Starting phenix.real_space_refine on Wed Sep 17 14:53:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgn_43212/09_2025/8vgn_43212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgn_43212/09_2025/8vgn_43212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vgn_43212/09_2025/8vgn_43212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgn_43212/09_2025/8vgn_43212.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgn_43212/09_2025/8vgn_43212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgn_43212/09_2025/8vgn_43212.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.031 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 54 5.16 5 C 5836 2.51 5 N 1500 2.21 5 O 1760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9150 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1668 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1623 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199} Chain: "G" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1284 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 1 Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1668 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "I" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1284 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 1 Chain: "L" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1623 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199} Time building chain proxies: 2.57, per 1000 atoms: 0.28 Number of scatterers: 9150 At special positions: 0 Unit cell: (62.6919, 154.39, 124.448, 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 54 16.00 O 1760 8.00 N 1500 7.00 C 5836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 167 " - pdb=" SG CYS G 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS H 220 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 167 " - pdb=" SG CYS I 183 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 350.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 22 sheets defined 29.7% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.686A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 191 through 196 removed outlier: 4.386A pdb=" N THR A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.518A pdb=" N ALA B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'G' and resid 48 through 71 Processing helix chain 'G' and resid 79 through 84 Processing helix chain 'G' and resid 85 through 98 Processing helix chain 'G' and resid 99 through 102 Processing helix chain 'G' and resid 114 through 143 Processing helix chain 'G' and resid 152 through 157 Processing helix chain 'G' and resid 171 through 176 removed outlier: 3.832A pdb=" N ASN G 176 " --> pdb=" O SER G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 219 removed outlier: 4.569A pdb=" N ASN G 214 " --> pdb=" O GLY G 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.686A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 131 through 133 No H-bonds generated for 'chain 'H' and resid 131 through 133' Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 191 through 196 removed outlier: 4.388A pdb=" N THR H 195 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 208 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 79 through 84 Processing helix chain 'I' and resid 85 through 98 Processing helix chain 'I' and resid 99 through 102 Processing helix chain 'I' and resid 114 through 143 Processing helix chain 'I' and resid 152 through 157 Processing helix chain 'I' and resid 171 through 176 removed outlier: 3.831A pdb=" N ASN I 176 " --> pdb=" O SER I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 219 removed outlier: 4.562A pdb=" N ASN I 214 " --> pdb=" O GLY I 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.518A pdb=" N ALA L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.021A pdb=" N ASN A 33 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N MET A 34 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 12 removed outlier: 7.034A pdb=" N CYS A 92 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TRP A 103 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG A 94 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 100A" --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 128 removed outlier: 5.710A pdb=" N TYR A 180 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 136 removed outlier: 5.710A pdb=" N TYR A 180 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 155 through 158 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.243A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLN B 37 " --> pdb=" O PRO B 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.243A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 118 removed outlier: 5.061A pdb=" N SER B 131 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU B 181 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL B 133 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU B 179 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU B 135 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER B 177 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN B 137 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 175 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB4, first strand: chain 'H' and resid 9 through 12 removed outlier: 4.023A pdb=" N ASN H 33 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 9 through 12 removed outlier: 7.036A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG H 94 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP H 100A" --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.709A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 135 through 136 removed outlier: 5.709A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 155 through 158 Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.245A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN L 37 " --> pdb=" O PRO L 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.245A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.064A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 153 through 154 514 hydrogen bonds defined for protein. 1332 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: 1.66 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2828 1.34 - 1.46: 2141 1.46 - 1.58: 4323 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 9374 Sorted by residual: bond pdb=" C GLU A 216 " pdb=" N PRO A 217 " ideal model delta sigma weight residual 1.334 1.352 -0.019 8.40e-03 1.42e+04 4.92e+00 bond pdb=" C GLU H 216 " pdb=" N PRO H 217 " ideal model delta sigma weight residual 1.334 1.351 -0.017 8.40e-03 1.42e+04 4.23e+00 bond pdb=" CG1 ILE G 95 " pdb=" CD1 ILE G 95 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.04e+00 bond pdb=" CG1 ILE I 95 " pdb=" CD1 ILE I 95 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.91e+00 bond pdb=" CB ARG L 61 " pdb=" CG ARG L 61 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.50e+00 ... (remaining 9369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 11954 1.59 - 3.18: 659 3.18 - 4.76: 109 4.76 - 6.35: 14 6.35 - 7.94: 10 Bond angle restraints: 12746 Sorted by residual: angle pdb=" N GLY G 75 " pdb=" CA GLY G 75 " pdb=" C GLY G 75 " ideal model delta sigma weight residual 111.52 118.49 -6.97 1.31e+00 5.83e-01 2.83e+01 angle pdb=" N GLY I 75 " pdb=" CA GLY I 75 " pdb=" C GLY I 75 " ideal model delta sigma weight residual 111.52 118.34 -6.82 1.31e+00 5.83e-01 2.71e+01 angle pdb=" N GLY G 91 " pdb=" CA GLY G 91 " pdb=" C GLY G 91 " ideal model delta sigma weight residual 112.64 116.80 -4.16 1.21e+00 6.83e-01 1.18e+01 angle pdb=" N GLY I 91 " pdb=" CA GLY I 91 " pdb=" C GLY I 91 " ideal model delta sigma weight residual 112.64 116.71 -4.07 1.21e+00 6.83e-01 1.13e+01 angle pdb=" N LYS I 142 " pdb=" CA LYS I 142 " pdb=" C LYS I 142 " ideal model delta sigma weight residual 113.72 117.63 -3.91 1.30e+00 5.92e-01 9.04e+00 ... (remaining 12741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 5123 17.26 - 34.53: 369 34.53 - 51.79: 62 51.79 - 69.06: 28 69.06 - 86.32: 16 Dihedral angle restraints: 5598 sinusoidal: 2120 harmonic: 3478 Sorted by residual: dihedral pdb=" CA PRO A 153 " pdb=" C PRO A 153 " pdb=" N VAL A 154 " pdb=" CA VAL A 154 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA PRO H 153 " pdb=" C PRO H 153 " pdb=" N VAL H 154 " pdb=" CA VAL H 154 " ideal model delta harmonic sigma weight residual 180.00 151.47 28.53 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA LYS H 218 " pdb=" C LYS H 218 " pdb=" N SER H 219 " pdb=" CA SER H 219 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 5595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1120 0.058 - 0.115: 276 0.115 - 0.173: 45 0.173 - 0.231: 1 0.231 - 0.288: 2 Chirality restraints: 1444 Sorted by residual: chirality pdb=" CA PHE H 150 " pdb=" N PHE H 150 " pdb=" C PHE H 150 " pdb=" CB PHE H 150 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA PHE A 150 " pdb=" N PHE A 150 " pdb=" C PHE A 150 " pdb=" CB PHE A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA PRO L 141 " pdb=" N PRO L 141 " pdb=" C PRO L 141 " pdb=" CB PRO L 141 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 1441 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 142 " -0.315 9.50e-02 1.11e+02 1.42e-01 1.56e+01 pdb=" NE ARG B 142 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 142 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG B 142 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 142 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 142 " -0.317 9.50e-02 1.11e+02 1.43e-01 1.56e+01 pdb=" NE ARG L 142 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG L 142 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG L 142 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG L 142 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 52 " -0.002 2.00e-02 2.50e+03 2.37e-02 1.12e+01 pdb=" CG TYR A 52 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR A 52 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 52 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 52 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR A 52 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 52 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR A 52 " -0.034 2.00e-02 2.50e+03 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2495 2.81 - 3.33: 8974 3.33 - 3.86: 16041 3.86 - 4.38: 19495 4.38 - 4.90: 32489 Nonbonded interactions: 79494 Sorted by model distance: nonbonded pdb=" OE2 GLU L 123 " pdb=" NZ LYS L 126 " model vdw 2.290 3.120 nonbonded pdb=" OE2 GLU B 123 " pdb=" NZ LYS B 126 " model vdw 2.290 3.120 nonbonded pdb=" OE1 GLU I 150 " pdb=" NH1 ARG I 156 " model vdw 2.307 3.120 nonbonded pdb=" OE1 GLU G 150 " pdb=" NH1 ARG G 156 " model vdw 2.310 3.120 nonbonded pdb=" OE2 GLU I 213 " pdb=" NZ LYS I 217 " model vdw 2.365 3.120 ... (remaining 79489 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'I' } 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: 4.580 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.170 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.006 0.056 9386 Z= 0.241 Angle : 0.832 7.940 12770 Z= 0.466 Chirality : 0.051 0.288 1444 Planarity : 0.008 0.143 1598 Dihedral : 14.287 86.319 3338 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.13 % Favored : 94.53 % Rotamer: Outliers : 0.78 % Allowed : 3.52 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.56 (0.23), residues: 1188 helix: -0.92 (0.26), residues: 270 sheet: 0.31 (0.25), residues: 418 loop : -0.48 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.004 ARG B 142 TYR 0.034 0.008 TYR H 52 PHE 0.038 0.003 PHE H 100D TRP 0.031 0.003 TRP L 91 HIS 0.007 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00569 ( 9374) covalent geometry : angle 0.83162 (12746) SS BOND : bond 0.00453 ( 12) SS BOND : angle 1.15736 ( 24) hydrogen bonds : bond 0.17546 ( 478) hydrogen bonds : angle 8.25395 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8008 (t0) cc_final: 0.7565 (t70) REVERT: G 49 SER cc_start: 0.8224 (m) cc_final: 0.7981 (p) REVERT: G 117 MET cc_start: 0.8221 (mtp) cc_final: 0.7212 (mmm) REVERT: G 119 MET cc_start: 0.7190 (mmt) cc_final: 0.6958 (mmt) REVERT: G 149 MET cc_start: 0.8089 (mmt) cc_final: 0.7859 (mmp) REVERT: G 213 GLU cc_start: 0.8559 (tp30) cc_final: 0.8185 (tm-30) REVERT: G 216 TRP cc_start: 0.7980 (m100) cc_final: 0.7332 (m-10) REVERT: H 72 ASP cc_start: 0.7999 (t0) cc_final: 0.7542 (t70) REVERT: I 49 SER cc_start: 0.8232 (m) cc_final: 0.7877 (p) REVERT: I 117 MET cc_start: 0.8248 (mtp) cc_final: 0.7218 (mmm) REVERT: I 119 MET cc_start: 0.7100 (mmt) cc_final: 0.6881 (mmt) REVERT: I 149 MET cc_start: 0.8076 (mmt) cc_final: 0.7840 (mmp) REVERT: I 213 GLU cc_start: 0.8544 (tp30) cc_final: 0.8181 (tm-30) REVERT: I 216 TRP cc_start: 0.7990 (m100) cc_final: 0.7340 (m-10) outliers start: 8 outliers final: 0 residues processed: 173 average time/residue: 0.7039 time to fit residues: 128.9784 Evaluate side-chains 110 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN B 53 ASN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 ASN G 204 GLN H 61 GLN I 171 ASN I 204 GLN L 53 ASN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.123169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.071856 restraints weight = 14758.397| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.42 r_work: 0.2790 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9386 Z= 0.259 Angle : 0.744 7.527 12770 Z= 0.389 Chirality : 0.047 0.189 1444 Planarity : 0.005 0.050 1598 Dihedral : 5.733 29.650 1278 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.83 % Allowed : 8.79 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.59 (0.24), residues: 1188 helix: 1.21 (0.30), residues: 270 sheet: 0.44 (0.24), residues: 422 loop : 0.04 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 24 TYR 0.025 0.002 TYR I 86 PHE 0.024 0.002 PHE A 100D TRP 0.028 0.002 TRP I 89 HIS 0.005 0.002 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 9374) covalent geometry : angle 0.74367 (12746) SS BOND : bond 0.00754 ( 12) SS BOND : angle 0.93416 ( 24) hydrogen bonds : bond 0.04565 ( 478) hydrogen bonds : angle 5.61085 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8151 (t0) cc_final: 0.7905 (t70) REVERT: A 216 GLU cc_start: 0.8189 (pm20) cc_final: 0.6274 (pm20) REVERT: A 218 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7464 (pttp) REVERT: B 170 ASP cc_start: 0.8307 (t0) cc_final: 0.8025 (t0) REVERT: G 71 MET cc_start: 0.8965 (mtm) cc_final: 0.8619 (mtp) REVERT: G 117 MET cc_start: 0.8192 (mtp) cc_final: 0.7563 (mmm) REVERT: G 149 MET cc_start: 0.8234 (mmt) cc_final: 0.7937 (mmp) REVERT: G 213 GLU cc_start: 0.8241 (tp30) cc_final: 0.7886 (tm-30) REVERT: G 216 TRP cc_start: 0.8101 (m100) cc_final: 0.7237 (m-10) REVERT: H 72 ASP cc_start: 0.8142 (t0) cc_final: 0.7892 (t70) REVERT: H 216 GLU cc_start: 0.8216 (pm20) cc_final: 0.6310 (pm20) REVERT: H 218 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7448 (pttp) REVERT: I 117 MET cc_start: 0.8252 (mtp) cc_final: 0.7608 (mmm) REVERT: I 119 MET cc_start: 0.7435 (mmt) cc_final: 0.7222 (tpp) REVERT: I 149 MET cc_start: 0.8239 (mmt) cc_final: 0.7972 (mmp) REVERT: I 213 GLU cc_start: 0.8236 (tp30) cc_final: 0.7891 (tm-30) REVERT: I 216 TRP cc_start: 0.8103 (m100) cc_final: 0.7196 (m-10) REVERT: L 79 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: L 170 ASP cc_start: 0.8329 (t0) cc_final: 0.8034 (t0) outliers start: 29 outliers final: 8 residues processed: 156 average time/residue: 0.7269 time to fit residues: 119.8983 Evaluate side-chains 119 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain H residue 218 LYS Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 183 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.0050 chunk 77 optimal weight: 0.8980 chunk 83 optimal weight: 0.0370 chunk 62 optimal weight: 0.9990 chunk 54 optimal weight: 0.0870 chunk 114 optimal weight: 0.0020 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 87 optimal weight: 0.6980 overall best weight: 0.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS B 137 ASN B 189 HIS H 3 GLN H 168 HIS L 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.129394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.078913 restraints weight = 14688.538| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.45 r_work: 0.2957 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9386 Z= 0.108 Angle : 0.592 7.785 12770 Z= 0.308 Chirality : 0.042 0.184 1444 Planarity : 0.004 0.050 1598 Dihedral : 4.806 19.691 1278 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.76 % Allowed : 11.62 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.20 (0.25), residues: 1188 helix: 2.37 (0.32), residues: 266 sheet: 0.69 (0.24), residues: 428 loop : 0.11 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 47 TYR 0.016 0.001 TYR G 86 PHE 0.009 0.001 PHE G 200 TRP 0.017 0.001 TRP G 89 HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9374) covalent geometry : angle 0.59273 (12746) SS BOND : bond 0.00208 ( 12) SS BOND : angle 0.39255 ( 24) hydrogen bonds : bond 0.03542 ( 478) hydrogen bonds : angle 4.84980 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8085 (t0) cc_final: 0.7686 (t70) REVERT: B 53 ASN cc_start: 0.9120 (m110) cc_final: 0.8885 (m110) REVERT: B 170 ASP cc_start: 0.8396 (t0) cc_final: 0.8124 (t0) REVERT: B 199 GLN cc_start: 0.8958 (tt0) cc_final: 0.8728 (tt0) REVERT: G 46 MET cc_start: 0.4978 (ttp) cc_final: 0.4633 (mpt) REVERT: G 48 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6013 (mp0) REVERT: G 71 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8567 (mtp) REVERT: G 117 MET cc_start: 0.7871 (mtp) cc_final: 0.7028 (mpp) REVERT: G 119 MET cc_start: 0.7641 (tpp) cc_final: 0.7297 (tpt) REVERT: G 149 MET cc_start: 0.8086 (mmt) cc_final: 0.7795 (mmp) REVERT: G 213 GLU cc_start: 0.8208 (tp30) cc_final: 0.7819 (tm-30) REVERT: G 216 TRP cc_start: 0.8070 (m100) cc_final: 0.7091 (m-10) REVERT: G 217 LYS cc_start: 0.7974 (mmpt) cc_final: 0.7767 (mmpt) REVERT: H 72 ASP cc_start: 0.8052 (t0) cc_final: 0.7638 (t70) REVERT: I 117 MET cc_start: 0.7748 (mtp) cc_final: 0.6723 (mmm) REVERT: I 119 MET cc_start: 0.6975 (mmt) cc_final: 0.6590 (tpt) REVERT: I 149 MET cc_start: 0.8079 (mmt) cc_final: 0.7843 (mmp) REVERT: I 213 GLU cc_start: 0.8175 (tp30) cc_final: 0.7797 (tm-30) REVERT: I 215 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7626 (mm-30) REVERT: I 216 TRP cc_start: 0.8052 (m100) cc_final: 0.7082 (m-10) REVERT: L 53 ASN cc_start: 0.9132 (m110) cc_final: 0.8877 (m110) REVERT: L 79 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7845 (mm-30) REVERT: L 82 ASP cc_start: 0.9028 (m-30) cc_final: 0.8807 (m-30) REVERT: L 170 ASP cc_start: 0.8411 (t0) cc_final: 0.8131 (t0) REVERT: L 199 GLN cc_start: 0.8869 (tt0) cc_final: 0.8652 (tt0) outliers start: 18 outliers final: 1 residues processed: 159 average time/residue: 0.6938 time to fit residues: 116.8653 Evaluate side-chains 120 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain G residue 71 MET Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 5 GLN A 61 GLN A 159 ASN A 168 HIS ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN H 3 GLN H 5 GLN H 61 GLN H 159 ASN H 168 HIS I 140 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.124763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.072530 restraints weight = 14552.925| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.42 r_work: 0.2819 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9386 Z= 0.196 Angle : 0.646 6.420 12770 Z= 0.332 Chirality : 0.044 0.149 1444 Planarity : 0.004 0.033 1598 Dihedral : 4.865 20.805 1278 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.37 % Allowed : 13.96 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.01 (0.25), residues: 1188 helix: 1.91 (0.31), residues: 272 sheet: 0.70 (0.24), residues: 428 loop : 0.03 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 24 TYR 0.022 0.002 TYR I 86 PHE 0.016 0.002 PHE G 200 TRP 0.029 0.001 TRP G 89 HIS 0.004 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 9374) covalent geometry : angle 0.64575 (12746) SS BOND : bond 0.00386 ( 12) SS BOND : angle 0.71788 ( 24) hydrogen bonds : bond 0.03994 ( 478) hydrogen bonds : angle 4.87020 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8157 (t0) cc_final: 0.7705 (t70) REVERT: A 159 ASN cc_start: 0.7933 (m-40) cc_final: 0.7650 (m110) REVERT: A 199 ILE cc_start: 0.8592 (pp) cc_final: 0.8301 (tp) REVERT: A 216 GLU cc_start: 0.8303 (pm20) cc_final: 0.6786 (pm20) REVERT: B 79 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8105 (mm-30) REVERT: B 170 ASP cc_start: 0.8523 (t0) cc_final: 0.8181 (t0) REVERT: G 46 MET cc_start: 0.5473 (ttp) cc_final: 0.4456 (mpt) REVERT: G 48 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6065 (mp0) REVERT: G 71 MET cc_start: 0.8944 (mtm) cc_final: 0.8574 (mtp) REVERT: G 117 MET cc_start: 0.7976 (mtp) cc_final: 0.7394 (mmm) REVERT: G 119 MET cc_start: 0.7658 (tpp) cc_final: 0.7286 (tpt) REVERT: G 149 MET cc_start: 0.8080 (mmt) cc_final: 0.7817 (mmp) REVERT: G 213 GLU cc_start: 0.8338 (tp30) cc_final: 0.8026 (tm-30) REVERT: G 216 TRP cc_start: 0.8084 (m100) cc_final: 0.7069 (m-10) REVERT: H 72 ASP cc_start: 0.8149 (t0) cc_final: 0.7716 (t70) REVERT: H 159 ASN cc_start: 0.7927 (m-40) cc_final: 0.7644 (m110) REVERT: H 199 ILE cc_start: 0.8577 (pp) cc_final: 0.8289 (tp) REVERT: H 216 GLU cc_start: 0.8331 (pm20) cc_final: 0.6814 (pm20) REVERT: I 117 MET cc_start: 0.7663 (mtp) cc_final: 0.6989 (mmm) REVERT: I 119 MET cc_start: 0.7135 (mmt) cc_final: 0.6827 (tpt) REVERT: I 149 MET cc_start: 0.8100 (mmt) cc_final: 0.7834 (mmp) REVERT: I 213 GLU cc_start: 0.8268 (tp30) cc_final: 0.8049 (tm-30) REVERT: I 216 TRP cc_start: 0.8072 (m100) cc_final: 0.7136 (m-10) REVERT: L 79 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7981 (mm-30) REVERT: L 170 ASP cc_start: 0.8534 (t0) cc_final: 0.8186 (t0) outliers start: 14 outliers final: 2 residues processed: 132 average time/residue: 0.7832 time to fit residues: 109.0344 Evaluate side-chains 118 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 76 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 5 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 ASN H 3 GLN H 5 GLN L 189 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.125861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074066 restraints weight = 14565.294| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.39 r_work: 0.2851 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9386 Z= 0.148 Angle : 0.602 6.207 12770 Z= 0.310 Chirality : 0.042 0.145 1444 Planarity : 0.004 0.039 1598 Dihedral : 4.710 19.033 1278 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.37 % Allowed : 13.77 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.15 (0.25), residues: 1188 helix: 2.11 (0.31), residues: 272 sheet: 0.80 (0.23), residues: 434 loop : 0.03 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 24 TYR 0.019 0.001 TYR I 86 PHE 0.014 0.001 PHE G 200 TRP 0.023 0.001 TRP I 89 HIS 0.008 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9374) covalent geometry : angle 0.60236 (12746) SS BOND : bond 0.00316 ( 12) SS BOND : angle 0.50623 ( 24) hydrogen bonds : bond 0.03677 ( 478) hydrogen bonds : angle 4.65726 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8142 (t0) cc_final: 0.7663 (t70) REVERT: A 81 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8714 (tt0) REVERT: A 159 ASN cc_start: 0.8008 (m-40) cc_final: 0.7794 (m110) REVERT: A 199 ILE cc_start: 0.8382 (pp) cc_final: 0.8144 (tp) REVERT: A 216 GLU cc_start: 0.8100 (pm20) cc_final: 0.7820 (pp20) REVERT: B 79 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8115 (mm-30) REVERT: B 145 LYS cc_start: 0.8824 (ptmm) cc_final: 0.8208 (pptt) REVERT: B 167 ASP cc_start: 0.8400 (t0) cc_final: 0.7963 (t0) REVERT: B 169 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8737 (pptt) REVERT: B 170 ASP cc_start: 0.8570 (t0) cc_final: 0.8034 (t0) REVERT: G 46 MET cc_start: 0.5409 (ttp) cc_final: 0.4429 (mpt) REVERT: G 48 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6185 (mp0) REVERT: G 71 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8570 (mtp) REVERT: G 117 MET cc_start: 0.7699 (mtp) cc_final: 0.7158 (mmm) REVERT: G 119 MET cc_start: 0.7626 (tpp) cc_final: 0.7280 (tpt) REVERT: G 149 MET cc_start: 0.8055 (mmt) cc_final: 0.7774 (mmp) REVERT: G 213 GLU cc_start: 0.8304 (tp30) cc_final: 0.8023 (tm-30) REVERT: G 216 TRP cc_start: 0.8095 (m100) cc_final: 0.7107 (m-10) REVERT: H 72 ASP cc_start: 0.8175 (t0) cc_final: 0.7680 (t70) REVERT: H 199 ILE cc_start: 0.8389 (pp) cc_final: 0.8148 (tp) REVERT: H 216 GLU cc_start: 0.8121 (pm20) cc_final: 0.7808 (pp20) REVERT: I 117 MET cc_start: 0.7529 (mtp) cc_final: 0.7229 (tpp) REVERT: I 119 MET cc_start: 0.7143 (mmt) cc_final: 0.6829 (tpt) REVERT: I 149 MET cc_start: 0.8005 (mmt) cc_final: 0.7737 (mmp) REVERT: I 213 GLU cc_start: 0.8272 (tp30) cc_final: 0.8001 (tm-30) REVERT: I 216 TRP cc_start: 0.8067 (m100) cc_final: 0.7052 (m-10) REVERT: L 79 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8100 (mm-30) REVERT: L 167 ASP cc_start: 0.8401 (t0) cc_final: 0.7972 (t0) REVERT: L 169 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8779 (pptt) REVERT: L 170 ASP cc_start: 0.8577 (t0) cc_final: 0.8038 (t0) outliers start: 14 outliers final: 3 residues processed: 130 average time/residue: 0.7949 time to fit residues: 108.8499 Evaluate side-chains 120 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain G residue 71 MET Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 169 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 13 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 5 GLN A 61 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN H 61 GLN I 166 ASN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.124666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.072528 restraints weight = 14508.855| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.42 r_work: 0.2824 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9386 Z= 0.177 Angle : 0.617 6.460 12770 Z= 0.316 Chirality : 0.043 0.150 1444 Planarity : 0.004 0.043 1598 Dihedral : 4.713 20.328 1278 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.66 % Allowed : 13.38 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.20 (0.25), residues: 1188 helix: 2.13 (0.31), residues: 272 sheet: 0.88 (0.23), residues: 434 loop : 0.02 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 24 TYR 0.020 0.002 TYR I 86 PHE 0.015 0.001 PHE G 200 TRP 0.026 0.001 TRP G 89 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9374) covalent geometry : angle 0.61694 (12746) SS BOND : bond 0.00333 ( 12) SS BOND : angle 0.50907 ( 24) hydrogen bonds : bond 0.03805 ( 478) hydrogen bonds : angle 4.66833 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8209 (t0) cc_final: 0.7729 (t70) REVERT: A 81 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8704 (tt0) REVERT: A 216 GLU cc_start: 0.8198 (pm20) cc_final: 0.7951 (pp20) REVERT: B 79 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8157 (mm-30) REVERT: B 160 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: B 167 ASP cc_start: 0.8430 (t0) cc_final: 0.8024 (t0) REVERT: B 169 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8826 (pptt) REVERT: B 170 ASP cc_start: 0.8625 (t0) cc_final: 0.8140 (t0) REVERT: G 46 MET cc_start: 0.5859 (ttp) cc_final: 0.4579 (mpt) REVERT: G 48 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6187 (mp0) REVERT: G 71 MET cc_start: 0.8943 (mtm) cc_final: 0.8574 (mtp) REVERT: G 117 MET cc_start: 0.7792 (mtp) cc_final: 0.7426 (tpp) REVERT: G 149 MET cc_start: 0.7932 (mmt) cc_final: 0.7693 (mmp) REVERT: G 213 GLU cc_start: 0.8321 (tp30) cc_final: 0.8061 (tm-30) REVERT: H 72 ASP cc_start: 0.8189 (t0) cc_final: 0.7701 (t70) REVERT: H 216 GLU cc_start: 0.8211 (pm20) cc_final: 0.7952 (pp20) REVERT: I 117 MET cc_start: 0.7682 (mtp) cc_final: 0.7335 (tpp) REVERT: I 119 MET cc_start: 0.7171 (mmt) cc_final: 0.6804 (tpt) REVERT: I 149 MET cc_start: 0.7936 (mmt) cc_final: 0.7715 (mmp) REVERT: I 213 GLU cc_start: 0.8294 (tp30) cc_final: 0.8054 (tm-30) REVERT: L 79 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8155 (mm-30) REVERT: L 167 ASP cc_start: 0.8423 (t0) cc_final: 0.8019 (t0) REVERT: L 169 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8820 (pptt) REVERT: L 170 ASP cc_start: 0.8634 (t0) cc_final: 0.8144 (t0) outliers start: 17 outliers final: 5 residues processed: 130 average time/residue: 0.7816 time to fit residues: 107.1041 Evaluate side-chains 122 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 169 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 5 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 ASN H 5 GLN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.125191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073402 restraints weight = 14581.028| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.39 r_work: 0.2840 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9386 Z= 0.151 Angle : 0.601 6.753 12770 Z= 0.309 Chirality : 0.042 0.143 1444 Planarity : 0.004 0.047 1598 Dihedral : 4.621 19.328 1278 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.76 % Allowed : 13.77 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.34 (0.25), residues: 1188 helix: 2.30 (0.31), residues: 272 sheet: 1.00 (0.24), residues: 434 loop : 0.03 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 24 TYR 0.018 0.001 TYR I 86 PHE 0.014 0.001 PHE G 200 TRP 0.023 0.001 TRP G 89 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9374) covalent geometry : angle 0.60162 (12746) SS BOND : bond 0.00318 ( 12) SS BOND : angle 0.48398 ( 24) hydrogen bonds : bond 0.03650 ( 478) hydrogen bonds : angle 4.57983 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8181 (t0) cc_final: 0.7691 (t70) REVERT: A 81 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8713 (tt0) REVERT: B 79 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8141 (mm-30) REVERT: B 169 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8777 (pptt) REVERT: B 170 ASP cc_start: 0.8668 (t0) cc_final: 0.8114 (t0) REVERT: G 46 MET cc_start: 0.5831 (ttp) cc_final: 0.4535 (mpt) REVERT: G 48 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6206 (mp0) REVERT: G 71 MET cc_start: 0.8953 (mtm) cc_final: 0.8577 (mtp) REVERT: G 119 MET cc_start: 0.7746 (tpp) cc_final: 0.7395 (tpt) REVERT: G 149 MET cc_start: 0.7893 (mmt) cc_final: 0.7677 (mmp) REVERT: G 213 GLU cc_start: 0.8365 (tp30) cc_final: 0.8085 (tm-30) REVERT: G 216 TRP cc_start: 0.8073 (m100) cc_final: 0.7025 (m-10) REVERT: H 72 ASP cc_start: 0.8180 (t0) cc_final: 0.7666 (t70) REVERT: H 216 GLU cc_start: 0.8298 (pm20) cc_final: 0.8081 (pp20) REVERT: I 119 MET cc_start: 0.7188 (mmt) cc_final: 0.6800 (tpt) REVERT: I 149 MET cc_start: 0.7897 (mmt) cc_final: 0.7678 (mmp) REVERT: I 213 GLU cc_start: 0.8307 (tp30) cc_final: 0.8019 (tm-30) REVERT: I 216 TRP cc_start: 0.8196 (m100) cc_final: 0.7123 (m-10) REVERT: L 79 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8128 (mm-30) REVERT: L 169 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8801 (pptt) REVERT: L 170 ASP cc_start: 0.8670 (t0) cc_final: 0.8117 (t0) outliers start: 18 outliers final: 6 residues processed: 129 average time/residue: 0.7527 time to fit residues: 102.5472 Evaluate side-chains 122 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 169 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 114 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 61 GLN A 159 ASN B 199 GLN H 5 GLN H 61 GLN H 159 ASN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.123052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.071191 restraints weight = 14567.522| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.43 r_work: 0.2769 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 9386 Z= 0.292 Angle : 0.704 8.467 12770 Z= 0.360 Chirality : 0.046 0.162 1444 Planarity : 0.005 0.050 1598 Dihedral : 5.003 24.317 1278 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.05 % Allowed : 13.28 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.10 (0.24), residues: 1188 helix: 1.88 (0.31), residues: 272 sheet: 0.93 (0.23), residues: 432 loop : -0.04 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 24 TYR 0.024 0.002 TYR I 86 PHE 0.020 0.002 PHE H 150 TRP 0.025 0.002 TRP G 89 HIS 0.006 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00683 ( 9374) covalent geometry : angle 0.70392 (12746) SS BOND : bond 0.00429 ( 12) SS BOND : angle 0.63613 ( 24) hydrogen bonds : bond 0.04286 ( 478) hydrogen bonds : angle 4.87796 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8212 (t0) cc_final: 0.7727 (t70) REVERT: A 81 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8773 (tt0) REVERT: B 79 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8171 (mm-30) REVERT: B 169 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8791 (pptt) REVERT: B 170 ASP cc_start: 0.8695 (t0) cc_final: 0.8164 (t0) REVERT: G 71 MET cc_start: 0.8879 (mtm) cc_final: 0.8504 (mtp) REVERT: G 93 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8051 (mtp) REVERT: G 119 MET cc_start: 0.7712 (tpp) cc_final: 0.7335 (tpt) REVERT: G 149 MET cc_start: 0.7926 (mmt) cc_final: 0.7709 (mmp) REVERT: G 213 GLU cc_start: 0.8346 (tp30) cc_final: 0.8034 (tm-30) REVERT: G 216 TRP cc_start: 0.8199 (m100) cc_final: 0.7298 (m-10) REVERT: H 72 ASP cc_start: 0.8203 (t0) cc_final: 0.7714 (t70) REVERT: H 216 GLU cc_start: 0.8333 (pm20) cc_final: 0.8129 (pp20) REVERT: I 93 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8013 (mtp) REVERT: I 119 MET cc_start: 0.7124 (mmt) cc_final: 0.6691 (tpt) REVERT: I 149 MET cc_start: 0.7886 (mmt) cc_final: 0.7659 (mmp) REVERT: I 213 GLU cc_start: 0.8324 (tp30) cc_final: 0.8015 (tm-30) REVERT: I 216 TRP cc_start: 0.8231 (m100) cc_final: 0.7268 (m-10) REVERT: L 79 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: L 169 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8789 (pptt) REVERT: L 170 ASP cc_start: 0.8698 (t0) cc_final: 0.8172 (t0) outliers start: 21 outliers final: 6 residues processed: 129 average time/residue: 0.7594 time to fit residues: 103.3982 Evaluate side-chains 118 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 183 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 73 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN G 166 ASN H 5 GLN I 166 ASN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.124295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.072340 restraints weight = 14519.656| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.40 r_work: 0.2817 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9386 Z= 0.165 Angle : 0.635 7.979 12770 Z= 0.326 Chirality : 0.042 0.146 1444 Planarity : 0.005 0.057 1598 Dihedral : 4.758 21.024 1278 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.07 % Allowed : 14.94 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.14 (0.24), residues: 1188 helix: 2.11 (0.31), residues: 272 sheet: 0.80 (0.24), residues: 424 loop : 0.03 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 24 TYR 0.019 0.001 TYR I 86 PHE 0.015 0.001 PHE G 200 TRP 0.024 0.001 TRP I 89 HIS 0.007 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9374) covalent geometry : angle 0.63496 (12746) SS BOND : bond 0.00335 ( 12) SS BOND : angle 0.52883 ( 24) hydrogen bonds : bond 0.03697 ( 478) hydrogen bonds : angle 4.65217 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8234 (t0) cc_final: 0.7732 (t70) REVERT: A 81 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8740 (tt0) REVERT: B 79 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8157 (mm-30) REVERT: B 169 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8823 (pptt) REVERT: B 170 ASP cc_start: 0.8707 (t0) cc_final: 0.8153 (t0) REVERT: G 46 MET cc_start: 0.5962 (ttp) cc_final: 0.4225 (mpt) REVERT: G 48 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6181 (mp0) REVERT: G 71 MET cc_start: 0.8904 (mtm) cc_final: 0.8542 (mtp) REVERT: G 117 MET cc_start: 0.8591 (mtp) cc_final: 0.8006 (tpt) REVERT: G 119 MET cc_start: 0.7634 (tpp) cc_final: 0.7337 (tpt) REVERT: G 149 MET cc_start: 0.7880 (mmt) cc_final: 0.7657 (mmp) REVERT: G 213 GLU cc_start: 0.8288 (tp30) cc_final: 0.7955 (tm-30) REVERT: G 214 ASN cc_start: 0.8347 (t0) cc_final: 0.7938 (t0) REVERT: G 216 TRP cc_start: 0.8167 (m100) cc_final: 0.7128 (m-10) REVERT: H 72 ASP cc_start: 0.8236 (t0) cc_final: 0.7748 (t70) REVERT: I 117 MET cc_start: 0.8479 (mtp) cc_final: 0.7956 (tpt) REVERT: I 119 MET cc_start: 0.7044 (mmt) cc_final: 0.6654 (tpt) REVERT: I 213 GLU cc_start: 0.8271 (tp30) cc_final: 0.7930 (tm-30) REVERT: I 215 GLU cc_start: 0.8554 (tt0) cc_final: 0.8181 (tt0) REVERT: I 216 TRP cc_start: 0.8242 (m100) cc_final: 0.7229 (m-10) REVERT: L 79 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8116 (mm-30) REVERT: L 169 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8846 (pptt) REVERT: L 170 ASP cc_start: 0.8702 (t0) cc_final: 0.8145 (t0) outliers start: 11 outliers final: 6 residues processed: 120 average time/residue: 0.7749 time to fit residues: 98.1854 Evaluate side-chains 117 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 183 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 99 optimal weight: 0.7980 chunk 1 optimal weight: 0.0470 chunk 18 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 61 GLN H 5 GLN H 61 GLN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.126118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.074847 restraints weight = 14445.558| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.40 r_work: 0.2864 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9386 Z= 0.125 Angle : 0.608 7.547 12770 Z= 0.313 Chirality : 0.041 0.144 1444 Planarity : 0.005 0.060 1598 Dihedral : 4.575 19.362 1278 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.07 % Allowed : 15.14 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.33 (0.25), residues: 1188 helix: 2.32 (0.31), residues: 272 sheet: 0.89 (0.24), residues: 424 loop : 0.13 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 24 TYR 0.016 0.001 TYR I 86 PHE 0.012 0.001 PHE G 200 TRP 0.020 0.001 TRP G 89 HIS 0.009 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9374) covalent geometry : angle 0.60824 (12746) SS BOND : bond 0.00308 ( 12) SS BOND : angle 0.45649 ( 24) hydrogen bonds : bond 0.03422 ( 478) hydrogen bonds : angle 4.46977 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8195 (t0) cc_final: 0.7690 (t70) REVERT: B 53 ASN cc_start: 0.9140 (m110) cc_final: 0.8842 (m110) REVERT: B 79 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8210 (mm-30) REVERT: B 169 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8887 (pptt) REVERT: B 170 ASP cc_start: 0.8737 (t0) cc_final: 0.8191 (t0) REVERT: G 46 MET cc_start: 0.5881 (ttp) cc_final: 0.4380 (mpt) REVERT: G 48 GLU cc_start: 0.7086 (mm-30) cc_final: 0.5952 (mp0) REVERT: G 71 MET cc_start: 0.8913 (mtm) cc_final: 0.8532 (mtp) REVERT: G 117 MET cc_start: 0.8562 (mtp) cc_final: 0.8192 (tpt) REVERT: G 119 MET cc_start: 0.7584 (tpp) cc_final: 0.7263 (tpt) REVERT: G 149 MET cc_start: 0.7881 (mmt) cc_final: 0.7666 (mmp) REVERT: G 213 GLU cc_start: 0.8252 (tp30) cc_final: 0.7914 (tm-30) REVERT: G 214 ASN cc_start: 0.8301 (t0) cc_final: 0.8013 (t0) REVERT: G 216 TRP cc_start: 0.8117 (m100) cc_final: 0.7008 (m-10) REVERT: H 72 ASP cc_start: 0.8219 (t0) cc_final: 0.7702 (t70) REVERT: I 48 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6806 (mm-30) REVERT: I 117 MET cc_start: 0.8451 (mtp) cc_final: 0.7907 (tpt) REVERT: I 119 MET cc_start: 0.7030 (mmt) cc_final: 0.6625 (tpt) REVERT: I 213 GLU cc_start: 0.8248 (tp30) cc_final: 0.7885 (tm-30) REVERT: I 215 GLU cc_start: 0.8481 (tt0) cc_final: 0.8030 (tt0) REVERT: I 216 TRP cc_start: 0.8192 (m100) cc_final: 0.7158 (m-10) REVERT: L 53 ASN cc_start: 0.9150 (m110) cc_final: 0.8860 (m110) REVERT: L 79 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8199 (mm-30) REVERT: L 169 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8884 (pptt) REVERT: L 170 ASP cc_start: 0.8736 (t0) cc_final: 0.8186 (t0) outliers start: 11 outliers final: 7 residues processed: 133 average time/residue: 0.7254 time to fit residues: 102.0883 Evaluate side-chains 123 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 183 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 67 optimal weight: 0.0270 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 75 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 159 ASN H 3 GLN ** L 189 HIS ** 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 = 0.3827 r_free = 0.3827 target = 0.125879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.074234 restraints weight = 14354.219| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.41 r_work: 0.2858 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9386 Z= 0.138 Angle : 0.626 7.485 12770 Z= 0.322 Chirality : 0.041 0.141 1444 Planarity : 0.004 0.052 1598 Dihedral : 4.573 19.259 1278 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.37 % Allowed : 15.62 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.41 (0.24), residues: 1188 helix: 2.36 (0.31), residues: 272 sheet: 0.98 (0.24), residues: 422 loop : 0.17 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 24 TYR 0.017 0.001 TYR I 86 PHE 0.013 0.001 PHE G 200 TRP 0.023 0.001 TRP I 89 HIS 0.009 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9374) covalent geometry : angle 0.62586 (12746) SS BOND : bond 0.00333 ( 12) SS BOND : angle 0.51241 ( 24) hydrogen bonds : bond 0.03506 ( 478) hydrogen bonds : angle 4.45937 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5527.17 seconds wall clock time: 95 minutes 0.37 seconds (5700.37 seconds total)