Starting phenix.real_space_refine on Fri Aug 22 20:46:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fy4_29552/08_2025/8fy4_29552.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fy4_29552/08_2025/8fy4_29552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fy4_29552/08_2025/8fy4_29552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fy4_29552/08_2025/8fy4_29552.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fy4_29552/08_2025/8fy4_29552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fy4_29552/08_2025/8fy4_29552.map" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 40 5.16 5 C 5016 2.51 5 N 1332 2.21 5 O 1412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7800 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1803 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain breaks: 2 Chain: "B" Number of atoms: 4326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4326 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 532} Chain breaks: 7 Chain: "C" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1671 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 189} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.00, per 1000 atoms: 0.26 Number of scatterers: 7800 At special positions: 0 Unit cell: (70.854, 80.976, 151.107, 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 40 16.00 O 1412 8.00 N 1332 7.00 C 5016 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: 0.64 Conformation dependent library (CDL) restraints added in 427.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 1 sheets defined 74.3% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 24 through 54 Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 67 through 82 removed outlier: 4.191A pdb=" N ILE A 82 " --> pdb=" O CYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.687A pdb=" N ASN A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.960A pdb=" N VAL A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 162 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.670A pdb=" N PHE A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.282A pdb=" N LEU A 240 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 40 removed outlier: 3.883A pdb=" N LEU B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 56 Processing helix chain 'B' and resid 59 through 74 removed outlier: 4.251A pdb=" N THR B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 108 through 122 removed outlier: 3.509A pdb=" N TYR B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 removed outlier: 3.949A pdb=" N PHE B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 163 through 180 Processing helix chain 'B' and resid 205 through 230 removed outlier: 3.606A pdb=" N ALA B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 removed outlier: 4.375A pdb=" N ARG B 237 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 265 through 276 Processing helix chain 'B' and resid 290 through 306 Processing helix chain 'B' and resid 308 through 329 removed outlier: 3.566A pdb=" N PHE B 314 " --> pdb=" O ASN B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.935A pdb=" N LYS B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 351 removed outlier: 3.528A pdb=" N LEU B 350 " --> pdb=" O CYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 369 Processing helix chain 'B' and resid 370 through 382 Processing helix chain 'B' and resid 388 through 403 Processing helix chain 'B' and resid 457 through 472 removed outlier: 3.757A pdb=" N ILE B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 547 Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 566 through 584 Processing helix chain 'B' and resid 586 through 594 removed outlier: 3.776A pdb=" N THR B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 637 through 656 Processing helix chain 'B' and resid 658 through 673 removed outlier: 3.851A pdb=" N ILE B 673 " --> pdb=" O ALA B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 695 through 706 removed outlier: 3.786A pdb=" N GLN B 701 " --> pdb=" O GLN B 697 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 703 " --> pdb=" O ALA B 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 40 Processing helix chain 'C' and resid 42 through 47 removed outlier: 3.581A pdb=" N SER C 47 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 64 through 78 removed outlier: 3.753A pdb=" N VAL C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 98 removed outlier: 3.603A pdb=" N ARG C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 109 through 117 removed outlier: 3.986A pdb=" N PHE C 113 " --> pdb=" O PHE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 150 removed outlier: 3.693A pdb=" N PHE C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN C 150 " --> pdb=" O PHE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 removed outlier: 4.032A pdb=" N ILE C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.847A pdb=" N GLU C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 224 through 233 Processing sheet with id=AA1, first strand: chain 'C' and resid 203 through 204 494 hydrogen bonds defined for protein. 1443 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: 1.24 Time building geometry restraints manager: 0.87 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: 2516 1.34 - 1.46: 1455 1.46 - 1.58: 3929 1.58 - 1.70: 0 1.70 - 1.81: 57 Bond restraints: 7957 Sorted by residual: bond pdb=" CB LYS B 176 " pdb=" CG LYS B 176 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CG LYS C 31 " pdb=" CD LYS C 31 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB GLN B 137 " pdb=" CG GLN B 137 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CB ASP A 237 " pdb=" CG ASP A 237 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB LYS C 31 " pdb=" CG LYS C 31 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 ... (remaining 7952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 10657 2.59 - 5.18: 89 5.18 - 7.77: 9 7.77 - 10.36: 2 10.36 - 12.95: 2 Bond angle restraints: 10759 Sorted by residual: angle pdb=" CB MET C 170 " pdb=" CG MET C 170 " pdb=" SD MET C 170 " ideal model delta sigma weight residual 112.70 125.65 -12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" CA LYS B 176 " pdb=" CB LYS B 176 " pdb=" CG LYS B 176 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CA LEU B 38 " pdb=" CB LEU B 38 " pdb=" CG LEU B 38 " ideal model delta sigma weight residual 116.30 128.27 -11.97 3.50e+00 8.16e-02 1.17e+01 angle pdb=" CB LYS C 31 " pdb=" CG LYS C 31 " pdb=" CD LYS C 31 " ideal model delta sigma weight residual 111.30 118.65 -7.35 2.30e+00 1.89e-01 1.02e+01 angle pdb=" CB LYS B 176 " pdb=" CG LYS B 176 " pdb=" CD LYS B 176 " ideal model delta sigma weight residual 111.30 118.16 -6.86 2.30e+00 1.89e-01 8.90e+00 ... (remaining 10754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 4345 17.75 - 35.50: 391 35.50 - 53.26: 100 53.26 - 71.01: 21 71.01 - 88.76: 4 Dihedral angle restraints: 4861 sinusoidal: 1959 harmonic: 2902 Sorted by residual: dihedral pdb=" CA ASP C 209 " pdb=" CB ASP C 209 " pdb=" CG ASP C 209 " pdb=" OD1 ASP C 209 " ideal model delta sinusoidal sigma weight residual -30.00 -86.66 56.66 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP C 259 " pdb=" CB ASP C 259 " pdb=" CG ASP C 259 " pdb=" OD1 ASP C 259 " ideal model delta sinusoidal sigma weight residual -30.00 -85.21 55.21 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CB MET B 285 " pdb=" CG MET B 285 " pdb=" SD MET B 285 " pdb=" CE MET B 285 " ideal model delta sinusoidal sigma weight residual 180.00 120.92 59.08 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 809 0.027 - 0.054: 263 0.054 - 0.081: 101 0.081 - 0.108: 45 0.108 - 0.136: 13 Chirality restraints: 1231 Sorted by residual: chirality pdb=" CA ILE B 424 " pdb=" N ILE B 424 " pdb=" C ILE B 424 " pdb=" CB ILE B 424 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CB ILE C 181 " pdb=" CA ILE C 181 " pdb=" CG1 ILE C 181 " pdb=" CG2 ILE C 181 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 453 " pdb=" N ILE B 453 " pdb=" C ILE B 453 " pdb=" CB ILE B 453 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1228 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 141 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO C 142 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 64 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" CD GLU C 64 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU C 64 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C 64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 163 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO C 164 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.020 5.00e-02 4.00e+02 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 387 2.73 - 3.27: 8194 3.27 - 3.82: 13833 3.82 - 4.36: 15628 4.36 - 4.90: 27191 Nonbonded interactions: 65233 Sorted by model distance: nonbonded pdb=" N GLN C 226 " pdb=" OE1 GLN C 226 " model vdw 2.189 3.120 nonbonded pdb=" O GLY C 45 " pdb=" OG1 THR C 163 " model vdw 2.206 3.040 nonbonded pdb=" O PHE A 214 " pdb=" OH TYR A 228 " model vdw 2.217 3.040 nonbonded pdb=" N GLN C 274 " pdb=" OE1 GLN C 274 " model vdw 2.218 3.120 nonbonded pdb=" N GLU A 179 " pdb=" OE1 GLU A 179 " model vdw 2.229 3.120 ... (remaining 65228 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.690 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.460 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 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 0.043 7957 Z= 0.116 Angle : 0.570 12.948 10759 Z= 0.280 Chirality : 0.036 0.136 1231 Planarity : 0.004 0.043 1371 Dihedral : 14.867 88.761 2965 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.87 % Allowed : 18.55 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.28), residues: 957 helix: 2.16 (0.21), residues: 681 sheet: None (None), residues: 0 loop : 0.27 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.017 0.001 TYR B 136 PHE 0.009 0.001 PHE B 284 TRP 0.006 0.001 TRP C 275 HIS 0.003 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7957) covalent geometry : angle 0.57035 (10759) hydrogen bonds : bond 0.13020 ( 494) hydrogen bonds : angle 4.31654 ( 1443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.331 Fit side-chains REVERT: A 31 GLU cc_start: 0.6566 (tt0) cc_final: 0.6320 (tt0) REVERT: A 67 ASP cc_start: 0.7051 (p0) cc_final: 0.6842 (p0) REVERT: A 138 SER cc_start: 0.7279 (m) cc_final: 0.6682 (p) REVERT: B 243 MET cc_start: 0.0653 (mmt) cc_final: 0.0161 (mmt) REVERT: B 285 MET cc_start: 0.3848 (mmp) cc_final: 0.2687 (mmp) REVERT: B 459 GLU cc_start: 0.6679 (mp0) cc_final: 0.6115 (mp0) REVERT: B 530 ASN cc_start: 0.5968 (t0) cc_final: 0.5729 (t0) REVERT: B 548 ASP cc_start: 0.6645 (t0) cc_final: 0.6314 (t0) REVERT: B 549 ASN cc_start: 0.7057 (m-40) cc_final: 0.6553 (p0) REVERT: B 551 MET cc_start: 0.7028 (mmm) cc_final: 0.6682 (mmp) REVERT: B 561 GLN cc_start: 0.7167 (mt0) cc_final: 0.6544 (mp10) REVERT: B 582 ILE cc_start: 0.6955 (OUTLIER) cc_final: 0.6711 (mt) REVERT: B 664 LYS cc_start: 0.6414 (ttmm) cc_final: 0.6190 (ttmt) REVERT: C 182 SER cc_start: 0.6862 (t) cc_final: 0.6594 (m) REVERT: C 190 GLU cc_start: 0.6851 (tp30) cc_final: 0.6497 (tp30) outliers start: 16 outliers final: 8 residues processed: 138 average time/residue: 0.6205 time to fit residues: 90.7183 Evaluate side-chains 116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 243 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.0040 chunk 45 optimal weight: 0.2980 overall best weight: 0.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 102 GLN A 135 ASN A 151 GLN A 216 GLN B 88 GLN B 163 GLN B 169 HIS ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN B 364 GLN B 383 GLN B 549 ASN B 561 GLN B 632 GLN B 695 ASN C 58 HIS C 185 GLN C 192 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.170806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.154259 restraints weight = 10504.026| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 1.56 r_work: 0.3931 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7957 Z= 0.149 Angle : 0.592 10.133 10759 Z= 0.297 Chirality : 0.038 0.153 1231 Planarity : 0.005 0.052 1371 Dihedral : 5.021 52.784 1060 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.55 % Allowed : 16.57 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.28), residues: 957 helix: 1.97 (0.20), residues: 690 sheet: None (None), residues: 0 loop : 0.15 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 224 TYR 0.016 0.002 TYR B 659 PHE 0.020 0.002 PHE B 295 TRP 0.008 0.002 TRP B 296 HIS 0.009 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7957) covalent geometry : angle 0.59245 (10759) hydrogen bonds : bond 0.03663 ( 494) hydrogen bonds : angle 3.54725 ( 1443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: B 176 LYS cc_start: 0.6971 (tmmt) cc_final: 0.6714 (tmmt) REVERT: B 243 MET cc_start: 0.0809 (mmt) cc_final: 0.0463 (mmt) REVERT: B 459 GLU cc_start: 0.7227 (mp0) cc_final: 0.6913 (mp0) REVERT: B 582 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6469 (mt) REVERT: C 190 GLU cc_start: 0.7406 (tp30) cc_final: 0.7093 (tp30) outliers start: 39 outliers final: 10 residues processed: 163 average time/residue: 0.6241 time to fit residues: 107.5208 Evaluate side-chains 127 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain C residue 68 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 0.0170 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 125 GLN A 200 GLN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN B 549 ASN B 554 ASN ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS C 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.156130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.139280 restraints weight = 10053.773| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.57 r_work: 0.3746 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 7957 Z= 0.189 Angle : 0.615 8.406 10759 Z= 0.308 Chirality : 0.040 0.164 1231 Planarity : 0.005 0.048 1371 Dihedral : 4.756 42.473 1052 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.13 % Allowed : 18.44 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.27), residues: 957 helix: 1.76 (0.20), residues: 693 sheet: None (None), residues: 0 loop : 0.17 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 663 TYR 0.018 0.002 TYR B 659 PHE 0.017 0.002 PHE C 247 TRP 0.007 0.001 TRP C 275 HIS 0.009 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 7957) covalent geometry : angle 0.61475 (10759) hydrogen bonds : bond 0.04316 ( 494) hydrogen bonds : angle 3.69423 ( 1443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8309 (mm) cc_final: 0.8067 (mp) REVERT: A 236 MET cc_start: 0.7524 (mtm) cc_final: 0.7142 (mtp) REVERT: B 123 ARG cc_start: 0.8090 (mpt-90) cc_final: 0.7667 (mtt-85) REVERT: B 143 GLU cc_start: 0.6512 (tm-30) cc_final: 0.6281 (tm-30) REVERT: B 176 LYS cc_start: 0.7056 (tmmt) cc_final: 0.6817 (tmmt) REVERT: B 243 MET cc_start: 0.1105 (mmt) cc_final: 0.0887 (mmt) REVERT: B 285 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.4898 (mmp) REVERT: B 291 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7060 (mp) REVERT: B 668 GLN cc_start: 0.7888 (tt0) cc_final: 0.7685 (tt0) REVERT: B 690 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7561 (mm-30) REVERT: C 64 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6869 (pp20) REVERT: C 68 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8059 (tt) REVERT: C 145 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7711 (ttpp) REVERT: C 172 VAL cc_start: 0.5935 (OUTLIER) cc_final: 0.5665 (t) REVERT: C 229 GLU cc_start: 0.7698 (tt0) cc_final: 0.7474 (tt0) outliers start: 44 outliers final: 11 residues processed: 180 average time/residue: 0.6692 time to fit residues: 126.7620 Evaluate side-chains 154 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 172 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 3 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 0.0570 chunk 50 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 73 optimal weight: 0.0370 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 216 GLN B 108 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN C 58 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.154196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137292 restraints weight = 10135.286| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.59 r_work: 0.3719 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7957 Z= 0.149 Angle : 0.542 8.217 10759 Z= 0.269 Chirality : 0.038 0.150 1231 Planarity : 0.005 0.065 1371 Dihedral : 4.111 34.803 1047 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.38 % Allowed : 21.70 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.27), residues: 957 helix: 1.83 (0.20), residues: 694 sheet: None (None), residues: 0 loop : 0.16 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 663 TYR 0.016 0.001 TYR B 355 PHE 0.021 0.001 PHE C 247 TRP 0.007 0.001 TRP B 296 HIS 0.008 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 7957) covalent geometry : angle 0.54175 (10759) hydrogen bonds : bond 0.03736 ( 494) hydrogen bonds : angle 3.51306 ( 1443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8316 (mm) cc_final: 0.8090 (mp) REVERT: A 236 MET cc_start: 0.7535 (mtm) cc_final: 0.7289 (mtt) REVERT: B 123 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7771 (mtt-85) REVERT: B 143 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6486 (tm-30) REVERT: B 176 LYS cc_start: 0.7111 (tmmt) cc_final: 0.6840 (tmmt) REVERT: B 243 MET cc_start: 0.1436 (mmt) cc_final: 0.1235 (mmt) REVERT: B 265 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7445 (m-40) REVERT: B 285 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5102 (mmp) REVERT: B 690 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7525 (mm-30) REVERT: C 64 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6930 (pp20) REVERT: C 68 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8113 (tt) REVERT: C 150 GLN cc_start: 0.5819 (OUTLIER) cc_final: 0.5611 (pp30) REVERT: C 172 VAL cc_start: 0.6039 (OUTLIER) cc_final: 0.5788 (t) outliers start: 29 outliers final: 12 residues processed: 165 average time/residue: 0.6380 time to fit residues: 110.7897 Evaluate side-chains 165 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 226 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.9155 > 50: distance: 127 - 130: 4.020 distance: 130 - 131: 4.736 distance: 131 - 132: 5.835 distance: 131 - 134: 12.685 distance: 132 - 133: 5.557 distance: 132 - 136: 8.445 distance: 134 - 135: 9.528 distance: 136 - 137: 9.584 distance: 136 - 248: 8.134 distance: 137 - 138: 6.034 distance: 137 - 140: 5.104 distance: 138 - 139: 7.003 distance: 138 - 147: 9.681 distance: 139 - 245: 6.289 distance: 140 - 141: 3.349 distance: 141 - 142: 4.652 distance: 141 - 143: 7.278 distance: 142 - 144: 5.506 distance: 143 - 145: 5.632 distance: 144 - 146: 6.460 distance: 145 - 146: 3.596 distance: 147 - 153: 10.859 distance: 148 - 149: 3.874 distance: 148 - 151: 3.418 distance: 149 - 150: 13.488 distance: 151 - 152: 6.095 distance: 152 - 153: 7.264 distance: 154 - 155: 9.810 distance: 155 - 156: 6.573 distance: 155 - 158: 8.094 distance: 156 - 157: 9.729 distance: 156 - 160: 5.747 distance: 158 - 159: 5.491 distance: 160 - 161: 7.815 distance: 161 - 162: 7.311 distance: 161 - 164: 6.942 distance: 162 - 163: 37.875 distance: 162 - 168: 19.206 distance: 164 - 165: 6.330 distance: 164 - 166: 14.125 distance: 165 - 167: 7.822 distance: 168 - 169: 21.822 distance: 169 - 170: 10.862 distance: 169 - 172: 10.900 distance: 170 - 171: 18.822 distance: 170 - 176: 15.752 distance: 172 - 173: 10.063 distance: 173 - 174: 21.473 distance: 173 - 175: 34.253 distance: 176 - 177: 5.654 distance: 177 - 178: 8.995 distance: 177 - 180: 9.665 distance: 178 - 179: 15.613 distance: 178 - 182: 10.477 distance: 180 - 181: 11.009 distance: 182 - 183: 15.199 distance: 183 - 184: 10.516 distance: 183 - 186: 16.688 distance: 184 - 185: 12.522 distance: 184 - 190: 7.281 distance: 186 - 187: 14.898 distance: 187 - 188: 9.824 distance: 187 - 189: 12.608 distance: 190 - 191: 7.127 distance: 190 - 196: 11.611 distance: 191 - 192: 21.013 distance: 191 - 194: 8.524 distance: 192 - 193: 5.418 distance: 194 - 195: 13.285 distance: 197 - 198: 4.738 distance: 198 - 199: 15.683 distance: 198 - 201: 15.291 distance: 199 - 200: 17.072 distance: 199 - 202: 4.253