Starting phenix.real_space_refine on Mon May 12 18:18:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgn_43212/05_2025/8vgn_43212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgn_43212/05_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_43212/05_2025/8vgn_43212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgn_43212/05_2025/8vgn_43212.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgn_43212/05_2025/8vgn_43212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgn_43212/05_2025/8vgn_43212.cif" } resolution = 2.5 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.69, per 1000 atoms: 0.73 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: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.46 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: 2.89 Time building geometry restraints manager: 2.84 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: 0.01 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: 4.570 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.460 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.060 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (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 TRP 0.031 0.003 TRP L 91 HIS 0.007 0.001 HIS B 34 PHE 0.038 0.003 PHE H 100D TYR 0.034 0.008 TYR H 52 ARG 0.032 0.004 ARG B 142 Details of bonding type rmsd hydrogen bonds : bond 0.17546 ( 478) hydrogen bonds : angle 8.25395 ( 1332) SS BOND : bond 0.00453 ( 12) SS BOND : angle 1.15736 ( 24) covalent geometry : bond 0.00569 ( 9374) covalent geometry : angle 0.83162 (12746) *********************** 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 : 1.032 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: 0.7982 (p) REVERT: G 117 MET cc_start: 0.8221 (mtp) cc_final: 0.7627 (mmm) REVERT: G 119 MET cc_start: 0.7190 (mmt) cc_final: 0.6540 (tpt) 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: 0.8188 (tm-30) REVERT: G 215 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7563 (mm-30) REVERT: G 216 TRP cc_start: 0.7980 (m100) cc_final: 0.7339 (m-10) REVERT: H 3 GLN cc_start: 0.8799 (tt0) cc_final: 0.8544 (tt0) REVERT: H 5 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8318 (tp40) 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: 0.7244 (mmm) REVERT: I 119 MET cc_start: 0.7100 (mmt) cc_final: 0.6883 (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: 1.3364 time to fit residues: 245.4288 Evaluate side-chains 114 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 47 optimal weight: 0.2980 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 GLN L 53 ASN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.125360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.074872 restraints weight = 14630.436| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.37 r_work: 0.2848 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9386 Z= 0.163 Angle : 0.685 6.453 12770 Z= 0.360 Chirality : 0.045 0.159 1444 Planarity : 0.005 0.050 1598 Dihedral : 5.643 29.435 1278 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.86 % Allowed : 9.38 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1188 helix: 1.44 (0.30), residues: 270 sheet: 0.42 (0.24), residues: 426 loop : 0.13 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 89 HIS 0.004 0.001 HIS B 189 PHE 0.020 0.002 PHE H 100D TYR 0.022 0.002 TYR G 86 ARG 0.010 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 478) hydrogen bonds : angle 5.46956 ( 1332) SS BOND : bond 0.00654 ( 12) SS BOND : angle 0.63510 ( 24) covalent geometry : bond 0.00365 ( 9374) covalent geometry : angle 0.68487 (12746) *********************** 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 157 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8103 (t0) cc_final: 0.7786 (t70) REVERT: A 199 ILE cc_start: 0.8295 (tp) cc_final: 0.8081 (tp) REVERT: B 170 ASP cc_start: 0.8269 (t0) cc_final: 0.7983 (t0) REVERT: G 49 SER cc_start: 0.8261 (m) cc_final: 0.8057 (p) REVERT: G 71 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8650 (mtp) REVERT: G 117 MET cc_start: 0.8009 (mtp) cc_final: 0.6827 (mmm) REVERT: G 118 ILE cc_start: 0.8412 (mm) cc_final: 0.8158 (mp) REVERT: G 119 MET cc_start: 0.7280 (mmt) cc_final: 0.6820 (tpt) REVERT: G 149 MET cc_start: 0.8210 (mmt) cc_final: 0.7942 (mmp) REVERT: G 213 GLU cc_start: 0.8198 (tp30) cc_final: 0.7836 (tm-30) REVERT: G 215 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7523 (mm-30) REVERT: G 216 TRP cc_start: 0.8093 (m100) cc_final: 0.7207 (m-10) REVERT: H 72 ASP cc_start: 0.8090 (t0) cc_final: 0.7711 (t70) REVERT: H 212 ASP cc_start: 0.9128 (m-30) cc_final: 0.8872 (m-30) REVERT: I 117 MET cc_start: 0.8200 (mtp) cc_final: 0.7019 (mmm) REVERT: I 118 ILE cc_start: 0.8520 (mm) cc_final: 0.8185 (mp) REVERT: I 119 MET cc_start: 0.7299 (mmt) cc_final: 0.6833 (tpt) REVERT: I 149 MET cc_start: 0.8221 (mmt) cc_final: 0.7906 (mmp) REVERT: I 213 GLU cc_start: 0.8190 (tp30) cc_final: 0.7861 (tm-30) REVERT: I 215 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7599 (mm-30) REVERT: I 216 TRP cc_start: 0.8103 (m100) cc_final: 0.7217 (m-10) REVERT: L 53 ASN cc_start: 0.9227 (m110) cc_final: 0.8967 (m110) REVERT: L 79 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: L 170 ASP cc_start: 0.8288 (t0) cc_final: 0.7996 (t0) outliers start: 19 outliers final: 2 residues processed: 154 average time/residue: 1.3557 time to fit residues: 221.3851 Evaluate side-chains 121 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain G residue 71 MET Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 171 ASN ** 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 = 0.3816 r_free = 0.3816 target = 0.124402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.072785 restraints weight = 14539.298| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.41 r_work: 0.2756 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9386 Z= 0.221 Angle : 0.686 8.101 12770 Z= 0.355 Chirality : 0.046 0.181 1444 Planarity : 0.004 0.036 1598 Dihedral : 5.237 22.261 1278 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.64 % Allowed : 10.94 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1188 helix: 1.79 (0.31), residues: 270 sheet: 0.56 (0.24), residues: 428 loop : 0.06 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 89 HIS 0.005 0.001 HIS B 189 PHE 0.021 0.002 PHE L 116 TYR 0.023 0.002 TYR I 86 ARG 0.008 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 478) hydrogen bonds : angle 5.21013 ( 1332) SS BOND : bond 0.00450 ( 12) SS BOND : angle 0.67941 ( 24) covalent geometry : bond 0.00515 ( 9374) covalent geometry : angle 0.68622 (12746) *********************** 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 159 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8067 (t0) cc_final: 0.7736 (t70) REVERT: B 170 ASP cc_start: 0.8301 (t0) cc_final: 0.7943 (t0) REVERT: B 199 GLN cc_start: 0.8904 (tt0) cc_final: 0.8702 (tt0) REVERT: G 46 MET cc_start: 0.5378 (ttp) cc_final: 0.4871 (mpt) REVERT: G 49 SER cc_start: 0.8337 (m) cc_final: 0.8109 (p) REVERT: G 71 MET cc_start: 0.8899 (mtm) cc_final: 0.8548 (mtp) REVERT: G 117 MET cc_start: 0.7980 (mtp) cc_final: 0.6866 (mmm) REVERT: G 118 ILE cc_start: 0.8355 (mm) cc_final: 0.8117 (mp) REVERT: G 149 MET cc_start: 0.8058 (mmt) cc_final: 0.7725 (mmp) REVERT: G 213 GLU cc_start: 0.8288 (tp30) cc_final: 0.7964 (tm-30) REVERT: G 215 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7666 (mm-30) REVERT: G 216 TRP cc_start: 0.8175 (m100) cc_final: 0.7240 (m-10) REVERT: H 72 ASP cc_start: 0.8050 (t0) cc_final: 0.7720 (t70) REVERT: H 201 ASN cc_start: 0.8427 (m-40) cc_final: 0.8221 (m-40) REVERT: H 216 GLU cc_start: 0.8405 (pm20) cc_final: 0.8123 (pp20) REVERT: I 93 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8051 (mtp) REVERT: I 117 MET cc_start: 0.8081 (mtp) cc_final: 0.6941 (mmm) REVERT: I 118 ILE cc_start: 0.8325 (mm) cc_final: 0.8108 (mp) REVERT: I 119 MET cc_start: 0.7157 (mmt) cc_final: 0.6701 (tpt) REVERT: I 149 MET cc_start: 0.8068 (mmt) cc_final: 0.7822 (mmp) REVERT: I 213 GLU cc_start: 0.8255 (tp30) cc_final: 0.7934 (tm-30) REVERT: I 215 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7568 (mm-30) REVERT: I 216 TRP cc_start: 0.8149 (m100) cc_final: 0.7119 (m-10) REVERT: L 170 ASP cc_start: 0.8311 (t0) cc_final: 0.7951 (t0) REVERT: L 199 GLN cc_start: 0.8888 (tt0) cc_final: 0.8683 (tt0) outliers start: 27 outliers final: 6 residues processed: 151 average time/residue: 1.3625 time to fit residues: 218.4827 Evaluate side-chains 126 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain L residue 12 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 64 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 61 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 61 GLN ** I 171 ASN ** 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 = 0.3818 r_free = 0.3818 target = 0.125051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.073317 restraints weight = 14504.361| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.39 r_work: 0.2842 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9386 Z= 0.164 Angle : 0.636 8.656 12770 Z= 0.328 Chirality : 0.044 0.179 1444 Planarity : 0.004 0.037 1598 Dihedral : 4.863 19.441 1278 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.15 % Allowed : 12.11 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.04 (0.25), residues: 1188 helix: 2.10 (0.32), residues: 272 sheet: 0.65 (0.24), residues: 428 loop : 0.02 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 89 HIS 0.004 0.001 HIS L 189 PHE 0.015 0.002 PHE L 116 TYR 0.019 0.002 TYR G 86 ARG 0.011 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 478) hydrogen bonds : angle 4.87764 ( 1332) SS BOND : bond 0.00435 ( 12) SS BOND : angle 0.61013 ( 24) covalent geometry : bond 0.00378 ( 9374) covalent geometry : angle 0.63558 (12746) *********************** 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 150 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8112 (t0) cc_final: 0.7717 (t70) REVERT: B 79 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8194 (mm-30) REVERT: B 167 ASP cc_start: 0.8237 (t0) cc_final: 0.7920 (t0) REVERT: B 169 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8552 (pptt) REVERT: B 170 ASP cc_start: 0.8485 (t0) cc_final: 0.8021 (t0) REVERT: G 46 MET cc_start: 0.5312 (ttp) cc_final: 0.5074 (mpt) REVERT: G 48 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6019 (mp0) REVERT: G 71 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8572 (mtp) REVERT: G 117 MET cc_start: 0.7933 (mtp) cc_final: 0.6884 (mmm) REVERT: G 118 ILE cc_start: 0.8299 (mm) cc_final: 0.8094 (mp) REVERT: G 119 MET cc_start: 0.7728 (tpp) cc_final: 0.7378 (tpt) REVERT: G 149 MET cc_start: 0.8124 (mmt) cc_final: 0.7835 (mmp) REVERT: G 215 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7652 (mm-30) REVERT: G 216 TRP cc_start: 0.8089 (m100) cc_final: 0.7115 (m-10) REVERT: H 72 ASP cc_start: 0.8102 (t0) cc_final: 0.7703 (t70) REVERT: I 117 MET cc_start: 0.7875 (mtp) cc_final: 0.6773 (mmm) REVERT: I 118 ILE cc_start: 0.8325 (mm) cc_final: 0.8118 (mp) REVERT: I 119 MET cc_start: 0.7173 (mmt) cc_final: 0.6770 (tpt) REVERT: I 149 MET cc_start: 0.8047 (mmt) cc_final: 0.7783 (mmp) REVERT: I 213 GLU cc_start: 0.8285 (tp30) cc_final: 0.8055 (tm-30) REVERT: I 215 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7495 (mm-30) REVERT: I 216 TRP cc_start: 0.8097 (m100) cc_final: 0.7155 (m-10) REVERT: L 79 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: L 170 ASP cc_start: 0.8485 (t0) cc_final: 0.8133 (t0) outliers start: 22 outliers final: 6 residues processed: 142 average time/residue: 1.3421 time to fit residues: 202.4382 Evaluate side-chains 127 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 33 ILE 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 49 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 ILE 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 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN G 140 ASN G 163 ASN G 166 ASN H 3 GLN I 163 ASN I 166 ASN ** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.124967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.073151 restraints weight = 14414.798| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.41 r_work: 0.2838 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3173 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= 0.161 Angle : 0.625 7.254 12770 Z= 0.322 Chirality : 0.044 0.168 1444 Planarity : 0.004 0.037 1598 Dihedral : 4.730 19.272 1278 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.95 % Allowed : 12.89 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1188 helix: 2.27 (0.32), residues: 272 sheet: 0.74 (0.24), residues: 428 loop : 0.02 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 89 HIS 0.005 0.001 HIS L 189 PHE 0.014 0.001 PHE G 200 TYR 0.019 0.002 TYR G 86 ARG 0.010 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 478) hydrogen bonds : angle 4.76120 ( 1332) SS BOND : bond 0.00418 ( 12) SS BOND : angle 0.49415 ( 24) covalent geometry : bond 0.00372 ( 9374) covalent geometry : angle 0.62565 (12746) *********************** 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 143 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8701 (mm-30) REVERT: A 72 ASP cc_start: 0.8149 (t0) cc_final: 0.7693 (t70) REVERT: B 79 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8200 (mm-30) REVERT: B 167 ASP cc_start: 0.8251 (t0) cc_final: 0.7937 (t0) REVERT: B 169 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8724 (pptt) REVERT: B 170 ASP cc_start: 0.8541 (t0) cc_final: 0.8079 (t0) REVERT: G 46 MET cc_start: 0.5613 (ttp) cc_final: 0.5314 (mpt) REVERT: G 48 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6087 (mp0) REVERT: G 71 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8574 (mtp) REVERT: G 117 MET cc_start: 0.7939 (mtp) cc_final: 0.6928 (mmm) REVERT: G 119 MET cc_start: 0.7706 (tpp) cc_final: 0.7361 (tpt) REVERT: G 149 MET cc_start: 0.7977 (mmt) cc_final: 0.7713 (mmp) REVERT: G 213 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7819 (tm-30) REVERT: G 215 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7546 (mm-30) REVERT: G 216 TRP cc_start: 0.8089 (m100) cc_final: 0.7063 (m-10) REVERT: H 72 ASP cc_start: 0.8186 (t0) cc_final: 0.7720 (t70) REVERT: H 216 GLU cc_start: 0.8386 (pm20) cc_final: 0.8120 (pp20) REVERT: I 117 MET cc_start: 0.7817 (mtp) cc_final: 0.7000 (mmm) REVERT: I 118 ILE cc_start: 0.8269 (mm) cc_final: 0.8052 (mp) REVERT: I 119 MET cc_start: 0.7143 (mmt) cc_final: 0.6776 (tpt) REVERT: I 149 MET cc_start: 0.7929 (mmt) cc_final: 0.7692 (mmp) REVERT: I 213 GLU cc_start: 0.8283 (tp30) cc_final: 0.8044 (tm-30) REVERT: I 216 TRP cc_start: 0.8074 (m100) cc_final: 0.7061 (m-10) REVERT: L 79 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: L 167 ASP cc_start: 0.8447 (t0) cc_final: 0.7991 (t0) REVERT: L 169 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8625 (pptt) REVERT: L 170 ASP cc_start: 0.8501 (t0) cc_final: 0.8015 (t0) outliers start: 20 outliers final: 6 residues processed: 137 average time/residue: 1.4152 time to fit residues: 205.5578 Evaluate side-chains 130 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 71 MET Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain I 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 53 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 168 HIS B 137 ASN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 5 GLN H 61 GLN I 140 ASN ** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.125023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073357 restraints weight = 14464.249| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.40 r_work: 0.2838 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9386 Z= 0.158 Angle : 0.614 6.724 12770 Z= 0.315 Chirality : 0.043 0.173 1444 Planarity : 0.004 0.043 1598 Dihedral : 4.656 19.517 1278 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.86 % Allowed : 13.38 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.33 (0.25), residues: 1188 helix: 2.36 (0.31), residues: 272 sheet: 0.90 (0.24), residues: 434 loop : 0.08 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 89 HIS 0.005 0.001 HIS L 189 PHE 0.014 0.001 PHE G 200 TYR 0.019 0.002 TYR I 86 ARG 0.011 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 478) hydrogen bonds : angle 4.66358 ( 1332) SS BOND : bond 0.00406 ( 12) SS BOND : angle 0.48099 ( 24) covalent geometry : bond 0.00366 ( 9374) covalent geometry : angle 0.61411 (12746) *********************** 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 140 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8689 (mm-30) REVERT: A 72 ASP cc_start: 0.8220 (t0) cc_final: 0.7729 (t70) REVERT: A 216 GLU cc_start: 0.8279 (pm20) cc_final: 0.7999 (pp20) REVERT: B 79 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8154 (mm-30) REVERT: B 169 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8753 (pptt) REVERT: B 170 ASP cc_start: 0.8607 (t0) cc_final: 0.8119 (t0) REVERT: G 46 MET cc_start: 0.5827 (ttp) cc_final: 0.5212 (mpt) REVERT: G 48 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6146 (mp0) REVERT: G 71 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8545 (mtp) REVERT: G 117 MET cc_start: 0.7894 (mtp) cc_final: 0.7090 (mmm) REVERT: G 119 MET cc_start: 0.7640 (tpp) cc_final: 0.7245 (tpt) REVERT: G 149 MET cc_start: 0.7936 (mmt) cc_final: 0.7675 (mmp) REVERT: G 213 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7906 (tm-30) REVERT: G 216 TRP cc_start: 0.8083 (m100) cc_final: 0.7116 (m-10) REVERT: H 10 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8714 (mm-30) REVERT: H 72 ASP cc_start: 0.8166 (t0) cc_final: 0.7677 (t70) REVERT: H 216 GLU cc_start: 0.8472 (pm20) cc_final: 0.8229 (pp20) REVERT: I 117 MET cc_start: 0.7768 (mtp) cc_final: 0.6841 (mmm) REVERT: I 119 MET cc_start: 0.7144 (mmt) cc_final: 0.6700 (tpt) REVERT: I 149 MET cc_start: 0.7920 (mmt) cc_final: 0.7685 (mmp) REVERT: I 213 GLU cc_start: 0.8276 (tp30) cc_final: 0.8017 (tm-30) REVERT: I 215 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7744 (mm-30) REVERT: I 216 TRP cc_start: 0.8092 (m100) cc_final: 0.7107 (m-10) REVERT: L 79 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: L 167 ASP cc_start: 0.8443 (t0) cc_final: 0.8193 (t0) REVERT: L 169 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8759 (pptt) REVERT: L 170 ASP cc_start: 0.8586 (t0) cc_final: 0.8123 (t0) outliers start: 19 outliers final: 5 residues processed: 139 average time/residue: 1.3475 time to fit residues: 198.8958 Evaluate side-chains 126 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS 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 G residue 100 LEU Chi-restraints excluded: chain I residue 118 ILE 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 83 optimal weight: 0.1980 chunk 112 optimal weight: 10.0000 chunk 106 optimal weight: 0.1980 chunk 102 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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** H 3 GLN H 5 GLN H 168 HIS ** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 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 = 0.3833 r_free = 0.3833 target = 0.126147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.074838 restraints weight = 14573.960| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.40 r_work: 0.2866 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9386 Z= 0.127 Angle : 0.592 6.722 12770 Z= 0.303 Chirality : 0.042 0.145 1444 Planarity : 0.004 0.046 1598 Dihedral : 4.480 18.317 1278 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.17 % Allowed : 15.04 % 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 (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: 1.38 (0.25), residues: 1188 helix: 2.53 (0.31), residues: 272 sheet: 0.87 (0.24), residues: 424 loop : 0.10 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 89 HIS 0.005 0.001 HIS B 189 PHE 0.012 0.001 PHE G 200 TYR 0.017 0.001 TYR I 86 ARG 0.012 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 478) hydrogen bonds : angle 4.53320 ( 1332) SS BOND : bond 0.00388 ( 12) SS BOND : angle 0.43326 ( 24) covalent geometry : bond 0.00289 ( 9374) covalent geometry : angle 0.59222 (12746) *********************** 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 136 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8694 (mm-30) REVERT: A 72 ASP cc_start: 0.8125 (t0) cc_final: 0.7631 (t70) REVERT: B 53 ASN cc_start: 0.9125 (m110) cc_final: 0.8799 (m110) REVERT: B 79 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8213 (mm-30) REVERT: B 169 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8813 (pptt) REVERT: B 170 ASP cc_start: 0.8679 (t0) cc_final: 0.8166 (t0) REVERT: G 46 MET cc_start: 0.5758 (ttp) cc_final: 0.5225 (mpt) REVERT: G 48 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6060 (mp0) REVERT: G 49 SER cc_start: 0.8253 (m) cc_final: 0.7940 (p) REVERT: G 71 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8592 (mtp) REVERT: G 117 MET cc_start: 0.7823 (mtp) cc_final: 0.7028 (mmm) REVERT: G 119 MET cc_start: 0.7592 (tpp) cc_final: 0.7210 (tpt) REVERT: G 149 MET cc_start: 0.7915 (mmt) cc_final: 0.7706 (mmp) REVERT: G 213 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7820 (tm-30) REVERT: G 216 TRP cc_start: 0.8094 (m100) cc_final: 0.7043 (m-10) REVERT: H 10 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8703 (mm-30) REVERT: H 72 ASP cc_start: 0.8115 (t0) cc_final: 0.7609 (t70) REVERT: H 199 ILE cc_start: 0.8697 (pp) cc_final: 0.8473 (tp) REVERT: H 216 GLU cc_start: 0.8484 (pm20) cc_final: 0.8246 (pp20) REVERT: I 117 MET cc_start: 0.7639 (mtp) cc_final: 0.6934 (mmm) REVERT: I 119 MET cc_start: 0.7118 (mmt) cc_final: 0.6686 (tpt) REVERT: I 149 MET cc_start: 0.7890 (mmt) cc_final: 0.7673 (mmp) REVERT: I 213 GLU cc_start: 0.8261 (tp30) cc_final: 0.8024 (tm-30) REVERT: I 216 TRP cc_start: 0.8072 (m100) cc_final: 0.7034 (m-10) REVERT: L 53 ASN cc_start: 0.9134 (m110) cc_final: 0.8813 (m110) REVERT: L 79 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8226 (mm-30) REVERT: L 167 ASP cc_start: 0.8403 (t0) cc_final: 0.8152 (t0) REVERT: L 169 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8709 (pptt) REVERT: L 170 ASP cc_start: 0.8616 (t0) cc_final: 0.8148 (t0) outliers start: 12 outliers final: 2 residues processed: 134 average time/residue: 1.4139 time to fit residues: 200.8534 Evaluate side-chains 123 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 218 LYS 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 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 36 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 60 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 48 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 H 3 GLN H 5 GLN H 61 GLN H 159 ASN I 171 ASN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.123952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.071667 restraints weight = 14757.794| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.43 r_work: 0.2802 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9386 Z= 0.209 Angle : 0.647 7.626 12770 Z= 0.331 Chirality : 0.044 0.151 1444 Planarity : 0.005 0.051 1598 Dihedral : 4.689 22.054 1278 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.27 % Allowed : 15.04 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.36 (0.24), residues: 1188 helix: 2.32 (0.31), residues: 272 sheet: 1.05 (0.24), residues: 432 loop : 0.01 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I 89 HIS 0.006 0.001 HIS L 189 PHE 0.016 0.002 PHE G 200 TYR 0.021 0.002 TYR I 86 ARG 0.013 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 478) hydrogen bonds : angle 4.70499 ( 1332) SS BOND : bond 0.00389 ( 12) SS BOND : angle 0.54510 ( 24) covalent geometry : bond 0.00487 ( 9374) covalent geometry : angle 0.64723 (12746) *********************** 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 128 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8695 (mm-30) REVERT: A 72 ASP cc_start: 0.8181 (t0) cc_final: 0.7688 (t70) REVERT: A 159 ASN cc_start: 0.7845 (m-40) cc_final: 0.7623 (m110) REVERT: A 199 ILE cc_start: 0.8636 (pp) cc_final: 0.8390 (tp) REVERT: A 216 GLU cc_start: 0.8259 (pm20) cc_final: 0.7931 (pp20) REVERT: B 79 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8182 (mm-30) REVERT: B 167 ASP cc_start: 0.8427 (t0) cc_final: 0.8012 (t0) REVERT: B 169 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8836 (pptt) REVERT: B 170 ASP cc_start: 0.8703 (t0) cc_final: 0.8190 (t0) REVERT: G 46 MET cc_start: 0.5974 (ttp) cc_final: 0.4970 (mpt) REVERT: G 48 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6052 (mp0) REVERT: G 49 SER cc_start: 0.8357 (m) cc_final: 0.7917 (t) REVERT: G 71 MET cc_start: 0.8948 (mtm) cc_final: 0.8553 (mtp) REVERT: G 117 MET cc_start: 0.7827 (mtp) cc_final: 0.7454 (tpp) REVERT: G 149 MET cc_start: 0.7844 (mmt) cc_final: 0.7642 (mmp) REVERT: G 213 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7813 (tm-30) REVERT: G 216 TRP cc_start: 0.8069 (m100) cc_final: 0.7106 (m-10) REVERT: H 10 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8701 (mm-30) REVERT: H 72 ASP cc_start: 0.8186 (t0) cc_final: 0.7671 (t70) REVERT: H 199 ILE cc_start: 0.8582 (pp) cc_final: 0.8368 (tp) REVERT: H 216 GLU cc_start: 0.8509 (pm20) cc_final: 0.8282 (pp20) REVERT: I 117 MET cc_start: 0.7826 (mtp) cc_final: 0.7395 (tpp) REVERT: I 149 MET cc_start: 0.7854 (mmt) cc_final: 0.7647 (mmp) REVERT: I 213 GLU cc_start: 0.8290 (tp30) cc_final: 0.8059 (tm-30) REVERT: I 216 TRP cc_start: 0.8096 (m100) cc_final: 0.7048 (m-10) REVERT: L 79 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8188 (mm-30) REVERT: L 167 ASP cc_start: 0.8457 (t0) cc_final: 0.8213 (t0) REVERT: L 169 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8740 (pptt) REVERT: L 170 ASP cc_start: 0.8615 (t0) cc_final: 0.8138 (t0) outliers start: 13 outliers final: 4 residues processed: 127 average time/residue: 1.5358 time to fit residues: 205.9634 Evaluate side-chains 118 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS 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 I residue 118 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 53 optimal weight: 0.0970 chunk 70 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN B 199 GLN H 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.123823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.071599 restraints weight = 14367.006| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.40 r_work: 0.2802 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9386 Z= 0.211 Angle : 0.652 7.467 12770 Z= 0.333 Chirality : 0.043 0.151 1444 Planarity : 0.005 0.055 1598 Dihedral : 4.717 22.130 1278 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.17 % Allowed : 15.53 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.37 (0.24), residues: 1188 helix: 2.39 (0.31), residues: 270 sheet: 1.04 (0.24), residues: 432 loop : -0.01 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 89 HIS 0.007 0.001 HIS B 189 PHE 0.016 0.002 PHE G 200 TYR 0.021 0.002 TYR I 86 ARG 0.014 0.002 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 478) hydrogen bonds : angle 4.72823 ( 1332) SS BOND : bond 0.00385 ( 12) SS BOND : angle 0.56578 ( 24) covalent geometry : bond 0.00492 ( 9374) covalent geometry : angle 0.65197 (12746) *********************** 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 122 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8726 (mm-30) REVERT: A 72 ASP cc_start: 0.8227 (t0) cc_final: 0.7740 (t70) REVERT: A 199 ILE cc_start: 0.8572 (pp) cc_final: 0.8364 (tp) REVERT: A 216 GLU cc_start: 0.8302 (pm20) cc_final: 0.7914 (pp20) REVERT: B 79 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8178 (mm-30) REVERT: B 169 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8854 (pptt) REVERT: B 170 ASP cc_start: 0.8725 (t0) cc_final: 0.8205 (t0) REVERT: G 46 MET cc_start: 0.6056 (ttp) cc_final: 0.4907 (mpt) REVERT: G 48 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6081 (mp0) REVERT: G 49 SER cc_start: 0.8374 (m) cc_final: 0.7933 (t) REVERT: G 71 MET cc_start: 0.8979 (mtm) cc_final: 0.8589 (mtp) REVERT: G 117 MET cc_start: 0.7898 (mtp) cc_final: 0.7550 (tpp) REVERT: G 149 MET cc_start: 0.7836 (mmt) cc_final: 0.7610 (mmp) REVERT: G 213 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7833 (tm-30) REVERT: G 216 TRP cc_start: 0.8071 (m100) cc_final: 0.7117 (m-10) REVERT: H 10 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8743 (mm-30) REVERT: H 72 ASP cc_start: 0.8246 (t0) cc_final: 0.7753 (t70) REVERT: H 216 GLU cc_start: 0.8518 (pm20) cc_final: 0.8311 (pp20) REVERT: I 50 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8555 (mttm) REVERT: I 117 MET cc_start: 0.7844 (mtp) cc_final: 0.7367 (tpp) REVERT: I 148 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7411 (mttm) REVERT: I 149 MET cc_start: 0.7858 (mmt) cc_final: 0.7645 (mmp) REVERT: I 213 GLU cc_start: 0.8313 (tp30) cc_final: 0.8079 (tm-30) REVERT: I 216 TRP cc_start: 0.8082 (m100) cc_final: 0.7113 (m-10) REVERT: L 79 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8200 (mm-30) REVERT: L 167 ASP cc_start: 0.8476 (t0) cc_final: 0.8234 (t0) REVERT: L 169 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8774 (pptt) REVERT: L 170 ASP cc_start: 0.8653 (t0) cc_final: 0.8182 (t0) outliers start: 12 outliers final: 3 residues processed: 118 average time/residue: 1.5228 time to fit residues: 190.0649 Evaluate side-chains 118 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 199 GLN Chi-restraints excluded: chain I residue 148 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 33 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 74 optimal weight: 0.0670 chunk 110 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 B 199 GLN H 5 GLN H 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.124913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.073068 restraints weight = 14611.442| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.40 r_work: 0.2826 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9386 Z= 0.152 Angle : 0.629 7.480 12770 Z= 0.321 Chirality : 0.042 0.142 1444 Planarity : 0.005 0.059 1598 Dihedral : 4.600 21.028 1278 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.88 % Allowed : 15.92 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.36 (0.24), residues: 1188 helix: 2.43 (0.30), residues: 272 sheet: 0.91 (0.24), residues: 422 loop : 0.10 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 89 HIS 0.009 0.001 HIS B 189 PHE 0.014 0.001 PHE G 200 TYR 0.019 0.001 TYR I 86 ARG 0.015 0.002 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 478) hydrogen bonds : angle 4.63805 ( 1332) SS BOND : bond 0.00335 ( 12) SS BOND : angle 0.49782 ( 24) covalent geometry : bond 0.00352 ( 9374) covalent geometry : angle 0.62876 (12746) ********************** 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 125 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8694 (mm-30) REVERT: A 72 ASP cc_start: 0.8226 (t0) cc_final: 0.7723 (t70) REVERT: A 216 GLU cc_start: 0.8307 (pm20) cc_final: 0.7928 (pp20) REVERT: B 79 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8175 (mm-30) REVERT: B 167 ASP cc_start: 0.8429 (t0) cc_final: 0.8042 (t0) REVERT: B 169 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8919 (pptt) REVERT: B 170 ASP cc_start: 0.8727 (t0) cc_final: 0.8221 (t0) REVERT: G 46 MET cc_start: 0.6066 (ttp) cc_final: 0.4979 (mpt) REVERT: G 48 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6021 (mp0) REVERT: G 49 SER cc_start: 0.8316 (m) cc_final: 0.7884 (t) REVERT: G 71 MET cc_start: 0.8964 (mtm) cc_final: 0.8569 (mtp) REVERT: G 117 MET cc_start: 0.7888 (mtp) cc_final: 0.7526 (tpp) REVERT: G 119 MET cc_start: 0.7627 (tpp) cc_final: 0.7303 (tpt) REVERT: G 149 MET cc_start: 0.7847 (mmt) cc_final: 0.7622 (mmp) REVERT: G 213 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7831 (tm-30) REVERT: G 216 TRP cc_start: 0.8060 (m100) cc_final: 0.7069 (m-10) REVERT: H 10 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8706 (mm-30) REVERT: H 72 ASP cc_start: 0.8215 (t0) cc_final: 0.7723 (t70) REVERT: H 216 GLU cc_start: 0.8537 (pm20) cc_final: 0.8335 (pp20) REVERT: I 50 LYS cc_start: 0.8771 (mmmm) cc_final: 0.8564 (mttm) REVERT: I 117 MET cc_start: 0.7822 (mtp) cc_final: 0.7368 (tpp) REVERT: I 119 MET cc_start: 0.7503 (tpp) cc_final: 0.7109 (tpt) REVERT: I 148 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7411 (mttm) REVERT: I 213 GLU cc_start: 0.8285 (tp30) cc_final: 0.8076 (tm-30) REVERT: I 216 TRP cc_start: 0.8071 (m100) cc_final: 0.7082 (m-10) REVERT: L 79 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8183 (mm-30) REVERT: L 167 ASP cc_start: 0.8439 (t0) cc_final: 0.8195 (t0) REVERT: L 169 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8781 (pptt) REVERT: L 170 ASP cc_start: 0.8657 (t0) cc_final: 0.8168 (t0) outliers start: 9 outliers final: 2 residues processed: 123 average time/residue: 1.6594 time to fit residues: 216.2506 Evaluate side-chains 120 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 I residue 148 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 63 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.124627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.072754 restraints weight = 14575.623| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.40 r_work: 0.2823 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9386 Z= 0.169 Angle : 0.635 7.461 12770 Z= 0.324 Chirality : 0.042 0.145 1444 Planarity : 0.005 0.059 1598 Dihedral : 4.618 21.301 1278 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.59 % Allowed : 16.50 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.38 (0.24), residues: 1188 helix: 2.25 (0.30), residues: 282 sheet: 1.08 (0.24), residues: 432 loop : 0.00 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I 89 HIS 0.009 0.001 HIS B 189 PHE 0.015 0.001 PHE G 200 TYR 0.020 0.001 TYR I 86 ARG 0.015 0.002 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 478) hydrogen bonds : angle 4.64982 ( 1332) SS BOND : bond 0.00336 ( 12) SS BOND : angle 0.51749 ( 24) covalent geometry : bond 0.00394 ( 9374) covalent geometry : angle 0.63548 (12746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9717.88 seconds wall clock time: 167 minutes 46.45 seconds (10066.45 seconds total)