Starting phenix.real_space_refine on Tue Feb 11 14:05:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y9a_10734/02_2025/6y9a_10734.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y9a_10734/02_2025/6y9a_10734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6y9a_10734/02_2025/6y9a_10734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y9a_10734/02_2025/6y9a_10734.map" model { file = "/net/cci-nas-00/data/ceres_data/6y9a_10734/02_2025/6y9a_10734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y9a_10734/02_2025/6y9a_10734.cif" } resolution = 4.2 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= 0.002 sd= 0.040 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 41 5.16 5 C 3829 2.51 5 N 965 2.21 5 O 1113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5948 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "B" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1644 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1684 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205} Time building chain proxies: 4.51, per 1000 atoms: 0.76 Number of scatterers: 5948 At special positions: 0 Unit cell: (61.864, 70.004, 154.66, 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 41 16.00 O 1113 8.00 N 965 7.00 C 3829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 937.1 milliseconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 37.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 45 through 51 removed outlier: 5.150A pdb=" N LYS A 50 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 71 Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.617A pdb=" N THR A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 84' Processing helix chain 'A' and resid 85 through 103 removed outlier: 3.865A pdb=" N TRP A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 143 removed outlier: 3.917A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 171 through 176 removed outlier: 4.401A pdb=" N ASN A 176 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 210 Processing helix chain 'B' and resid 45 through 51 removed outlier: 5.825A pdb=" N LYS B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 71 Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.646A pdb=" N VAL B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 100 removed outlier: 4.051A pdb=" N TRP B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 143 removed outlier: 3.710A pdb=" N LYS B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 171 through 176 removed outlier: 4.078A pdb=" N ASN B 176 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 212 removed outlier: 3.585A pdb=" N GLN B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'L' and resid 126 through 133 Processing helix chain 'L' and resid 188 through 193 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.723A pdb=" N LYS H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP H 59 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 19 through 21 removed outlier: 3.900A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET H 81 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR H 80 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.563A pdb=" N LEU H 130 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA H 143 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 190 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.635A pdb=" N THR H 157 " --> pdb=" O ASN H 205 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL H 204 " --> pdb=" O VAL H 213 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL H 213 " --> pdb=" O VAL H 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.739A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER L 22 " --> pdb=" O THR L 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.572A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR L 39 " --> pdb=" O ALA L 94 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.572A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN L 95 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 68 through 71 Processing sheet with id=AB1, first strand: chain 'L' and resid 120 through 123 removed outlier: 3.646A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU L 184 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS L 139 " --> pdb=" O SER L 182 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER L 182 " --> pdb=" O CYS L 139 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU L 141 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 158 through 159 removed outlier: 3.972A pdb=" N LYS L 150 " --> pdb=" O THR L 202 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR L 202 " --> pdb=" O LYS L 150 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN L 152 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU L 200 " --> pdb=" O GLN L 152 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS L 154 " --> pdb=" O ALA L 198 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR L 197 " --> pdb=" O PHE L 214 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE L 214 " --> pdb=" O TYR L 197 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS L 212 " --> pdb=" O CYS L 199 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL L 210 " --> pdb=" O VAL L 201 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 717 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.67 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: 1839 1.34 - 1.46: 1465 1.46 - 1.58: 2714 1.58 - 1.70: 2 1.70 - 1.82: 65 Bond restraints: 6085 Sorted by residual: bond pdb=" CB PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.61e+00 bond pdb=" CB PRO A 73 " pdb=" CG PRO A 73 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.70e+00 bond pdb=" CG1 ILE A 141 " pdb=" CD1 ILE A 141 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.50e+00 bond pdb=" CA THR B 180 " pdb=" C THR B 180 " ideal model delta sigma weight residual 1.520 1.504 0.015 1.40e-02 5.10e+03 1.21e+00 bond pdb=" N PRO B 73 " pdb=" CA PRO B 73 " ideal model delta sigma weight residual 1.469 1.482 -0.013 1.28e-02 6.10e+03 1.10e+00 ... (remaining 6080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 7992 2.04 - 4.09: 221 4.09 - 6.13: 35 6.13 - 8.18: 7 8.18 - 10.22: 2 Bond angle restraints: 8257 Sorted by residual: angle pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 112.00 105.14 6.86 1.40e+00 5.10e-01 2.40e+01 angle pdb=" CA PRO A 73 " pdb=" N PRO A 73 " pdb=" CD PRO A 73 " ideal model delta sigma weight residual 112.00 105.64 6.36 1.40e+00 5.10e-01 2.06e+01 angle pdb=" N LYS B 148 " pdb=" CA LYS B 148 " pdb=" C LYS B 148 " ideal model delta sigma weight residual 111.03 115.64 -4.61 1.11e+00 8.12e-01 1.73e+01 angle pdb=" N GLN A 181 " pdb=" CA GLN A 181 " pdb=" C GLN A 181 " ideal model delta sigma weight residual 111.28 106.77 4.51 1.09e+00 8.42e-01 1.71e+01 angle pdb=" N GLN B 181 " pdb=" CA GLN B 181 " pdb=" C GLN B 181 " ideal model delta sigma weight residual 111.28 107.01 4.27 1.09e+00 8.42e-01 1.54e+01 ... (remaining 8252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 3284 17.24 - 34.48: 278 34.48 - 51.72: 61 51.72 - 68.96: 10 68.96 - 86.20: 7 Dihedral angle restraints: 3640 sinusoidal: 1404 harmonic: 2236 Sorted by residual: dihedral pdb=" CB CYS L 139 " pdb=" SG CYS L 139 " pdb=" SG CYS L 199 " pdb=" CB CYS L 199 " ideal model delta sinusoidal sigma weight residual 93.00 176.92 -83.92 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS H 146 " pdb=" SG CYS H 146 " pdb=" SG CYS H 202 " pdb=" CB CYS H 202 " ideal model delta sinusoidal sigma weight residual 93.00 16.07 76.93 1 1.00e+01 1.00e-02 7.43e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 18.32 74.68 1 1.00e+01 1.00e-02 7.06e+01 ... (remaining 3637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 750 0.058 - 0.116: 171 0.116 - 0.175: 20 0.175 - 0.233: 3 0.233 - 0.291: 1 Chirality restraints: 945 Sorted by residual: chirality pdb=" CG LEU B 122 " pdb=" CB LEU B 122 " pdb=" CD1 LEU B 122 " pdb=" CD2 LEU B 122 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB VAL H 190 " pdb=" CA VAL H 190 " pdb=" CG1 VAL H 190 " pdb=" CG2 VAL H 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLN L 55 " pdb=" N GLN L 55 " pdb=" C GLN L 55 " pdb=" CB GLN L 55 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 942 not shown) Planarity restraints: 1030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 179 " 0.031 2.00e-02 2.50e+03 6.11e-02 3.73e+01 pdb=" C SER B 179 " -0.106 2.00e-02 2.50e+03 pdb=" O SER B 179 " 0.038 2.00e-02 2.50e+03 pdb=" N THR B 180 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 179 " -0.028 2.00e-02 2.50e+03 5.47e-02 3.00e+01 pdb=" C SER A 179 " 0.095 2.00e-02 2.50e+03 pdb=" O SER A 179 " -0.035 2.00e-02 2.50e+03 pdb=" N THR A 180 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 116 " -0.026 2.00e-02 2.50e+03 5.19e-02 2.69e+01 pdb=" C LYS B 116 " 0.090 2.00e-02 2.50e+03 pdb=" O LYS B 116 " -0.034 2.00e-02 2.50e+03 pdb=" N MET B 117 " -0.030 2.00e-02 2.50e+03 ... (remaining 1027 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 566 2.75 - 3.29: 6136 3.29 - 3.82: 9405 3.82 - 4.36: 10399 4.36 - 4.90: 17289 Nonbonded interactions: 43795 Sorted by model distance: nonbonded pdb=" O GLY H 103 " pdb=" OH TYR L 39 " model vdw 2.211 3.040 nonbonded pdb=" O TYR L 191 " pdb=" OH TYR L 197 " model vdw 2.271 3.040 nonbonded pdb=" O HIS L 194 " pdb=" NH2 ARG L 216 " model vdw 2.281 3.120 nonbonded pdb=" OG1 THR H 199 " pdb=" OE2 GLU H 218 " model vdw 2.312 3.040 nonbonded pdb=" ND2 ASN A 163 " pdb=" OD1 ASN A 166 " model vdw 2.328 3.120 ... (remaining 43790 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.070 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4803 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 6085 Z= 0.226 Angle : 0.809 10.221 8257 Z= 0.443 Chirality : 0.050 0.291 945 Planarity : 0.008 0.127 1030 Dihedral : 13.593 86.201 2192 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: -1.17 (0.29), residues: 766 helix: -0.51 (0.30), residues: 228 sheet: 0.10 (0.38), residues: 174 loop : -1.35 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 109 HIS 0.005 0.001 HIS B 63 PHE 0.040 0.002 PHE B 62 TYR 0.014 0.001 TYR L 197 ARG 0.005 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.4432 (mmm) cc_final: 0.4113 (mmm) REVERT: A 117 MET cc_start: 0.8031 (ptt) cc_final: 0.6042 (tpt) REVERT: B 149 MET cc_start: 0.7266 (mpp) cc_final: 0.6631 (mpp) REVERT: L 42 LEU cc_start: 0.6631 (tt) cc_final: 0.6234 (tt) REVERT: L 56 MET cc_start: 0.7262 (tmm) cc_final: 0.7059 (tmm) REVERT: L 146 PRO cc_start: 0.6978 (Cg_endo) cc_final: 0.6457 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1610 time to fit residues: 41.6369 Evaluate side-chains 155 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.0270 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 204 GLN B 120 ASN H 39 GLN H 161 ASN L 47 GLN L 194 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.155851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.122879 restraints weight = 15170.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.128116 restraints weight = 10340.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.132243 restraints weight = 7512.651| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6085 Z= 0.176 Angle : 0.617 6.695 8257 Z= 0.321 Chirality : 0.044 0.167 945 Planarity : 0.006 0.067 1030 Dihedral : 4.562 16.946 824 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: -0.08 (0.30), residues: 766 helix: 0.89 (0.32), residues: 245 sheet: 0.84 (0.41), residues: 160 loop : -1.15 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 33 HIS 0.004 0.001 HIS A 63 PHE 0.023 0.001 PHE B 62 TYR 0.017 0.001 TYR L 54 ARG 0.010 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7797 (ptt) cc_final: 0.6456 (tpt) REVERT: A 119 MET cc_start: 0.8961 (mmp) cc_final: 0.8716 (mmm) REVERT: A 164 ILE cc_start: 0.8116 (mt) cc_final: 0.7847 (mp) REVERT: A 176 ASN cc_start: 0.8110 (m-40) cc_final: 0.7678 (m-40) REVERT: A 190 PHE cc_start: 0.8909 (m-10) cc_final: 0.8505 (m-80) REVERT: B 58 MET cc_start: 0.8733 (ttm) cc_final: 0.8358 (ttt) REVERT: B 62 PHE cc_start: 0.8594 (m-80) cc_final: 0.8166 (m-80) REVERT: B 119 MET cc_start: 0.8561 (tpt) cc_final: 0.8336 (tpt) REVERT: B 131 MET cc_start: 0.7712 (mmp) cc_final: 0.7383 (mmm) REVERT: B 149 MET cc_start: 0.7425 (mpp) cc_final: 0.6728 (mpp) REVERT: B 150 GLU cc_start: 0.7716 (pp20) cc_final: 0.7350 (pp20) REVERT: B 184 TYR cc_start: 0.8229 (m-10) cc_final: 0.7735 (m-10) REVERT: B 211 ILE cc_start: 0.7460 (mm) cc_final: 0.7245 (mm) REVERT: H 3 GLN cc_start: 0.7764 (mp10) cc_final: 0.7550 (mp10) REVERT: H 35 ASN cc_start: 0.8744 (p0) cc_final: 0.8320 (p0) REVERT: H 36 TRP cc_start: 0.8040 (m100) cc_final: 0.7541 (m100) REVERT: H 59 ASP cc_start: 0.8192 (m-30) cc_final: 0.7832 (m-30) REVERT: H 73 ASP cc_start: 0.9302 (t0) cc_final: 0.9014 (t0) REVERT: H 99 ASN cc_start: 0.8337 (t0) cc_final: 0.7969 (p0) REVERT: H 100 VAL cc_start: 0.8928 (t) cc_final: 0.8294 (t) REVERT: H 128 PHE cc_start: 0.8873 (m-80) cc_final: 0.8672 (m-80) REVERT: H 201 ILE cc_start: 0.8351 (tp) cc_final: 0.8041 (tp) REVERT: L 79 LYS cc_start: 0.7901 (tptt) cc_final: 0.7285 (tppt) REVERT: L 80 ILE cc_start: 0.7226 (mp) cc_final: 0.6808 (mm) REVERT: L 91 TYR cc_start: 0.9044 (m-10) cc_final: 0.8392 (m-80) REVERT: L 123 PHE cc_start: 0.8155 (m-80) cc_final: 0.7712 (m-80) REVERT: L 175 ASP cc_start: 0.8687 (m-30) cc_final: 0.8438 (m-30) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1465 time to fit residues: 38.4464 Evaluate side-chains 159 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 19 optimal weight: 0.0010 chunk 34 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN L 143 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.128892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.096757 restraints weight = 17037.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.101446 restraints weight = 11355.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.105003 restraints weight = 8244.098| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6085 Z= 0.327 Angle : 0.760 7.512 8257 Z= 0.398 Chirality : 0.047 0.158 945 Planarity : 0.006 0.058 1030 Dihedral : 5.230 21.467 824 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.15 % Allowed : 4.95 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: -0.31 (0.30), residues: 766 helix: 0.48 (0.31), residues: 256 sheet: 0.17 (0.37), residues: 188 loop : -0.92 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 89 HIS 0.009 0.002 HIS L 31 PHE 0.025 0.002 PHE L 76 TYR 0.021 0.002 TYR L 197 ARG 0.010 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8436 (mt) cc_final: 0.8212 (mp) REVERT: A 190 PHE cc_start: 0.9466 (m-10) cc_final: 0.9158 (m-80) REVERT: B 119 MET cc_start: 0.8838 (tpt) cc_final: 0.8504 (tpt) REVERT: B 149 MET cc_start: 0.6828 (mpp) cc_final: 0.6201 (mpp) REVERT: B 150 GLU cc_start: 0.7275 (pp20) cc_final: 0.6760 (pp20) REVERT: B 161 TYR cc_start: 0.8033 (m-80) cc_final: 0.7478 (m-80) REVERT: B 184 TYR cc_start: 0.8318 (m-10) cc_final: 0.7975 (m-10) REVERT: B 188 SER cc_start: 0.9182 (t) cc_final: 0.8875 (p) REVERT: H 36 TRP cc_start: 0.8788 (m100) cc_final: 0.7866 (m100) REVERT: H 47 TRP cc_start: 0.9022 (t60) cc_final: 0.7725 (t60) REVERT: H 57 ASP cc_start: 0.8449 (m-30) cc_final: 0.8241 (m-30) REVERT: H 73 ASP cc_start: 0.9310 (t0) cc_final: 0.9018 (t0) REVERT: H 101 PHE cc_start: 0.8419 (m-80) cc_final: 0.8029 (m-80) REVERT: L 40 TRP cc_start: 0.7946 (m100) cc_final: 0.7534 (m100) REVERT: L 41 TYR cc_start: 0.8791 (m-80) cc_final: 0.8587 (m-10) REVERT: L 76 PHE cc_start: 0.7966 (m-80) cc_final: 0.7571 (m-80) REVERT: L 93 CYS cc_start: 0.4062 (m) cc_final: 0.2426 (m) REVERT: L 121 PHE cc_start: 0.8593 (m-80) cc_final: 0.8033 (m-80) REVERT: L 123 PHE cc_start: 0.9373 (m-80) cc_final: 0.9110 (m-80) REVERT: L 175 ASP cc_start: 0.8818 (m-30) cc_final: 0.8579 (m-30) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1373 time to fit residues: 34.7380 Evaluate side-chains 151 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 6.9990 chunk 44 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.131625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.100256 restraints weight = 15054.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.105382 restraints weight = 9494.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.109352 restraints weight = 6618.460| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6085 Z= 0.201 Angle : 0.632 6.961 8257 Z= 0.326 Chirality : 0.044 0.179 945 Planarity : 0.005 0.057 1030 Dihedral : 4.729 18.018 824 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: -0.08 (0.31), residues: 766 helix: 0.91 (0.32), residues: 260 sheet: 0.14 (0.38), residues: 184 loop : -0.91 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 89 HIS 0.007 0.001 HIS A 63 PHE 0.013 0.002 PHE B 62 TYR 0.017 0.002 TYR L 54 ARG 0.006 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TRP cc_start: 0.8780 (m-10) cc_final: 0.8544 (m100) REVERT: A 164 ILE cc_start: 0.8429 (mt) cc_final: 0.8114 (mp) REVERT: A 190 PHE cc_start: 0.9413 (m-10) cc_final: 0.8929 (m-80) REVERT: B 149 MET cc_start: 0.6752 (mpp) cc_final: 0.6113 (mpp) REVERT: B 150 GLU cc_start: 0.7327 (pp20) cc_final: 0.6774 (pp20) REVERT: B 161 TYR cc_start: 0.8187 (m-80) cc_final: 0.7589 (m-80) REVERT: B 176 ASN cc_start: 0.7953 (m-40) cc_final: 0.7350 (p0) REVERT: B 184 TYR cc_start: 0.8429 (m-10) cc_final: 0.8168 (m-10) REVERT: B 188 SER cc_start: 0.9144 (t) cc_final: 0.8822 (p) REVERT: H 36 TRP cc_start: 0.8809 (m100) cc_final: 0.7712 (m100) REVERT: H 47 TRP cc_start: 0.8869 (t60) cc_final: 0.7532 (t60) REVERT: H 73 ASP cc_start: 0.9328 (t0) cc_final: 0.9051 (t0) REVERT: H 101 PHE cc_start: 0.8715 (m-80) cc_final: 0.8063 (m-80) REVERT: L 40 TRP cc_start: 0.8090 (m100) cc_final: 0.7534 (m100) REVERT: L 56 MET cc_start: 0.8774 (tmm) cc_final: 0.8211 (tmm) REVERT: L 70 SER cc_start: 0.8701 (p) cc_final: 0.8302 (p) REVERT: L 87 ASP cc_start: 0.7625 (p0) cc_final: 0.7116 (p0) REVERT: L 148 GLU cc_start: 0.9505 (mp0) cc_final: 0.9239 (mp0) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1386 time to fit residues: 34.9289 Evaluate side-chains 157 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.128512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.097129 restraints weight = 15997.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.102034 restraints weight = 10220.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105763 restraints weight = 7224.476| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6085 Z= 0.220 Angle : 0.627 6.412 8257 Z= 0.327 Chirality : 0.043 0.174 945 Planarity : 0.005 0.057 1030 Dihedral : 4.739 18.787 824 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: -0.09 (0.31), residues: 766 helix: 0.86 (0.32), residues: 256 sheet: -0.01 (0.36), residues: 197 loop : -0.76 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 89 HIS 0.005 0.001 HIS A 63 PHE 0.013 0.002 PHE L 76 TYR 0.017 0.002 TYR L 54 ARG 0.004 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TRP cc_start: 0.8805 (m-10) cc_final: 0.8569 (m100) REVERT: A 164 ILE cc_start: 0.8499 (mt) cc_final: 0.8229 (mp) REVERT: A 190 PHE cc_start: 0.9458 (m-10) cc_final: 0.9119 (m-80) REVERT: B 58 MET cc_start: 0.9224 (ttt) cc_final: 0.8970 (ttt) REVERT: B 149 MET cc_start: 0.6818 (mpp) cc_final: 0.6169 (mpp) REVERT: B 150 GLU cc_start: 0.7281 (pp20) cc_final: 0.6692 (pp20) REVERT: B 161 TYR cc_start: 0.8271 (m-80) cc_final: 0.7492 (m-80) REVERT: B 168 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8366 (mm-30) REVERT: B 176 ASN cc_start: 0.7890 (m-40) cc_final: 0.7252 (p0) REVERT: B 184 TYR cc_start: 0.8511 (m-10) cc_final: 0.8137 (m-10) REVERT: B 188 SER cc_start: 0.9148 (t) cc_final: 0.8843 (p) REVERT: H 3 GLN cc_start: 0.8561 (mp10) cc_final: 0.8186 (mp10) REVERT: H 36 TRP cc_start: 0.8780 (m100) cc_final: 0.7650 (m100) REVERT: H 47 TRP cc_start: 0.8967 (t60) cc_final: 0.7618 (t60) REVERT: H 57 ASP cc_start: 0.8579 (m-30) cc_final: 0.8356 (m-30) REVERT: H 73 ASP cc_start: 0.9318 (t0) cc_final: 0.9041 (t0) REVERT: H 101 PHE cc_start: 0.8553 (m-80) cc_final: 0.8030 (m-80) REVERT: H 160 TRP cc_start: 0.7346 (m100) cc_final: 0.6709 (m100) REVERT: H 216 LYS cc_start: 0.8515 (tmtt) cc_final: 0.8231 (ptpt) REVERT: L 21 ILE cc_start: 0.8000 (tp) cc_final: 0.7799 (tp) REVERT: L 40 TRP cc_start: 0.8138 (m100) cc_final: 0.7591 (m100) REVERT: L 70 SER cc_start: 0.8877 (p) cc_final: 0.8133 (p) REVERT: L 76 PHE cc_start: 0.8284 (m-80) cc_final: 0.7904 (m-80) REVERT: L 87 ASP cc_start: 0.7422 (p0) cc_final: 0.7182 (p0) REVERT: L 121 PHE cc_start: 0.8773 (m-80) cc_final: 0.8079 (m-80) REVERT: L 123 PHE cc_start: 0.8472 (m-80) cc_final: 0.8006 (m-80) REVERT: L 148 GLU cc_start: 0.9508 (mp0) cc_final: 0.9172 (mp0) REVERT: L 175 ASP cc_start: 0.8929 (m-30) cc_final: 0.8671 (m-30) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1390 time to fit residues: 34.9612 Evaluate side-chains 156 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 176 ASN A 181 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.123231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.092535 restraints weight = 15946.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.097379 restraints weight = 10052.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.100994 restraints weight = 7025.362| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6085 Z= 0.267 Angle : 0.687 6.546 8257 Z= 0.357 Chirality : 0.045 0.178 945 Planarity : 0.005 0.060 1030 Dihedral : 5.041 20.554 824 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: -0.40 (0.31), residues: 766 helix: 0.57 (0.32), residues: 256 sheet: -0.26 (0.37), residues: 192 loop : -0.84 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 89 HIS 0.004 0.001 HIS L 31 PHE 0.013 0.002 PHE L 76 TYR 0.018 0.002 TYR L 54 ARG 0.004 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 HIS cc_start: 0.8923 (m-70) cc_final: 0.7752 (m-70) REVERT: A 85 TRP cc_start: 0.8910 (m-10) cc_final: 0.8648 (m100) REVERT: A 190 PHE cc_start: 0.9541 (m-10) cc_final: 0.9231 (m-80) REVERT: B 131 MET cc_start: 0.8536 (mmm) cc_final: 0.8185 (mmm) REVERT: B 161 TYR cc_start: 0.8429 (m-80) cc_final: 0.8102 (m-80) REVERT: B 171 ASN cc_start: 0.8926 (p0) cc_final: 0.8525 (p0) REVERT: B 176 ASN cc_start: 0.7860 (m-40) cc_final: 0.7173 (p0) REVERT: B 188 SER cc_start: 0.9128 (t) cc_final: 0.8816 (p) REVERT: H 3 GLN cc_start: 0.8674 (mp10) cc_final: 0.8303 (mp10) REVERT: H 22 CYS cc_start: 0.6376 (p) cc_final: 0.5910 (p) REVERT: H 36 TRP cc_start: 0.8903 (m100) cc_final: 0.8007 (m100) REVERT: H 47 TRP cc_start: 0.8857 (t60) cc_final: 0.7583 (t60) REVERT: H 57 ASP cc_start: 0.8532 (m-30) cc_final: 0.8009 (p0) REVERT: H 73 ASP cc_start: 0.9275 (t0) cc_final: 0.8979 (t0) REVERT: H 101 PHE cc_start: 0.8831 (m-80) cc_final: 0.8484 (m-80) REVERT: H 127 VAL cc_start: 0.8575 (m) cc_final: 0.8269 (m) REVERT: H 128 PHE cc_start: 0.9126 (m-80) cc_final: 0.8857 (m-80) REVERT: H 216 LYS cc_start: 0.8622 (tmtt) cc_final: 0.8408 (ptpt) REVERT: L 40 TRP cc_start: 0.8200 (m100) cc_final: 0.7676 (m100) REVERT: L 56 MET cc_start: 0.8899 (tmm) cc_final: 0.8340 (tmm) REVERT: L 70 SER cc_start: 0.8808 (p) cc_final: 0.8313 (p) REVERT: L 123 PHE cc_start: 0.8658 (m-80) cc_final: 0.8155 (m-80) REVERT: L 148 GLU cc_start: 0.9501 (mp0) cc_final: 0.9195 (mp0) REVERT: L 150 LYS cc_start: 0.8577 (tttp) cc_final: 0.8298 (tmtt) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1535 time to fit residues: 38.3511 Evaluate side-chains 152 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.0030 chunk 42 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 58 optimal weight: 0.0570 chunk 41 optimal weight: 1.9990 overall best weight: 0.4708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.129258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.097377 restraints weight = 15303.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.102430 restraints weight = 9700.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.106224 restraints weight = 6815.737| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6085 Z= 0.167 Angle : 0.630 6.694 8257 Z= 0.320 Chirality : 0.044 0.176 945 Planarity : 0.005 0.056 1030 Dihedral : 4.653 18.731 824 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: -0.13 (0.31), residues: 766 helix: 0.92 (0.32), residues: 258 sheet: -0.06 (0.36), residues: 199 loop : -0.89 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 33 HIS 0.004 0.001 HIS A 63 PHE 0.016 0.002 PHE B 62 TYR 0.021 0.001 TYR L 54 ARG 0.004 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 HIS cc_start: 0.8928 (m-70) cc_final: 0.7786 (m-70) REVERT: A 85 TRP cc_start: 0.8746 (m-10) cc_final: 0.8494 (m100) REVERT: A 149 MET cc_start: 0.6890 (tpt) cc_final: 0.6665 (tpt) REVERT: A 190 PHE cc_start: 0.9467 (m-10) cc_final: 0.9148 (m-80) REVERT: B 58 MET cc_start: 0.9282 (ttt) cc_final: 0.8946 (ttt) REVERT: B 131 MET cc_start: 0.8428 (mmm) cc_final: 0.8143 (mmm) REVERT: B 140 ASN cc_start: 0.8404 (m110) cc_final: 0.8198 (m110) REVERT: B 150 GLU cc_start: 0.7196 (pp20) cc_final: 0.6733 (pp20) REVERT: B 161 TYR cc_start: 0.8341 (m-80) cc_final: 0.7079 (m-80) REVERT: B 174 GLU cc_start: 0.9537 (tp30) cc_final: 0.9199 (mp0) REVERT: B 176 ASN cc_start: 0.7907 (m-40) cc_final: 0.7277 (p0) REVERT: B 184 TYR cc_start: 0.8511 (m-10) cc_final: 0.8227 (m-10) REVERT: H 3 GLN cc_start: 0.8622 (mp10) cc_final: 0.8253 (mp10) REVERT: H 22 CYS cc_start: 0.6181 (p) cc_final: 0.5797 (p) REVERT: H 36 TRP cc_start: 0.8851 (m100) cc_final: 0.7967 (m100) REVERT: H 47 TRP cc_start: 0.8936 (t60) cc_final: 0.7461 (t60) REVERT: H 73 ASP cc_start: 0.9294 (t0) cc_final: 0.8998 (t0) REVERT: H 101 PHE cc_start: 0.8398 (m-80) cc_final: 0.7868 (m-80) REVERT: H 216 LYS cc_start: 0.8636 (tmtt) cc_final: 0.8330 (ptpt) REVERT: L 40 TRP cc_start: 0.7982 (m100) cc_final: 0.7555 (m100) REVERT: L 70 SER cc_start: 0.8839 (p) cc_final: 0.8238 (p) REVERT: L 76 PHE cc_start: 0.8279 (m-80) cc_final: 0.7807 (m-80) REVERT: L 79 LYS cc_start: 0.8358 (tptt) cc_final: 0.8058 (tppt) REVERT: L 87 ASP cc_start: 0.7351 (p0) cc_final: 0.7037 (p0) REVERT: L 91 TYR cc_start: 0.8697 (m-10) cc_final: 0.8149 (m-80) REVERT: L 101 TYR cc_start: 0.8148 (m-10) cc_final: 0.7537 (m-10) REVERT: L 123 PHE cc_start: 0.8536 (m-80) cc_final: 0.7992 (m-80) REVERT: L 148 GLU cc_start: 0.9511 (mp0) cc_final: 0.9090 (mp0) REVERT: L 150 LYS cc_start: 0.8547 (tttp) cc_final: 0.8235 (tmtt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1435 time to fit residues: 36.0821 Evaluate side-chains 151 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 0.0670 chunk 65 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.131744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.099824 restraints weight = 15346.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.104628 restraints weight = 9956.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.108376 restraints weight = 7073.541| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6085 Z= 0.177 Angle : 0.628 6.376 8257 Z= 0.319 Chirality : 0.044 0.175 945 Planarity : 0.005 0.055 1030 Dihedral : 4.543 18.236 824 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: 0.07 (0.31), residues: 766 helix: 1.09 (0.33), residues: 258 sheet: 0.03 (0.37), residues: 199 loop : -0.75 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 33 HIS 0.004 0.001 HIS A 63 PHE 0.014 0.001 PHE B 62 TYR 0.013 0.001 TYR L 54 ARG 0.003 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 HIS cc_start: 0.8922 (m-70) cc_final: 0.7805 (m-70) REVERT: A 85 TRP cc_start: 0.8653 (m-10) cc_final: 0.8391 (m100) REVERT: A 190 PHE cc_start: 0.9435 (m-10) cc_final: 0.9120 (m-80) REVERT: B 58 MET cc_start: 0.9289 (ttt) cc_final: 0.8894 (ttt) REVERT: B 131 MET cc_start: 0.8353 (mmm) cc_final: 0.8094 (mmm) REVERT: B 150 GLU cc_start: 0.7289 (pp20) cc_final: 0.6808 (pp20) REVERT: B 176 ASN cc_start: 0.7898 (m-40) cc_final: 0.7195 (p0) REVERT: H 3 GLN cc_start: 0.8594 (mp10) cc_final: 0.8211 (mp10) REVERT: H 22 CYS cc_start: 0.6090 (p) cc_final: 0.5757 (p) REVERT: H 36 TRP cc_start: 0.8903 (m100) cc_final: 0.8013 (m100) REVERT: H 47 TRP cc_start: 0.8900 (t60) cc_final: 0.7443 (t60) REVERT: H 57 ASP cc_start: 0.8555 (m-30) cc_final: 0.8321 (m-30) REVERT: H 73 ASP cc_start: 0.9296 (t0) cc_final: 0.9020 (t0) REVERT: H 101 PHE cc_start: 0.8357 (m-80) cc_final: 0.7764 (m-80) REVERT: H 216 LYS cc_start: 0.8605 (tmtt) cc_final: 0.8275 (ptpt) REVERT: L 40 TRP cc_start: 0.7995 (m100) cc_final: 0.7631 (m100) REVERT: L 55 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8458 (mm-40) REVERT: L 70 SER cc_start: 0.8922 (p) cc_final: 0.8341 (p) REVERT: L 76 PHE cc_start: 0.8459 (m-80) cc_final: 0.7927 (m-80) REVERT: L 87 ASP cc_start: 0.7131 (p0) cc_final: 0.6864 (p0) REVERT: L 91 TYR cc_start: 0.8690 (m-10) cc_final: 0.8144 (m-80) REVERT: L 95 GLN cc_start: 0.8895 (pp30) cc_final: 0.8641 (pp30) REVERT: L 98 GLU cc_start: 0.9197 (pt0) cc_final: 0.8830 (pm20) REVERT: L 101 TYR cc_start: 0.8199 (m-10) cc_final: 0.7662 (m-10) REVERT: L 123 PHE cc_start: 0.8394 (m-80) cc_final: 0.7975 (m-80) REVERT: L 148 GLU cc_start: 0.9503 (mp0) cc_final: 0.9079 (mp0) REVERT: L 150 LYS cc_start: 0.8547 (tttp) cc_final: 0.8238 (tmtt) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1501 time to fit residues: 36.1966 Evaluate side-chains 147 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.126501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.094558 restraints weight = 14205.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099658 restraints weight = 8285.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.103498 restraints weight = 5569.094| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.6679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6085 Z= 0.309 Angle : 0.744 6.470 8257 Z= 0.384 Chirality : 0.046 0.175 945 Planarity : 0.006 0.057 1030 Dihedral : 5.149 20.524 824 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: -0.35 (0.31), residues: 766 helix: 0.68 (0.33), residues: 256 sheet: -0.36 (0.36), residues: 191 loop : -0.79 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 89 HIS 0.007 0.001 HIS L 31 PHE 0.016 0.002 PHE L 76 TYR 0.020 0.002 TYR L 54 ARG 0.003 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 HIS cc_start: 0.9118 (m-70) cc_final: 0.7960 (m-70) REVERT: A 64 ILE cc_start: 0.8936 (mm) cc_final: 0.8729 (mm) REVERT: A 190 PHE cc_start: 0.9556 (m-10) cc_final: 0.9263 (m-80) REVERT: B 58 MET cc_start: 0.9305 (ttt) cc_final: 0.8911 (ttt) REVERT: B 161 TYR cc_start: 0.8583 (m-80) cc_final: 0.7642 (m-80) REVERT: B 164 ILE cc_start: 0.9268 (mp) cc_final: 0.9028 (mp) REVERT: B 176 ASN cc_start: 0.7949 (m-40) cc_final: 0.7305 (p0) REVERT: B 188 SER cc_start: 0.9183 (t) cc_final: 0.8945 (p) REVERT: H 3 GLN cc_start: 0.8684 (mp10) cc_final: 0.8229 (mp10) REVERT: H 22 CYS cc_start: 0.7703 (p) cc_final: 0.6819 (p) REVERT: H 36 TRP cc_start: 0.9160 (m100) cc_final: 0.8219 (m100) REVERT: H 47 TRP cc_start: 0.8640 (t60) cc_final: 0.7606 (t60) REVERT: H 57 ASP cc_start: 0.8176 (m-30) cc_final: 0.7808 (p0) REVERT: H 73 ASP cc_start: 0.9070 (t0) cc_final: 0.8746 (t0) REVERT: H 101 PHE cc_start: 0.8420 (m-80) cc_final: 0.8095 (m-80) REVERT: H 150 ASP cc_start: 0.7063 (m-30) cc_final: 0.6859 (m-30) REVERT: H 160 TRP cc_start: 0.7536 (m100) cc_final: 0.7288 (m100) REVERT: H 216 LYS cc_start: 0.8856 (tmtt) cc_final: 0.8533 (ptpt) REVERT: L 50 GLN cc_start: 0.9382 (mt0) cc_final: 0.9026 (mp10) REVERT: L 76 PHE cc_start: 0.8304 (m-80) cc_final: 0.7887 (m-80) REVERT: L 79 LYS cc_start: 0.8544 (tptt) cc_final: 0.8301 (tppt) REVERT: L 123 PHE cc_start: 0.8808 (m-80) cc_final: 0.8525 (m-80) REVERT: L 148 GLU cc_start: 0.9359 (mp0) cc_final: 0.9068 (mp0) REVERT: L 150 LYS cc_start: 0.8588 (tttp) cc_final: 0.8329 (tmtt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1433 time to fit residues: 34.9674 Evaluate side-chains 148 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.256 > 50: distance: 1 - 2: 4.256 distance: 2 - 3: 4.650 distance: 2 - 5: 3.581 distance: 3 - 4: 17.754 distance: 3 - 9: 10.914 distance: 6 - 7: 3.980 distance: 10 - 11: 9.620 distance: 11 - 12: 21.691 distance: 11 - 17: 13.614 distance: 13 - 14: 11.686 distance: 13 - 15: 12.391 distance: 14 - 16: 5.088 distance: 17 - 18: 7.381 distance: 18 - 19: 9.567 distance: 18 - 21: 18.920 distance: 19 - 20: 10.897 distance: 19 - 24: 8.906 distance: 21 - 22: 3.644 distance: 21 - 23: 16.020 distance: 24 - 25: 10.860 distance: 25 - 26: 4.870 distance: 25 - 28: 21.069 distance: 26 - 27: 20.761 distance: 26 - 32: 28.751 distance: 28 - 29: 34.432 distance: 29 - 30: 16.081 distance: 30 - 31: 12.485 distance: 32 - 33: 17.686 distance: 33 - 34: 26.677 distance: 33 - 36: 18.201 distance: 34 - 35: 22.252 distance: 34 - 39: 10.679 distance: 36 - 37: 13.061 distance: 36 - 38: 34.445 distance: 39 - 40: 12.250 distance: 40 - 41: 10.336 distance: 40 - 43: 13.097 distance: 41 - 42: 11.307 distance: 41 - 48: 14.321 distance: 43 - 44: 5.108 distance: 44 - 45: 14.187 distance: 45 - 46: 7.654 distance: 45 - 47: 10.887 distance: 48 - 49: 9.340 distance: 49 - 50: 9.038 distance: 49 - 52: 19.220 distance: 50 - 51: 21.755 distance: 50 - 55: 32.850 distance: 52 - 53: 17.524 distance: 52 - 54: 26.449 distance: 55 - 56: 11.391 distance: 55 - 61: 25.916 distance: 56 - 57: 12.566 distance: 56 - 59: 14.343 distance: 57 - 58: 34.080 distance: 57 - 62: 18.839 distance: 59 - 60: 18.350 distance: 60 - 61: 20.738 distance: 62 - 63: 23.980 distance: 63 - 64: 9.826 distance: 63 - 66: 20.683 distance: 64 - 65: 7.708 distance: 64 - 70: 13.538 distance: 66 - 67: 40.691 distance: 67 - 68: 16.265 distance: 67 - 69: 31.364