Starting phenix.real_space_refine on Fri Jul 25 07:07:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gr0_51516/07_2025/9gr0_51516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gr0_51516/07_2025/9gr0_51516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gr0_51516/07_2025/9gr0_51516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gr0_51516/07_2025/9gr0_51516.map" model { file = "/net/cci-nas-00/data/ceres_data/9gr0_51516/07_2025/9gr0_51516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gr0_51516/07_2025/9gr0_51516.cif" } resolution = 2.61 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= 0.002 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 26 5.16 5 C 4556 2.51 5 N 1269 2.21 5 O 1354 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-5711/modules/chem_data/mon_lib" Total number of atoms: 7213 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 65 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 65 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "B" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3427 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 22, 'TRANS': 420} Chain breaks: 1 Chain: "C" Number of atoms: 3439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3439 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 21, 'TRANS': 422} Chain breaks: 1 Chain: "B" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'FAD': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'FAD': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 5.93, per 1000 atoms: 0.82 Number of scatterers: 7213 At special positions: 0 Unit cell: (81.2, 83.52, 114.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 8 15.00 O 1354 8.00 N 1269 7.00 C 4556 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: 2.07 Conformation dependent library (CDL) restraints added in 794.1 milliseconds 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1630 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 16 sheets defined 30.8% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'B' and resid 140 through 154 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.526A pdb=" N SER B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 286 through 300 Processing helix chain 'B' and resid 309 through 326 Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.683A pdb=" N GLY B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.423A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 471 Processing helix chain 'B' and resid 584 through 594 removed outlier: 3.589A pdb=" N ALA B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 607 removed outlier: 3.642A pdb=" N LEU B 607 " --> pdb=" O GLU B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 154 Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.654A pdb=" N ILE C 220 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 274 through 280 Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 309 through 326 Processing helix chain 'C' and resid 345 through 359 Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.742A pdb=" N LYS C 408 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 470 Processing helix chain 'C' and resid 584 through 594 removed outlier: 3.637A pdb=" N ALA C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 606 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 239 Processing sheet with id=AA2, first strand: chain 'F' and resid 234 through 239 removed outlier: 6.254A pdb=" N LEU F 235 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE B 508 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET F 237 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 224 through 229 removed outlier: 6.859A pdb=" N VAL B 132 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 160 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE B 134 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 162 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 136 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N HIS B 131 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR B 253 " --> pdb=" O HIS B 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 229 removed outlier: 6.859A pdb=" N VAL B 132 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 160 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE B 134 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 162 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 136 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N HIS B 131 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR B 253 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 192 through 193 Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AA7, first strand: chain 'B' and resid 362 through 364 removed outlier: 6.721A pdb=" N VAL B 330 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N MET B 364 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN B 332 " --> pdb=" O MET B 364 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 375 Processing sheet with id=AA9, first strand: chain 'B' and resid 421 through 422 removed outlier: 5.921A pdb=" N PHE B 421 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N TYR B 443 " --> pdb=" O PHE B 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 224 through 229 removed outlier: 8.217A pdb=" N ARG C 158 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS C 131 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR C 253 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N MET C 242 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU C 236 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS C 244 " --> pdb=" O VAL C 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 224 through 229 removed outlier: 8.217A pdb=" N ARG C 158 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS C 131 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR C 253 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 433 " --> pdb=" O ALA C 429 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 192 through 194 Processing sheet with id=AB4, first strand: chain 'C' and resid 262 through 264 Processing sheet with id=AB5, first strand: chain 'C' and resid 281 through 282 removed outlier: 6.292A pdb=" N THR C 282 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER C 302 " --> pdb=" O HIS C 393 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL C 395 " --> pdb=" O SER C 302 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR C 304 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 330 " --> pdb=" O LYS C 362 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N MET C 364 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN C 332 " --> pdb=" O MET C 364 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 369 through 375 Processing sheet with id=AB7, first strand: chain 'C' and resid 421 through 422 removed outlier: 5.932A pdb=" N PHE C 421 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N TYR C 443 " --> pdb=" O PHE C 421 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1437 1.33 - 1.45: 1696 1.45 - 1.57: 4156 1.57 - 1.69: 16 1.69 - 1.81: 44 Bond restraints: 7349 Sorted by residual: bond pdb=" CB VAL C 423 " pdb=" CG1 VAL C 423 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.90e+00 bond pdb=" CA ASP C 237 " pdb=" CB ASP C 237 " ideal model delta sigma weight residual 1.533 1.558 -0.025 2.29e-02 1.91e+03 1.20e+00 bond pdb=" N PRO C 173 " pdb=" CA PRO C 173 " ideal model delta sigma weight residual 1.465 1.484 -0.019 2.03e-02 2.43e+03 8.67e-01 bond pdb=" CA ARG C 172 " pdb=" C ARG C 172 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.26e-02 6.30e+03 7.74e-01 bond pdb=" CA VAL C 550 " pdb=" C VAL C 550 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.10e-02 2.27e+03 6.82e-01 ... (remaining 7344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 9613 1.21 - 2.42: 285 2.42 - 3.64: 47 3.64 - 4.85: 9 4.85 - 6.06: 8 Bond angle restraints: 9962 Sorted by residual: angle pdb=" N VAL C 238 " pdb=" CA VAL C 238 " pdb=" C VAL C 238 " ideal model delta sigma weight residual 111.81 109.32 2.49 8.60e-01 1.35e+00 8.38e+00 angle pdb=" N PRO C 173 " pdb=" CA PRO C 173 " pdb=" C PRO C 173 " ideal model delta sigma weight residual 110.70 113.91 -3.21 1.22e+00 6.72e-01 6.91e+00 angle pdb=" N ARG C 172 " pdb=" CA ARG C 172 " pdb=" C ARG C 172 " ideal model delta sigma weight residual 109.81 115.35 -5.54 2.21e+00 2.05e-01 6.29e+00 angle pdb=" N ARG B 172 " pdb=" CA ARG B 172 " pdb=" C ARG B 172 " ideal model delta sigma weight residual 109.81 115.31 -5.50 2.21e+00 2.05e-01 6.19e+00 angle pdb=" N PRO B 173 " pdb=" CA PRO B 173 " pdb=" C PRO B 173 " ideal model delta sigma weight residual 110.70 113.52 -2.82 1.22e+00 6.72e-01 5.34e+00 ... (remaining 9957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 3964 16.67 - 33.34: 374 33.34 - 50.02: 111 50.02 - 66.69: 33 66.69 - 83.36: 12 Dihedral angle restraints: 4494 sinusoidal: 1947 harmonic: 2547 Sorted by residual: dihedral pdb=" CA LYS C 177 " pdb=" C LYS C 177 " pdb=" N GLU C 178 " pdb=" CA GLU C 178 " ideal model delta harmonic sigma weight residual -180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ARG C 450 " pdb=" C ARG C 450 " pdb=" N ARG C 451 " pdb=" CA ARG C 451 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASP B 237 " pdb=" CB ASP B 237 " pdb=" CG ASP B 237 " pdb=" OD1 ASP B 237 " ideal model delta sinusoidal sigma weight residual -30.00 -87.13 57.13 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 4491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 580 0.026 - 0.052: 290 0.052 - 0.078: 96 0.078 - 0.104: 83 0.104 - 0.130: 49 Chirality restraints: 1098 Sorted by residual: chirality pdb=" CA VAL C 423 " pdb=" N VAL C 423 " pdb=" C VAL C 423 " pdb=" CB VAL C 423 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA VAL B 564 " pdb=" N VAL B 564 " pdb=" C VAL B 564 " pdb=" CB VAL B 564 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA VAL C 564 " pdb=" N VAL C 564 " pdb=" C VAL C 564 " pdb=" CB VAL C 564 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1095 not shown) Planarity restraints: 1254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 132 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO C 133 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 133 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 133 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 174 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C PRO C 174 " -0.029 2.00e-02 2.50e+03 pdb=" O PRO C 174 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU C 175 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 172 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO C 173 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 173 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 173 " 0.023 5.00e-02 4.00e+02 ... (remaining 1251 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 386 2.73 - 3.27: 6671 3.27 - 3.82: 11653 3.82 - 4.36: 14940 4.36 - 4.90: 25567 Nonbonded interactions: 59217 Sorted by model distance: nonbonded pdb=" OE2 GLU B 453 " pdb=" O HOH B 801 " model vdw 2.191 3.040 nonbonded pdb=" OE1 GLU B 336 " pdb=" O2B NAD B 702 " model vdw 2.224 3.040 nonbonded pdb=" OD2 ASP B 499 " pdb=" OG SER B 501 " model vdw 2.266 3.040 nonbonded pdb=" O2A FAD B 701 " pdb=" O HOH B 802 " model vdw 2.284 3.040 nonbonded pdb=" NH1 ARG C 172 " pdb=" O ARG C 285 " model vdw 2.286 3.120 ... (remaining 59212 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 'F' } ncs_group { reference = (chain 'B' and (resid 129 through 610 or resid 701 through 702)) selection = (chain 'C' and (resid 129 through 510 or resid 551 through 610 or resid 701 thro \ ugh 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.370 Find NCS groups from input model: 0.310 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:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 : 0.003 0.045 7349 Z= 0.127 Angle : 0.526 6.062 9962 Z= 0.279 Chirality : 0.045 0.130 1098 Planarity : 0.005 0.049 1254 Dihedral : 15.364 83.359 2864 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 18.01 % Favored : 81.99 % 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: -0.17 (0.28), residues: 891 helix: 1.15 (0.35), residues: 247 sheet: 0.64 (0.35), residues: 214 loop : -1.30 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 351 HIS 0.004 0.001 HIS C 455 PHE 0.015 0.002 PHE B 482 TYR 0.009 0.001 TYR B 567 ARG 0.005 0.000 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.15769 ( 288) hydrogen bonds : angle 6.55552 ( 873) covalent geometry : bond 0.00291 ( 7349) covalent geometry : angle 0.52581 ( 9962) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.827 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 1.4388 time to fit residues: 170.3115 Evaluate side-chains 75 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/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-5711/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-5711/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-5711/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: 66.5726 > 50: distance: 32 - 60: 6.629 distance: 39 - 44: 11.682 distance: 40 - 67: 12.305 distance: 44 - 45: 7.967 distance: 45 - 46: 27.379 distance: 45 - 48: 37.929 distance: 46 - 47: 14.404 distance: 46 - 51: 45.756 distance: 48 - 49: 55.032 distance: 48 - 50: 18.954 distance: 51 - 52: 10.559 distance: 52 - 53: 22.630 distance: 52 - 55: 27.264 distance: 53 - 54: 31.032 distance: 53 - 60: 18.796 distance: 55 - 56: 17.526 distance: 56 - 57: 18.964 distance: 57 - 58: 23.379 distance: 58 - 59: 29.270 distance: 60 - 61: 10.163 distance: 61 - 62: 12.861 distance: 61 - 64: 8.079 distance: 62 - 63: 21.280 distance: 62 - 67: 17.585 distance: 64 - 65: 18.097 distance: 64 - 66: 20.850 distance: 67 - 68: 6.962 distance: 68 - 69: 14.180 distance: 68 - 71: 24.645 distance: 69 - 70: 23.264 distance: 69 - 75: 16.348 distance: 71 - 72: 15.585 distance: 72 - 73: 21.641 distance: 72 - 74: 7.901 distance: 75 - 76: 8.735 distance: 76 - 77: 23.850 distance: 76 - 79: 22.430 distance: 77 - 78: 15.565 distance: 77 - 86: 14.201 distance: 79 - 80: 22.593 distance: 80 - 81: 18.596 distance: 81 - 82: 15.105 distance: 82 - 83: 27.890 distance: 83 - 84: 20.886 distance: 83 - 85: 21.697 distance: 86 - 87: 9.860 distance: 86 - 162: 20.773 distance: 87 - 88: 10.103 distance: 87 - 90: 8.757 distance: 88 - 89: 6.102 distance: 88 - 97: 13.637 distance: 89 - 159: 8.378 distance: 90 - 91: 8.185 distance: 91 - 92: 13.716 distance: 91 - 93: 4.690 distance: 93 - 95: 9.576 distance: 94 - 96: 32.078 distance: 95 - 96: 24.136 distance: 97 - 98: 13.058 distance: 98 - 99: 12.342 distance: 98 - 101: 13.159 distance: 99 - 100: 28.410 distance: 99 - 106: 9.784 distance: 101 - 102: 17.699 distance: 102 - 103: 20.151 distance: 103 - 104: 31.198 distance: 104 - 105: 22.010 distance: 106 - 107: 19.355 distance: 107 - 108: 23.144 distance: 107 - 110: 17.635 distance: 108 - 109: 35.642 distance: 108 - 115: 22.940 distance: 110 - 111: 19.656 distance: 111 - 112: 10.618 distance: 112 - 113: 23.205 distance: 112 - 114: 12.261 distance: 115 - 116: 8.029 distance: 116 - 117: 21.449 distance: 116 - 119: 24.358 distance: 117 - 118: 28.011 distance: 117 - 129: 8.429 distance: 119 - 120: 27.564 distance: 120 - 121: 14.877 distance: 120 - 122: 19.601 distance: 121 - 123: 25.916 distance: 122 - 124: 27.076 distance: 122 - 125: 7.293 distance: 123 - 124: 14.946 distance: 124 - 126: 19.672 distance: 125 - 127: 21.591 distance: 126 - 128: 17.742 distance: 127 - 128: 18.015 distance: 129 - 130: 13.684 distance: 130 - 131: 27.287 distance: 130 - 133: 16.283 distance: 131 - 132: 6.170 distance: 131 - 137: 14.050 distance: 133 - 134: 17.241 distance: 134 - 135: 14.276 distance: 134 - 136: 18.905