Starting phenix.real_space_refine on Fri Aug 22 17:30:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7li9_23364/08_2025/7li9_23364.cif Found real_map, /net/cci-nas-00/data/ceres_data/7li9_23364/08_2025/7li9_23364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7li9_23364/08_2025/7li9_23364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7li9_23364/08_2025/7li9_23364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7li9_23364/08_2025/7li9_23364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7li9_23364/08_2025/7li9_23364.map" } resolution = 3.9 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= -0.000 sd= 0.032 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 S 34 5.16 5 Cl 1 4.86 5 C 4090 2.51 5 N 966 2.21 5 O 1083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 6174 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4305 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 23, 'TRANS': 515} Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 100 Unusual residues: {' CL': 1, 'D10': 3, 'D12': 2, 'HP6': 2, 'LNK': 1, 'SRO': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Time building chain proxies: 1.72, per 1000 atoms: 0.28 Number of scatterers: 6174 At special positions: 0 Unit cell: (68.929, 74.5395, 122.63, 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) Cl 1 17.00 S 34 16.00 O 1083 8.00 N 966 7.00 C 4090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 347.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 7 sheets defined 52.4% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 99 through 113 removed outlier: 4.928A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.657A pdb=" N TRP A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 190 removed outlier: 4.148A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.567A pdb=" N SER A 199 " --> pdb=" O PRO A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 252 through 268 removed outlier: 3.770A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 removed outlier: 3.676A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.771A pdb=" N ILE A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.957A pdb=" N LYS A 319 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 320 " --> pdb=" O TRP A 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 316 through 320' Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.738A pdb=" N GLY A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 349 removed outlier: 3.774A pdb=" N ALA A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 391 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.734A pdb=" N VAL A 397 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 4.068A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 451 removed outlier: 3.587A pdb=" N GLY A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 450 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.632A pdb=" N VAL A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 515 removed outlier: 4.036A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 529 Processing helix chain 'A' and resid 534 through 558 removed outlier: 3.514A pdb=" N ARG A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 541 " --> pdb=" O TRP A 537 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N SER A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Proline residue: A 546 - end of helix Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.841A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.551A pdb=" N LEU A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 599 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR A 600 " --> pdb=" O ARG A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 613 removed outlier: 3.583A pdb=" N THR A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 4.092A pdb=" N TYR B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 51' Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.689A pdb=" N SER B 44 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.696A pdb=" N TYR C 73 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN C 113 " --> pdb=" O ASN C 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 89 removed outlier: 3.522A pdb=" N SER C 96 " --> pdb=" O SER C 89 " (cutoff:3.500A) 268 hydrogen bonds defined for protein. 756 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: 0.93 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1817 1.34 - 1.46: 1646 1.46 - 1.58: 2835 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6347 Sorted by residual: bond pdb=" CD1 SRO A 910 " pdb=" NE1 SRO A 910 " ideal model delta sigma weight residual 1.377 1.324 0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" CD1 SRO A 909 " pdb=" NE1 SRO A 909 " ideal model delta sigma weight residual 1.377 1.324 0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" CD2 SRO A 909 " pdb=" CE2 SRO A 909 " ideal model delta sigma weight residual 1.419 1.370 0.049 2.00e-02 2.50e+03 6.02e+00 bond pdb=" CD2 SRO A 910 " pdb=" CE2 SRO A 910 " ideal model delta sigma weight residual 1.419 1.370 0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" CB SRO A 910 " pdb=" CG SRO A 910 " ideal model delta sigma weight residual 1.498 1.527 -0.029 2.00e-02 2.50e+03 2.14e+00 ... (remaining 6342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 8270 1.10 - 2.20: 212 2.20 - 3.30: 61 3.30 - 4.40: 51 4.40 - 5.50: 15 Bond angle restraints: 8609 Sorted by residual: angle pdb=" C ALA C 74 " pdb=" N ALA C 75 " pdb=" CA ALA C 75 " ideal model delta sigma weight residual 121.54 126.26 -4.72 1.91e+00 2.74e-01 6.10e+00 angle pdb=" N SER B 122 " pdb=" CA SER B 122 " pdb=" C SER B 122 " ideal model delta sigma weight residual 111.11 113.76 -2.65 1.20e+00 6.94e-01 4.88e+00 angle pdb=" N PHE A 287 " pdb=" CA PHE A 287 " pdb=" C PHE A 287 " ideal model delta sigma weight residual 109.81 114.29 -4.48 2.21e+00 2.05e-01 4.11e+00 angle pdb=" N ILE B 67 " pdb=" CA ILE B 67 " pdb=" C ILE B 67 " ideal model delta sigma weight residual 111.48 109.58 1.90 9.40e-01 1.13e+00 4.09e+00 angle pdb=" N PRO A 403 " pdb=" CA PRO A 403 " pdb=" C PRO A 403 " ideal model delta sigma weight residual 114.68 112.59 2.09 1.04e+00 9.25e-01 4.03e+00 ... (remaining 8604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.59: 3431 20.59 - 41.17: 187 41.17 - 61.76: 19 61.76 - 82.35: 6 82.35 - 102.94: 8 Dihedral angle restraints: 3651 sinusoidal: 1445 harmonic: 2206 Sorted by residual: dihedral pdb=" C1 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sinusoidal sigma weight residual -175.09 -72.15 -102.94 1 3.00e+01 1.11e-03 1.31e+01 dihedral pdb=" C1 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" C4 NAG D 2 " ideal model delta sinusoidal sigma weight residual -52.39 49.80 -102.19 1 3.00e+01 1.11e-03 1.29e+01 dihedral pdb=" N2 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sinusoidal sigma weight residual 62.25 164.33 -102.08 1 3.00e+01 1.11e-03 1.29e+01 ... (remaining 3648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 912 0.087 - 0.175: 30 0.175 - 0.262: 0 0.262 - 0.350: 0 0.350 - 0.437: 1 Chirality restraints: 943 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-02 2.50e+03 4.78e+02 chirality pdb=" CA ILE C 41 " pdb=" N ILE C 41 " pdb=" C ILE C 41 " pdb=" CB ILE C 41 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA VAL C 82 " pdb=" N VAL C 82 " pdb=" C VAL C 82 " pdb=" CB VAL C 82 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 940 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 338 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A 339 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 287 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 288 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 498 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO A 499 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " 0.016 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1976 2.83 - 3.35: 5574 3.35 - 3.86: 9998 3.86 - 4.38: 11021 4.38 - 4.90: 19411 Nonbonded interactions: 47980 Sorted by model distance: nonbonded pdb=" O SER A 214 " pdb=" OG SER A 214 " model vdw 2.309 3.040 nonbonded pdb=" O SER B 49 " pdb=" OG SER B 49 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR A 110 " pdb=" O ALA A 398 " model vdw 2.321 3.040 nonbonded pdb=" O SER A 190 " pdb=" OG SER A 190 " model vdw 2.330 3.040 nonbonded pdb=" NE2 GLN C 114 " pdb=" O SER C 119 " model vdw 2.345 3.120 ... (remaining 47975 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 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: 4.200 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.550 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 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 0.065 6353 Z= 0.135 Angle : 0.681 22.061 8621 Z= 0.299 Chirality : 0.040 0.437 943 Planarity : 0.003 0.037 1049 Dihedral : 13.558 102.936 2242 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.52 (0.26), residues: 761 helix: -1.06 (0.24), residues: 349 sheet: -2.81 (0.55), residues: 76 loop : -3.68 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 38 TYR 0.008 0.001 TYR A 175 PHE 0.007 0.001 PHE A 287 TRP 0.003 0.000 TRP A 317 HIS 0.002 0.000 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6347) covalent geometry : angle 0.55946 ( 8609) SS BOND : bond 0.00127 ( 3) SS BOND : angle 0.21786 ( 6) hydrogen bonds : bond 0.17743 ( 268) hydrogen bonds : angle 5.67003 ( 756) Misc. bond : bond 0.00024 ( 1) link_BETA1-4 : bond 0.06547 ( 1) link_BETA1-4 : angle 20.83721 ( 3) link_NAG-ASN : bond 0.00129 ( 1) link_NAG-ASN : angle 1.20753 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 VAL cc_start: 0.8386 (m) cc_final: 0.8005 (p) REVERT: C 62 GLN cc_start: 0.8423 (tt0) cc_final: 0.8184 (tt0) REVERT: C 114 GLN cc_start: 0.8014 (pp30) cc_final: 0.7472 (pp30) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.0931 time to fit residues: 19.3344 Evaluate side-chains 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN A 254 GLN A 332 GLN B 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.159599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.137505 restraints weight = 9063.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.139135 restraints weight = 6509.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139896 restraints weight = 5515.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140605 restraints weight = 4875.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141579 restraints weight = 4271.021| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6353 Z= 0.167 Angle : 0.629 9.688 8621 Z= 0.314 Chirality : 0.042 0.202 943 Planarity : 0.004 0.040 1049 Dihedral : 8.667 65.714 928 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.95 % Allowed : 13.20 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.41 (0.29), residues: 761 helix: -0.13 (0.27), residues: 349 sheet: -2.61 (0.58), residues: 84 loop : -3.01 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 59 TYR 0.028 0.002 TYR A 312 PHE 0.020 0.002 PHE A 531 TRP 0.015 0.002 TRP A 306 HIS 0.003 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 6347) covalent geometry : angle 0.62096 ( 8609) SS BOND : bond 0.00265 ( 3) SS BOND : angle 0.92574 ( 6) hydrogen bonds : bond 0.03530 ( 268) hydrogen bonds : angle 4.19719 ( 756) Misc. bond : bond 0.00122 ( 1) link_BETA1-4 : bond 0.02127 ( 1) link_BETA1-4 : angle 4.92419 ( 3) link_NAG-ASN : bond 0.00261 ( 1) link_NAG-ASN : angle 1.84489 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8203 (tt) REVERT: C 114 GLN cc_start: 0.8590 (pp30) cc_final: 0.7931 (pp30) outliers start: 19 outliers final: 12 residues processed: 113 average time/residue: 0.0812 time to fit residues: 12.2890 Evaluate side-chains 105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128903 restraints weight = 9079.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129112 restraints weight = 6996.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130106 restraints weight = 6245.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.130915 restraints weight = 5454.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130989 restraints weight = 4814.440| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6353 Z= 0.161 Angle : 0.567 7.853 8621 Z= 0.283 Chirality : 0.042 0.156 943 Planarity : 0.004 0.039 1049 Dihedral : 6.586 57.626 928 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.64 % Allowed : 17.86 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.97 (0.30), residues: 761 helix: 0.17 (0.27), residues: 348 sheet: -2.42 (0.53), residues: 94 loop : -2.65 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 234 TYR 0.015 0.001 TYR A 185 PHE 0.026 0.002 PHE A 531 TRP 0.013 0.001 TRP B 130 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6347) covalent geometry : angle 0.55902 ( 8609) SS BOND : bond 0.00283 ( 3) SS BOND : angle 0.83785 ( 6) hydrogen bonds : bond 0.03335 ( 268) hydrogen bonds : angle 3.98171 ( 756) Misc. bond : bond 0.00178 ( 1) link_BETA1-4 : bond 0.02461 ( 1) link_BETA1-4 : angle 5.03674 ( 3) link_NAG-ASN : bond 0.00579 ( 1) link_NAG-ASN : angle 0.79165 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.246 Fit side-chains REVERT: A 295 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8334 (tt) REVERT: C 114 GLN cc_start: 0.8838 (pp30) cc_final: 0.7997 (pp30) outliers start: 17 outliers final: 14 residues processed: 112 average time/residue: 0.0688 time to fit residues: 10.6285 Evaluate side-chains 103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.0000 chunk 0 optimal weight: 20.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126061 restraints weight = 9220.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125139 restraints weight = 8445.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126839 restraints weight = 8592.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127310 restraints weight = 6256.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127903 restraints weight = 5646.444| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6353 Z= 0.145 Angle : 0.553 8.256 8621 Z= 0.276 Chirality : 0.041 0.135 943 Planarity : 0.004 0.038 1049 Dihedral : 5.869 53.475 928 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.11 % Allowed : 18.94 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.30), residues: 761 helix: 0.40 (0.28), residues: 349 sheet: -2.27 (0.53), residues: 94 loop : -2.41 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 234 TYR 0.013 0.001 TYR B 50 PHE 0.031 0.002 PHE A 531 TRP 0.009 0.001 TRP B 130 HIS 0.002 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6347) covalent geometry : angle 0.54656 ( 8609) SS BOND : bond 0.00274 ( 3) SS BOND : angle 0.88637 ( 6) hydrogen bonds : bond 0.03073 ( 268) hydrogen bonds : angle 3.96405 ( 756) Misc. bond : bond 0.00016 ( 1) link_BETA1-4 : bond 0.02356 ( 1) link_BETA1-4 : angle 4.51620 ( 3) link_NAG-ASN : bond 0.00259 ( 1) link_NAG-ASN : angle 0.78338 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 37 GLN cc_start: 0.8113 (mp10) cc_final: 0.7888 (mp10) REVERT: C 102 MET cc_start: 0.7025 (tmm) cc_final: 0.6686 (ttp) REVERT: C 114 GLN cc_start: 0.8924 (pp30) cc_final: 0.8624 (pp30) outliers start: 20 outliers final: 14 residues processed: 107 average time/residue: 0.0665 time to fit residues: 9.9974 Evaluate side-chains 104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 127 LYS 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: 70.6385 > 50: distance: 1 - 19: 31.515 distance: 5 - 30: 30.333 distance: 12 - 38: 30.442 distance: 15 - 19: 27.919 distance: 16 - 46: 34.673 distance: 19 - 20: 15.756 distance: 20 - 21: 23.841 distance: 20 - 23: 27.240 distance: 21 - 22: 11.262 distance: 21 - 30: 25.908 distance: 22 - 52: 33.811 distance: 23 - 24: 21.176 distance: 24 - 25: 26.800 distance: 24 - 26: 34.209 distance: 25 - 27: 32.676 distance: 26 - 28: 21.364 distance: 27 - 29: 29.373 distance: 28 - 29: 22.438 distance: 30 - 31: 23.359 distance: 31 - 32: 14.620 distance: 31 - 34: 34.173 distance: 32 - 33: 8.423 distance: 32 - 38: 32.288 distance: 33 - 59: 41.544 distance: 34 - 35: 25.817 distance: 35 - 36: 40.981 distance: 35 - 37: 36.471 distance: 38 - 39: 5.773 distance: 39 - 40: 7.358 distance: 39 - 42: 31.654 distance: 40 - 41: 17.110 distance: 40 - 46: 29.850 distance: 41 - 67: 15.227 distance: 42 - 43: 7.644 distance: 43 - 44: 26.679 distance: 43 - 45: 23.255 distance: 46 - 47: 35.925 distance: 47 - 48: 20.125 distance: 47 - 50: 44.409 distance: 48 - 52: 9.257 distance: 50 - 51: 26.339 distance: 52 - 53: 12.777 distance: 53 - 54: 29.106 distance: 53 - 56: 17.917 distance: 54 - 55: 20.097 distance: 54 - 59: 41.443 distance: 56 - 57: 34.593 distance: 56 - 58: 25.588 distance: 59 - 60: 39.517 distance: 60 - 61: 41.740 distance: 60 - 63: 21.258 distance: 61 - 62: 61.974 distance: 61 - 67: 31.926 distance: 63 - 64: 19.430 distance: 63 - 65: 51.135 distance: 64 - 66: 28.131 distance: 67 - 68: 25.297 distance: 68 - 69: 10.131 distance: 69 - 70: 39.411 distance: 69 - 71: 38.304 distance: 71 - 72: 5.320 distance: 72 - 73: 9.459 distance: 72 - 75: 25.186 distance: 73 - 74: 19.285 distance: 73 - 83: 39.826 distance: 75 - 76: 8.200 distance: 76 - 77: 24.931 distance: 76 - 78: 22.595 distance: 77 - 79: 31.097 distance: 78 - 80: 16.336 distance: 79 - 81: 10.204 distance: 80 - 81: 30.028 distance: 81 - 82: 16.516 distance: 83 - 84: 17.390 distance: 84 - 85: 42.345 distance: 84 - 87: 38.240 distance: 85 - 86: 49.165 distance: 85 - 88: 30.078 distance: 88 - 89: 18.997 distance: 89 - 90: 15.813 distance: 89 - 92: 7.759 distance: 90 - 91: 20.174 distance: 90 - 95: 20.690 distance: 92 - 93: 25.337 distance: 92 - 94: 23.607