Starting phenix.real_space_refine on Wed Mar 12 03:38:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qnu_4609/03_2025/6qnu_4609.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qnu_4609/03_2025/6qnu_4609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qnu_4609/03_2025/6qnu_4609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qnu_4609/03_2025/6qnu_4609.map" model { file = "/net/cci-nas-00/data/ceres_data/6qnu_4609/03_2025/6qnu_4609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qnu_4609/03_2025/6qnu_4609.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 22 5.16 5 C 4655 2.51 5 N 1169 2.21 5 O 1404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7250 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1400 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 2 Chain: "B" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1424 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 11, 'TRANS': 169} Chain breaks: 2 Chain: "C" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1409 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain breaks: 2 Chain: "D" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1541 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 4 Chain: "E" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1476 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain breaks: 5 Time building chain proxies: 4.66, per 1000 atoms: 0.64 Number of scatterers: 7250 At special positions: 0 Unit cell: (94.963, 105.633, 93.896, 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 22 16.00 O 1404 8.00 N 1169 7.00 C 4655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 995.3 milliseconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1742 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 17 sheets defined 2.8% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.583A pdb=" N ASN B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'C' and resid 226 through 230 removed outlier: 4.153A pdb=" N PHE C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 270 removed outlier: 4.424A pdb=" N GLY E 269 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 197 removed outlier: 3.508A pdb=" N VAL A 269 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA4, first strand: chain 'B' and resid 188 through 196 removed outlier: 3.734A pdb=" N LEU B 289 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASN B 293 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 132 through 133 removed outlier: 4.175A pdb=" N LEU C 305 " --> pdb=" O GLY C 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 132 through 133 removed outlier: 3.652A pdb=" N PHE C 312 " --> pdb=" O GLY C 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 188 through 197 removed outlier: 5.542A pdb=" N ASN C 293 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.401A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU D 191 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE D 151 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG D 193 " --> pdb=" O TYR D 149 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR D 149 " --> pdb=" O ARG D 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.854A pdb=" N ILE D 171 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 170 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 222 through 223 removed outlier: 3.722A pdb=" N VAL D 222 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLU D 240 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU D 287 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR D 242 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 259 through 263 removed outlier: 3.753A pdb=" N VAL D 303 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 324 " --> pdb=" O VAL D 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 114 through 120 removed outlier: 6.511A pdb=" N PHE E 115 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ARG E 212 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY E 117 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU E 214 " --> pdb=" O GLY E 117 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL E 119 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 190 " --> pdb=" O ALA E 207 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR E 187 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU E 154 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR E 189 " --> pdb=" O VAL E 152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 131 removed outlier: 6.724A pdb=" N ILE E 171 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 222 through 223 removed outlier: 3.521A pdb=" N VAL E 222 " --> pdb=" O PHE E 247 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 229 through 232 removed outlier: 6.681A pdb=" N GLY E 230 " --> pdb=" O LYS E 329 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 259 through 261 Processing sheet with id=AB8, first strand: chain 'E' and resid 272 through 277 188 hydrogen bonds defined for protein. 507 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: 1.64 Time building geometry restraints manager: 1.97 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: 2260 1.34 - 1.46: 1349 1.46 - 1.57: 3752 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 7399 Sorted by residual: bond pdb=" C GLU E 155 " pdb=" N PRO E 156 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.68e+00 bond pdb=" C GLU D 155 " pdb=" N PRO D 156 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.44e+00 bond pdb=" CA THR A 304 " pdb=" CB THR A 304 " ideal model delta sigma weight residual 1.530 1.559 -0.029 1.69e-02 3.50e+03 2.95e+00 bond pdb=" CA TYR D 158 " pdb=" C TYR D 158 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.64e+00 bond pdb=" CA TYR E 158 " pdb=" C TYR E 158 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.63e+00 ... (remaining 7394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 9719 2.17 - 4.34: 270 4.34 - 6.51: 39 6.51 - 8.68: 18 8.68 - 10.85: 4 Bond angle restraints: 10050 Sorted by residual: angle pdb=" C ALA A 303 " pdb=" N THR A 304 " pdb=" CA THR A 304 " ideal model delta sigma weight residual 121.54 129.81 -8.27 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C ASN D 219 " pdb=" N ILE D 220 " pdb=" CA ILE D 220 " ideal model delta sigma weight residual 122.13 130.06 -7.93 1.85e+00 2.92e-01 1.84e+01 angle pdb=" N ILE D 315 " pdb=" CA ILE D 315 " pdb=" C ILE D 315 " ideal model delta sigma weight residual 113.71 109.68 4.03 9.50e-01 1.11e+00 1.80e+01 angle pdb=" C ASP D 218 " pdb=" N ASN D 219 " pdb=" CA ASN D 219 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 angle pdb=" N TRP D 257 " pdb=" CA TRP D 257 " pdb=" C TRP D 257 " ideal model delta sigma weight residual 114.04 109.06 4.98 1.24e+00 6.50e-01 1.62e+01 ... (remaining 10045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 3940 16.84 - 33.69: 390 33.69 - 50.53: 66 50.53 - 67.37: 11 67.37 - 84.22: 6 Dihedral angle restraints: 4413 sinusoidal: 1724 harmonic: 2689 Sorted by residual: dihedral pdb=" CA LEU A 273 " pdb=" C LEU A 273 " pdb=" N ASN A 274 " pdb=" CA ASN A 274 " ideal model delta harmonic sigma weight residual -180.00 -138.37 -41.63 0 5.00e+00 4.00e-02 6.93e+01 dihedral pdb=" CA LEU B 273 " pdb=" C LEU B 273 " pdb=" N ASN B 274 " pdb=" CA ASN B 274 " ideal model delta harmonic sigma weight residual -180.00 -145.15 -34.85 0 5.00e+00 4.00e-02 4.86e+01 dihedral pdb=" CA ASP D 218 " pdb=" C ASP D 218 " pdb=" N ASN D 219 " pdb=" CA ASN D 219 " ideal model delta harmonic sigma weight residual -180.00 -145.28 -34.72 0 5.00e+00 4.00e-02 4.82e+01 ... (remaining 4410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 845 0.053 - 0.106: 236 0.106 - 0.159: 77 0.159 - 0.211: 7 0.211 - 0.264: 5 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA TYR E 158 " pdb=" N TYR E 158 " pdb=" C TYR E 158 " pdb=" CB TYR E 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA TYR D 158 " pdb=" N TYR D 158 " pdb=" C TYR D 158 " pdb=" CB TYR D 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE C 306 " pdb=" CA ILE C 306 " pdb=" CG1 ILE C 306 " pdb=" CG2 ILE C 306 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1167 not shown) Planarity restraints: 1269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 275 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" C LYS B 275 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS B 275 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG B 276 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 219 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C ASN E 219 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN E 219 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE E 220 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 308 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 309 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " -0.030 5.00e-02 4.00e+02 ... (remaining 1266 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2300 2.84 - 3.35: 5486 3.35 - 3.87: 11611 3.87 - 4.38: 12135 4.38 - 4.90: 22568 Nonbonded interactions: 54100 Sorted by model distance: nonbonded pdb=" OH TYR B 257 " pdb=" OE2 GLU B 299 " model vdw 2.324 3.040 nonbonded pdb=" OE1 GLU C 194 " pdb=" OH TYR C 196 " model vdw 2.328 3.040 nonbonded pdb=" OG1 THR C 135 " pdb=" O LEU C 158 " model vdw 2.349 3.040 nonbonded pdb=" O LEU A 204 " pdb=" OG SER A 208 " model vdw 2.351 3.040 nonbonded pdb=" OE1 GLU E 170 " pdb=" OH TYR E 172 " model vdw 2.392 3.040 ... (remaining 54095 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' and (resid 130 through 218 or resid 225 through 239 or resid 245 thro \ ugh 318)) selection = (chain 'C' and (resid 130 through 218 or resid 225 through 318)) } ncs_group { reference = (chain 'D' and (resid 108 through 134 or resid 146 through 193 or resid 206 thro \ ugh 233 or resid 238 through 291 or resid 299 through 331)) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.490 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.660 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 0.045 7399 Z= 0.286 Angle : 0.909 10.852 10050 Z= 0.494 Chirality : 0.057 0.264 1170 Planarity : 0.006 0.054 1269 Dihedral : 13.913 84.215 2671 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.61 % Allowed : 5.89 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -4.05 (0.24), residues: 880 helix: -4.32 (0.26), residues: 24 sheet: -1.61 (0.27), residues: 323 loop : -3.50 (0.21), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 134 HIS 0.005 0.001 HIS B 246 PHE 0.019 0.002 PHE D 301 TYR 0.022 0.002 TYR A 170 ARG 0.004 0.001 ARG E 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 182 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 162 LYS cc_start: 0.8376 (mttt) cc_final: 0.8081 (mtpp) REVERT: A 163 ASN cc_start: 0.8567 (t0) cc_final: 0.8292 (t0) REVERT: B 150 GLN cc_start: 0.8680 (mp-120) cc_final: 0.8340 (mt0) REVERT: D 112 GLN cc_start: 0.7803 (mt0) cc_final: 0.7533 (tt0) REVERT: D 164 LEU cc_start: 0.8552 (tp) cc_final: 0.8283 (tp) REVERT: E 208 GLN cc_start: 0.7162 (mt0) cc_final: 0.6729 (mt0) outliers start: 5 outliers final: 2 residues processed: 187 average time/residue: 0.2589 time to fit residues: 60.0055 Evaluate side-chains 124 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 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 130 ASN A 151 ASN A 168 ASN A 246 HIS A 249 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN C 249 ASN D 208 GLN D 210 GLN D 236 GLN E 126 HIS E 183 HIS E 217 ASN E 312 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.155733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.135086 restraints weight = 10779.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.138421 restraints weight = 6097.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140452 restraints weight = 4094.264| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7399 Z= 0.236 Angle : 0.627 6.671 10050 Z= 0.326 Chirality : 0.045 0.179 1170 Planarity : 0.004 0.037 1269 Dihedral : 5.976 30.901 973 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 2.33 % Allowed : 12.88 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.34 (0.26), residues: 880 helix: -2.59 (0.70), residues: 19 sheet: -1.52 (0.26), residues: 356 loop : -2.82 (0.24), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 134 HIS 0.011 0.001 HIS B 246 PHE 0.009 0.001 PHE D 301 TYR 0.016 0.001 TYR A 170 ARG 0.005 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.866 Fit side-chains REVERT: A 162 LYS cc_start: 0.8273 (mttt) cc_final: 0.7840 (mtpp) REVERT: A 163 ASN cc_start: 0.8658 (t0) cc_final: 0.8395 (t0) REVERT: B 150 GLN cc_start: 0.8331 (mp-120) cc_final: 0.8063 (mt0) REVERT: C 147 TYR cc_start: 0.6050 (t80) cc_final: 0.5387 (t80) REVERT: C 314 TYR cc_start: 0.8499 (p90) cc_final: 0.8215 (p90) REVERT: D 112 GLN cc_start: 0.7801 (mt0) cc_final: 0.7293 (tt0) REVERT: E 166 LYS cc_start: 0.8364 (mmtm) cc_final: 0.7534 (ttmt) REVERT: E 257 TRP cc_start: 0.8464 (OUTLIER) cc_final: 0.7815 (t-100) outliers start: 19 outliers final: 10 residues processed: 142 average time/residue: 0.2089 time to fit residues: 38.8216 Evaluate side-chains 127 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 257 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS E 126 HIS E 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.155545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.134854 restraints weight = 10842.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138025 restraints weight = 6174.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140292 restraints weight = 4201.474| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7399 Z= 0.220 Angle : 0.606 8.167 10050 Z= 0.312 Chirality : 0.045 0.166 1170 Planarity : 0.004 0.031 1269 Dihedral : 5.631 28.756 972 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.94 % Allowed : 13.74 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.26), residues: 880 helix: -1.93 (0.84), residues: 19 sheet: -1.31 (0.27), residues: 358 loop : -2.54 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 134 HIS 0.006 0.001 HIS B 246 PHE 0.017 0.001 PHE E 247 TYR 0.018 0.001 TYR B 179 ARG 0.004 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.788 Fit side-chains REVERT: A 162 LYS cc_start: 0.8245 (mttt) cc_final: 0.7818 (mtpp) REVERT: A 163 ASN cc_start: 0.8639 (t0) cc_final: 0.8363 (t0) REVERT: B 150 GLN cc_start: 0.8350 (mp-120) cc_final: 0.8053 (mt0) REVERT: C 147 TYR cc_start: 0.5674 (t80) cc_final: 0.5113 (t80) REVERT: C 314 TYR cc_start: 0.8486 (p90) cc_final: 0.8177 (p90) REVERT: D 112 GLN cc_start: 0.7746 (mt0) cc_final: 0.7505 (tt0) outliers start: 24 outliers final: 17 residues processed: 138 average time/residue: 0.2019 time to fit residues: 37.1412 Evaluate side-chains 133 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.152551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.131250 restraints weight = 10965.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.134688 restraints weight = 6208.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136714 restraints weight = 4158.598| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7399 Z= 0.299 Angle : 0.639 7.112 10050 Z= 0.329 Chirality : 0.047 0.163 1170 Planarity : 0.004 0.030 1269 Dihedral : 5.743 31.586 972 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 4.17 % Allowed : 14.72 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.86 (0.27), residues: 880 helix: -1.18 (1.01), residues: 19 sheet: -1.28 (0.27), residues: 356 loop : -2.46 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 134 HIS 0.002 0.001 HIS E 126 PHE 0.020 0.002 PHE D 247 TYR 0.017 0.002 TYR A 170 ARG 0.003 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.815 Fit side-chains REVERT: A 162 LYS cc_start: 0.8320 (mttt) cc_final: 0.7912 (mtpp) REVERT: B 150 GLN cc_start: 0.8380 (mp-120) cc_final: 0.8040 (mt0) REVERT: C 147 TYR cc_start: 0.5817 (t80) cc_final: 0.5154 (t80) REVERT: C 314 TYR cc_start: 0.8565 (p90) cc_final: 0.8352 (p90) REVERT: E 247 PHE cc_start: 0.8840 (t80) cc_final: 0.8626 (t80) REVERT: E 257 TRP cc_start: 0.8761 (OUTLIER) cc_final: 0.8212 (t-100) outliers start: 34 outliers final: 22 residues processed: 143 average time/residue: 0.1877 time to fit residues: 36.0975 Evaluate side-chains 133 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 68 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN E 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.154735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134076 restraints weight = 10812.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137156 restraints weight = 6179.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139321 restraints weight = 4236.626| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7399 Z= 0.213 Angle : 0.599 6.276 10050 Z= 0.308 Chirality : 0.046 0.160 1170 Planarity : 0.004 0.029 1269 Dihedral : 5.429 26.992 972 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.61 % Favored : 92.27 % Rotamer: Outliers : 3.93 % Allowed : 16.69 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.27), residues: 880 helix: -1.14 (1.00), residues: 19 sheet: -1.25 (0.27), residues: 358 loop : -2.30 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 134 HIS 0.005 0.001 HIS B 246 PHE 0.019 0.001 PHE D 247 TYR 0.020 0.001 TYR B 179 ARG 0.006 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.923 Fit side-chains REVERT: A 162 LYS cc_start: 0.8254 (mttt) cc_final: 0.7822 (mtpp) REVERT: A 163 ASN cc_start: 0.8674 (t0) cc_final: 0.8370 (t0) REVERT: B 150 GLN cc_start: 0.8268 (mp-120) cc_final: 0.7917 (mt0) REVERT: C 147 TYR cc_start: 0.5658 (t80) cc_final: 0.5071 (t80) REVERT: E 166 LYS cc_start: 0.8359 (mmtm) cc_final: 0.7605 (ttmm) REVERT: E 257 TRP cc_start: 0.8781 (OUTLIER) cc_final: 0.8220 (t-100) outliers start: 32 outliers final: 27 residues processed: 143 average time/residue: 0.1955 time to fit residues: 38.0299 Evaluate side-chains 134 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 55 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.155832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.134959 restraints weight = 10773.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138370 restraints weight = 6004.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140419 restraints weight = 3999.566| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7399 Z= 0.187 Angle : 0.577 6.250 10050 Z= 0.297 Chirality : 0.045 0.156 1170 Planarity : 0.003 0.028 1269 Dihedral : 5.245 25.598 972 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.17 % Allowed : 17.30 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.27), residues: 880 helix: -0.94 (1.05), residues: 19 sheet: -1.17 (0.27), residues: 358 loop : -2.20 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 134 HIS 0.002 0.001 HIS B 246 PHE 0.016 0.001 PHE D 247 TYR 0.022 0.001 TYR B 179 ARG 0.006 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.812 Fit side-chains REVERT: A 162 LYS cc_start: 0.8191 (mttt) cc_final: 0.7768 (mtpp) REVERT: A 163 ASN cc_start: 0.8682 (t0) cc_final: 0.8412 (t0) REVERT: B 150 GLN cc_start: 0.8294 (mp-120) cc_final: 0.7949 (mt0) REVERT: C 147 TYR cc_start: 0.5550 (t80) cc_final: 0.4977 (t80) REVERT: E 257 TRP cc_start: 0.8743 (OUTLIER) cc_final: 0.8144 (t-100) outliers start: 34 outliers final: 24 residues processed: 137 average time/residue: 0.1834 time to fit residues: 34.0303 Evaluate side-chains 135 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** B 130 ASN ** 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 = 0.3975 r_free = 0.3975 target = 0.154653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134018 restraints weight = 10872.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.137348 restraints weight = 6218.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139305 restraints weight = 4193.820| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7399 Z= 0.225 Angle : 0.598 6.297 10050 Z= 0.308 Chirality : 0.046 0.161 1170 Planarity : 0.004 0.032 1269 Dihedral : 5.244 26.621 972 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 4.17 % Allowed : 17.18 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.28), residues: 880 helix: -0.80 (1.08), residues: 19 sheet: -1.16 (0.27), residues: 358 loop : -2.15 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 290 HIS 0.003 0.001 HIS E 126 PHE 0.018 0.001 PHE D 272 TYR 0.019 0.001 TYR B 179 ARG 0.006 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.793 Fit side-chains REVERT: A 162 LYS cc_start: 0.8219 (mttt) cc_final: 0.7791 (mtpp) REVERT: A 163 ASN cc_start: 0.8694 (t0) cc_final: 0.8399 (t0) REVERT: B 150 GLN cc_start: 0.8295 (mp-120) cc_final: 0.7942 (mt0) REVERT: E 247 PHE cc_start: 0.8800 (t80) cc_final: 0.8579 (t80) REVERT: E 257 TRP cc_start: 0.8782 (OUTLIER) cc_final: 0.8194 (t-100) outliers start: 34 outliers final: 27 residues processed: 135 average time/residue: 0.1730 time to fit residues: 32.2276 Evaluate side-chains 135 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 74 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.149054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128051 restraints weight = 11118.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.131333 restraints weight = 6265.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133450 restraints weight = 4220.852| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 7399 Z= 0.380 Angle : 0.697 6.539 10050 Z= 0.360 Chirality : 0.049 0.158 1170 Planarity : 0.004 0.039 1269 Dihedral : 5.876 33.405 972 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 4.66 % Allowed : 17.55 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.70 (0.27), residues: 880 helix: -0.53 (1.16), residues: 19 sheet: -1.27 (0.27), residues: 343 loop : -2.28 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 290 HIS 0.004 0.001 HIS E 126 PHE 0.024 0.002 PHE D 247 TYR 0.019 0.002 TYR A 314 ARG 0.008 0.001 ARG E 243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.895 Fit side-chains REVERT: B 150 GLN cc_start: 0.8224 (mp-120) cc_final: 0.7895 (mt0) REVERT: D 183 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.6650 (m-70) REVERT: E 247 PHE cc_start: 0.8761 (t80) cc_final: 0.8546 (t80) REVERT: E 257 TRP cc_start: 0.8897 (OUTLIER) cc_final: 0.8336 (t-100) outliers start: 38 outliers final: 34 residues processed: 134 average time/residue: 0.1809 time to fit residues: 33.5476 Evaluate side-chains 138 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 70.3471 > 50: distance: 1 - 159: 3.648 distance: 70 - 72: 23.035 distance: 72 - 73: 22.114 distance: 73 - 74: 53.069 distance: 73 - 76: 20.766 distance: 74 - 75: 41.915 distance: 74 - 81: 61.976 distance: 76 - 77: 41.398 distance: 77 - 78: 48.827 distance: 78 - 79: 13.627 distance: 79 - 80: 27.587 distance: 81 - 82: 37.705 distance: 82 - 83: 57.948 distance: 82 - 85: 45.542 distance: 83 - 84: 39.044 distance: 83 - 90: 57.833 distance: 85 - 86: 45.821 distance: 86 - 87: 33.028 distance: 87 - 88: 20.111 distance: 87 - 89: 22.025 distance: 90 - 91: 19.742 distance: 91 - 92: 32.919 distance: 91 - 94: 53.309 distance: 92 - 93: 45.274 distance: 92 - 98: 51.404 distance: 94 - 95: 34.427 distance: 95 - 96: 31.935 distance: 95 - 97: 23.788 distance: 98 - 99: 28.407 distance: 98 - 104: 58.888 distance: 99 - 100: 39.429 distance: 99 - 102: 6.996 distance: 100 - 101: 20.759 distance: 100 - 105: 57.321 distance: 102 - 103: 33.773 distance: 103 - 104: 52.491 distance: 105 - 106: 10.226 distance: 106 - 107: 23.110 distance: 106 - 109: 35.261 distance: 107 - 108: 37.432 distance: 107 - 113: 23.032 distance: 109 - 110: 50.645 distance: 110 - 111: 22.281 distance: 110 - 112: 30.753 distance: 113 - 114: 51.876 distance: 114 - 115: 42.801 distance: 114 - 117: 55.160 distance: 115 - 116: 29.254 distance: 115 - 119: 40.565 distance: 117 - 118: 40.857 distance: 119 - 120: 40.387 distance: 119 - 192: 32.241 distance: 120 - 121: 65.663 distance: 120 - 123: 40.647 distance: 121 - 122: 26.517 distance: 121 - 128: 38.782 distance: 122 - 189: 27.080 distance: 123 - 124: 56.349 distance: 124 - 125: 49.073 distance: 125 - 126: 30.886 distance: 126 - 127: 20.787 distance: 128 - 129: 56.329 distance: 129 - 130: 41.611 distance: 129 - 132: 50.330 distance: 130 - 131: 40.853 distance: 130 - 136: 19.592 distance: 132 - 133: 57.550 distance: 133 - 134: 43.889 distance: 133 - 135: 41.026 distance: 136 - 137: 17.540 distance: 136 - 179: 28.328 distance: 137 - 138: 41.452 distance: 137 - 140: 29.565 distance: 138 - 139: 47.723 distance: 138 - 143: 69.065 distance: 139 - 176: 28.154 distance: 140 - 141: 33.497 distance: 140 - 142: 23.912 distance: 143 - 144: 45.512 distance: 144 - 145: 58.877 distance: 144 - 147: 25.059 distance: 145 - 146: 68.983 distance: 145 - 151: 34.847 distance: 147 - 148: 54.774 distance: 148 - 149: 56.249 distance: 148 - 150: 51.595