Starting phenix.real_space_refine on Wed Jun 4 11:17:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qlu_53234/06_2025/9qlu_53234_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qlu_53234/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9qlu_53234/06_2025/9qlu_53234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qlu_53234/06_2025/9qlu_53234.map" model { file = "/net/cci-nas-00/data/ceres_data/9qlu_53234/06_2025/9qlu_53234_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qlu_53234/06_2025/9qlu_53234_neut.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 4.72, per 1000 atoms: 2.00 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: 0.59 Conformation dependent library (CDL) restraints added in 326.2 milliseconds 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: 0.28 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: 0.58 Time building geometry restraints manager: 0.71 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.170 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.700 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (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 HIS 0.003 0.001 HIS E 118 PHE 0.004 0.001 PHE A 149 TYR 0.017 0.006 TYR B 138 ARG 0.009 0.002 ARG A 110 Details of bonding type rmsd hydrogen bonds : bond 0.10610 ( 72) hydrogen bonds : angle 7.58083 ( 216) covalent geometry : bond 0.00364 ( 2395) covalent geometry : angle 0.67559 ( 3230) *********************** 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 : 0.261 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: 1.5912 time to fit residues: 97.0827 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 : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.106662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086917 restraints weight = 2345.184| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.95 r_work: 0.3273 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1907 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= 0.197 Angle : 0.645 5.993 3230 Z= 0.321 Chirality : 0.047 0.126 360 Planarity : 0.003 0.020 435 Dihedral : 5.200 14.047 350 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.92 % Allowed : 12.92 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.36), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 145 PHE 0.005 0.001 PHE C 148 TYR 0.014 0.003 TYR B 138 ARG 0.002 0.000 ARG D 110 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 72) hydrogen bonds : angle 5.80016 ( 216) covalent geometry : bond 0.00439 ( 2395) covalent geometry : angle 0.64522 ( 3230) *********************** 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 43 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.257 Fit side-chains REVERT: B 117 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: D 117 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: E 101 ARG cc_start: 0.8369 (ttm170) cc_final: 0.6347 (tpt170) REVERT: E 117 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: E 131 MET cc_start: 0.8868 (ttp) cc_final: 0.8648 (ttm) outliers start: 7 outliers final: 0 residues processed: 36 average time/residue: 1.5670 time to fit residues: 57.5290 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 : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain E residue 117 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 0.0570 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- 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 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 = 0.3801 r_free = 0.3801 target = 0.114417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.095123 restraints weight = 2339.282| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.91 r_work: 0.3421 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2395 Z= 0.094 Angle : 0.497 4.570 3230 Z= 0.251 Chirality : 0.044 0.124 360 Planarity : 0.002 0.030 435 Dihedral : 4.299 11.541 350 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.92 % Allowed : 13.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.36), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 118 PHE 0.003 0.001 PHE D 154 TYR 0.009 0.002 TYR C 138 ARG 0.004 0.000 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.02759 ( 72) hydrogen bonds : angle 5.26537 ( 216) covalent geometry : bond 0.00202 ( 2395) covalent geometry : angle 0.49674 ( 3230) *********************** 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 49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.259 Fit side-chains REVERT: E 101 ARG cc_start: 0.8322 (ttm170) cc_final: 0.6461 (tpt170) outliers start: 7 outliers final: 1 residues processed: 42 average time/residue: 1.4029 time to fit residues: 60.1133 Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.109510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090160 restraints weight = 2343.264| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.92 r_work: 0.3277 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2272 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= 0.354 Angle : 0.706 5.318 3230 Z= 0.363 Chirality : 0.051 0.127 360 Planarity : 0.005 0.058 435 Dihedral : 5.127 13.233 350 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 5.42 % Allowed : 12.92 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.37), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 145 PHE 0.008 0.002 PHE A 154 TYR 0.013 0.003 TYR B 138 ARG 0.003 0.001 ARG A 110 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 72) hydrogen bonds : angle 5.46855 ( 216) covalent geometry : bond 0.00760 ( 2395) covalent geometry : angle 0.70609 ( 3230) *********************** 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 52 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.269 Fit side-chains REVERT: A 117 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7442 (tp-100) REVERT: B 117 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: D 117 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7860 (tp40) REVERT: E 101 ARG cc_start: 0.8395 (ttm170) cc_final: 0.6299 (tpt170) REVERT: E 117 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: E 131 MET cc_start: 0.8984 (ttp) cc_final: 0.8744 (ttm) outliers start: 13 outliers final: 0 residues processed: 44 average time/residue: 1.3606 time to fit residues: 61.1374 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 : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain B residue 117 GLN 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 24 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3702 r_free = 0.3702 target = 0.108939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.089604 restraints weight = 2384.009| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.93 r_work: 0.3308 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2395 Z= 0.224 Angle : 0.593 5.019 3230 Z= 0.303 Chirality : 0.047 0.126 360 Planarity : 0.004 0.042 435 Dihedral : 4.859 12.883 350 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.37), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 145 PHE 0.005 0.001 PHE A 154 TYR 0.011 0.002 TYR B 138 ARG 0.004 0.001 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 72) hydrogen bonds : angle 5.34323 ( 216) covalent geometry : bond 0.00479 ( 2395) covalent geometry : angle 0.59308 ( 3230) *********************** 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 48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.276 Fit side-chains REVERT: E 101 ARG cc_start: 0.8346 (ttm170) cc_final: 0.6272 (tpt170) REVERT: E 117 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: E 131 MET cc_start: 0.8926 (ttp) cc_final: 0.8682 (ttm) outliers start: 10 outliers final: 1 residues processed: 43 average time/residue: 1.4076 time to fit residues: 61.7647 Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain E residue 117 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 2 optimal weight: 0.0770 chunk 5 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.7344 ------------------------------------------------------------------------------- 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** ** 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 142 ASN ** 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 = 0.3723 r_free = 0.3723 target = 0.110458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.090862 restraints weight = 2343.005| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.94 r_work: 0.3333 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2395 Z= 0.189 Angle : 0.561 5.695 3230 Z= 0.286 Chirality : 0.046 0.125 360 Planarity : 0.003 0.037 435 Dihedral : 4.650 12.593 350 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.37), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 118 PHE 0.005 0.001 PHE A 154 TYR 0.010 0.002 TYR B 138 ARG 0.003 0.001 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 72) hydrogen bonds : angle 5.27027 ( 216) covalent geometry : bond 0.00404 ( 2395) covalent geometry : angle 0.56087 ( 3230) *********************** 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 44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.286 Fit side-chains REVERT: E 101 ARG cc_start: 0.8330 (ttm170) cc_final: 0.6297 (tpt170) REVERT: E 117 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8034 (tt0) outliers start: 7 outliers final: 1 residues processed: 41 average time/residue: 1.4877 time to fit residues: 62.2227 Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain E residue 117 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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** ** 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 = 0.3708 r_free = 0.3708 target = 0.109012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.089428 restraints weight = 2389.465| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.95 r_work: 0.3308 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2395 Z= 0.260 Angle : 0.619 6.664 3230 Z= 0.316 Chirality : 0.047 0.125 360 Planarity : 0.004 0.038 435 Dihedral : 4.885 12.966 350 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.75 % Allowed : 15.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.38), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 118 PHE 0.006 0.001 PHE A 154 TYR 0.011 0.003 TYR B 138 ARG 0.006 0.001 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 72) hydrogen bonds : angle 5.36214 ( 216) covalent geometry : bond 0.00556 ( 2395) covalent geometry : angle 0.61939 ( 3230) *********************** 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 47 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.257 Fit side-chains REVERT: A 117 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7646 (tp-100) REVERT: E 101 ARG cc_start: 0.8375 (ttm170) cc_final: 0.6322 (tpt170) REVERT: E 117 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: E 143 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8579 (tt) outliers start: 9 outliers final: 1 residues processed: 43 average time/residue: 1.3673 time to fit residues: 60.0059 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 : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- 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** ** 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 142 ASN ** 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 = 0.3737 r_free = 0.3737 target = 0.111249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.091335 restraints weight = 2391.454| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.96 r_work: 0.3315 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2395 Z= 0.195 Angle : 0.566 5.342 3230 Z= 0.289 Chirality : 0.046 0.126 360 Planarity : 0.003 0.028 435 Dihedral : 4.663 12.851 350 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.92 % Allowed : 15.42 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.38), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 118 PHE 0.005 0.001 PHE A 154 TYR 0.010 0.002 TYR B 138 ARG 0.004 0.001 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 72) hydrogen bonds : angle 5.26077 ( 216) covalent geometry : bond 0.00416 ( 2395) covalent geometry : angle 0.56602 ( 3230) *********************** 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 44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.270 Fit side-chains REVERT: C 143 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8119 (tt) REVERT: E 101 ARG cc_start: 0.8345 (ttm170) cc_final: 0.6312 (tpt170) REVERT: E 117 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7992 (tt0) outliers start: 7 outliers final: 1 residues processed: 40 average time/residue: 1.3503 time to fit residues: 55.1800 Evaluate side-chains 40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain E residue 117 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 142 ASN ** 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 = 0.3726 r_free = 0.3726 target = 0.110220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.090420 restraints weight = 2346.901| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.93 r_work: 0.3322 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2395 Z= 0.226 Angle : 0.589 5.149 3230 Z= 0.301 Chirality : 0.046 0.127 360 Planarity : 0.003 0.027 435 Dihedral : 4.747 13.037 350 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.17 % Allowed : 14.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.37), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 118 PHE 0.005 0.001 PHE A 154 TYR 0.011 0.002 TYR B 138 ARG 0.005 0.001 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 72) hydrogen bonds : angle 5.26156 ( 216) covalent geometry : bond 0.00482 ( 2395) covalent geometry : angle 0.58874 ( 3230) *********************** 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 47 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.276 Fit side-chains REVERT: C 143 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8114 (tt) REVERT: E 101 ARG cc_start: 0.8358 (ttm170) cc_final: 0.6332 (tpt170) REVERT: E 117 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: E 143 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8573 (tt) outliers start: 10 outliers final: 1 residues processed: 41 average time/residue: 1.3694 time to fit residues: 57.3504 Evaluate side-chains 40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN 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 = 0.3793 r_free = 0.3793 target = 0.115293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.095082 restraints weight = 2201.933| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.95 r_work: 0.3372 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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 : 0.003 0.020 2395 Z= 0.143 Angle : 0.522 4.551 3230 Z= 0.267 Chirality : 0.045 0.127 360 Planarity : 0.003 0.024 435 Dihedral : 4.411 12.195 350 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.33 % Allowed : 14.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.37), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 118 PHE 0.004 0.001 PHE A 154 TYR 0.009 0.002 TYR B 138 ARG 0.005 0.001 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.03113 ( 72) hydrogen bonds : angle 5.09065 ( 216) covalent geometry : bond 0.00307 ( 2395) covalent geometry : angle 0.52211 ( 3230) ********************** 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 43 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.248 Fit side-chains REVERT: C 117 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7576 (tp-100) REVERT: D 117 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8138 (tp40) REVERT: E 101 ARG cc_start: 0.8327 (ttm170) cc_final: 0.6282 (tpt170) REVERT: E 117 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: E 143 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8561 (tt) outliers start: 8 outliers final: 1 residues processed: 40 average time/residue: 1.4157 time to fit residues: 57.7842 Evaluate side-chains 38 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain C residue 117 GLN Chi-restraints excluded: chain D 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 25 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.113692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.093265 restraints weight = 2218.773| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.98 r_work: 0.3368 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 2395 Z= 0.282 Angle : 1.545 59.122 3230 Z= 0.906 Chirality : 0.064 0.854 360 Planarity : 0.003 0.024 435 Dihedral : 4.432 12.227 350 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.67 % Allowed : 17.08 % Favored : 81.25 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.37), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 118 PHE 0.004 0.001 PHE A 154 TYR 0.009 0.002 TYR B 138 ARG 0.005 0.001 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 72) hydrogen bonds : angle 5.09653 ( 216) covalent geometry : bond 0.00574 ( 2395) covalent geometry : angle 1.54469 ( 3230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2748.41 seconds wall clock time: 47 minutes 33.61 seconds (2853.61 seconds total)