers start: 8 outliers final: 0 residues processed: 40 average time/residue: 0.5319 time to fit residues: 21.7327 Evaluate side-chains 35 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 117 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 0.0770 chunk 28 optimal weight: 6.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 117 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.112048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.093025 restraints weight = 2362.284| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.87 r_work: 0.3393 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2395 Z= 0.107 Angle : 0.489 3.527 3230 Z= 0.251 Chirality : 0.044 0.125 360 Planarity : 0.002 0.017 435 Dihedral : 4.106 11.238 350 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.92 % Allowed : 14.58 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.38), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 110 TYR 0.008 0.002 TYR E 138 PHE 0.003 0.001 PHE D 154 HIS 0.002 0.000 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 2395) covalent geometry : angle 0.48929 ( 3230) hydrogen bonds : bond 0.02810 ( 72) hydrogen bonds : angle 4.91907 ( 216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.054 Fit side-chains REVERT: E 101 ARG cc_start: 0.8329 (ttm170) cc_final: 0.6375 (tpt170) REVERT: E 117 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: E 131 MET cc_start: 0.8828 (ttp) cc_final: 0.8608 (ttm) REVERT: E 136 THR cc_start: 0.8522 (m) cc_final: 0.8302 (t) REVERT: E 143 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8459 (tt) outliers start: 7 outliers final: 1 residues processed: 34 average time/residue: 0.5160 time to fit residues: 17.8578 Evaluate side-chains 33 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 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 = 0.3668 r_free = 0.3668 target = 0.103306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084243 restraints weight = 2481.069| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.93 r_work: 0.3252 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 2395 Z= 0.308 Angle : 0.654 5.476 3230 Z= 0.336 Chirality : 0.049 0.128 360 Planarity : 0.004 0.043 435 Dihedral : 4.893 13.314 350 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.92 % Allowed : 15.00 % Favored : 82.08 % 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 aren not related in a simple way. whole: -1.85 (0.38), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 110 TYR 0.012 0.003 TYR B 138 PHE 0.007 0.002 PHE A 154 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00661 ( 2395) covalent geometry : angle 0.65388 ( 3230) hydrogen bonds : bond 0.04081 ( 72) hydrogen bonds : angle 5.27943 ( 216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.058 Fit side-chains REVERT: B 117 GLN cc_start: 0.8414 (tt0) cc_final: 0.8210 (tp40) REVERT: C 117 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8308 (tp40) REVERT: E 101 ARG cc_start: 0.8387 (ttm170) cc_final: 0.6286 (tpt170) REVERT: E 117 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: E 143 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8575 (tt) outliers start: 7 outliers final: 1 residues processed: 37 average time/residue: 0.4930 time to fit residues: 18.5737 Evaluate side-chains 38 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain C residue 117 GLN Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 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 = 0.3733 r_free = 0.3733 target = 0.108400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089485 restraints weight = 2442.391| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.89 r_work: 0.3341 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2395 Z= 0.159 Angle : 0.533 4.028 3230 Z= 0.274 Chirality : 0.045 0.127 360 Planarity : 0.003 0.023 435 Dihedral : 4.438 12.425 350 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.08 % Allowed : 15.83 % Favored : 82.08 % 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 aren not related in a simple way. whole: -1.87 (0.38), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 110 TYR 0.009 0.002 TYR B 138 PHE 0.004 0.001 PHE A 154 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 2395) covalent geometry : angle 0.53290 ( 3230) hydrogen bonds : bond 0.03251 ( 72) hydrogen bonds : angle 5.08337 ( 216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.091 Fit side-chains REVERT: B 117 GLN cc_start: 0.8324 (tt0) cc_final: 0.8097 (tp40) REVERT: C 117 GLN cc_start: 0.8506 (tp40) cc_final: 0.8265 (tp40) REVERT: E 101 ARG cc_start: 0.8335 (ttm170) cc_final: 0.6400 (tpt170) REVERT: E 117 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: E 143 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8533 (tt) outliers start: 5 outliers final: 1 residues processed: 37 average time/residue: 0.5503 time to fit residues: 20.7480 Evaluate side-chains 38 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 0.0270 chunk 20 optimal weight: 0.9980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 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 = 0.3793 r_free = 0.3793 target = 0.115810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.095439 restraints weight = 2253.865| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.00 r_work: 0.3404 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2395 Z= 0.116 Angle : 0.496 3.483 3230 Z= 0.255 Chirality : 0.044 0.126 360 Planarity : 0.002 0.016 435 Dihedral : 4.136 11.465 350 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.50 % Allowed : 14.58 % Favored : 82.92 % 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 aren not related in a simple way. whole: -1.88 (0.38), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 110 TYR 0.008 0.002 TYR E 138 PHE 0.003 0.001 PHE D 154 HIS 0.002 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 2395) covalent geometry : angle 0.49594 ( 3230) hydrogen bonds : bond 0.02855 ( 72) hydrogen bonds : angle 4.91316 ( 216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.20 seconds wall clock time: 22 minutes 12.54 seconds (1332.54 seconds total)