Starting phenix.real_space_refine on Thu Jul 2 03:57:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fdk_31546/07_2026/7fdk_31546.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fdk_31546/07_2026/7fdk_31546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7fdk_31546/07_2026/7fdk_31546.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fdk_31546/07_2026/7fdk_31546.cif" model { file = "/net/cci-nas-00/data/ceres_data/7fdk_31546/07_2026/7fdk_31546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fdk_31546/07_2026/7fdk_31546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fdk_31546/07_2026/7fdk_31546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fdk_31546/07_2026/7fdk_31546.map" } resolution = 3.69 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= 0.004 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 37 5.16 5 C 4113 2.51 5 N 1076 2.21 5 O 1223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6449 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4867 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4860 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 26, 'TRANS': 570} Conformer: "B" Number of residues, atoms: 597, 4860 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 26, 'TRANS': 570} bond proxies already assigned to first conformer: 4986 Chain: "E" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1540 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "A" 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 chiralities: 2 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.14, per 1000 atoms: 0.33 Number of scatterers: 6449 At special positions: 0 Unit cell: (118.56, 83.2, 80.08, 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 37 16.00 O 1223 8.00 N 1076 7.00 C 4113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 53 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 604.6 milliseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 50.8% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.883A pdb=" N ASN A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 79 removed outlier: 4.058A pdb=" N SER A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.614A pdb=" N THR A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 Proline residue: A 178 - end of helix removed outlier: 3.962A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 231 removed outlier: 4.171A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.540A pdb=" N LYS A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.561A pdb=" N THR A 282 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.526A pdb=" N ALA A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.808A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.248A pdb=" N ALA A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 removed outlier: 4.328A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 465 removed outlier: 4.036A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.549A pdb=" N ARG A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.439A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 4.528A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.529A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 383 through 390 Processing helix chain 'E' and resid 403 through 407 removed outlier: 3.638A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.524A pdb=" N ASP E 442 " --> pdb=" O SER E 438 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.405A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.426A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 355 removed outlier: 4.005A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 270 hydrogen bonds defined for protein. 788 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: 0.86 Time building geometry restraints manager: 0.65 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: 2071 1.34 - 1.46: 1721 1.46 - 1.58: 2781 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6631 Sorted by residual: bond pdb=" C LYS A 359 " pdb=" N MET A 360 " ideal model delta sigma weight residual 1.330 1.535 -0.205 1.23e-02 6.61e+03 2.79e+02 bond pdb=" C ILE A 358 " pdb=" N LYS A 359 " ideal model delta sigma weight residual 1.331 1.551 -0.221 1.66e-02 3.63e+03 1.77e+02 bond pdb=" C ALA E 397 " pdb=" N ASP E 398 " ideal model delta sigma weight residual 1.328 1.432 -0.104 1.42e-02 4.96e+03 5.37e+01 bond pdb=" C ASP E 398 " pdb=" N SER E 399 " ideal model delta sigma weight residual 1.332 1.392 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" C SER A 563 " pdb=" N GLU A 564 " ideal model delta sigma weight residual 1.335 1.231 0.104 3.04e-02 1.08e+03 1.16e+01 ... (remaining 6626 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 8756 2.24 - 4.47: 219 4.47 - 6.71: 29 6.71 - 8.95: 2 8.95 - 11.18: 4 Bond angle restraints: 9010 Sorted by residual: angle pdb=" O ILE A 358 " pdb=" C ILE A 358 " pdb=" N LYS A 359 " ideal model delta sigma weight residual 123.26 134.44 -11.18 1.08e+00 8.57e-01 1.07e+02 angle pdb=" CA ILE A 358 " pdb=" C ILE A 358 " pdb=" N LYS A 359 " ideal model delta sigma weight residual 116.31 105.62 10.69 1.14e+00 7.69e-01 8.79e+01 angle pdb=" N GLN A 86 " pdb=" CA GLN A 86 " pdb=" C GLN A 86 " ideal model delta sigma weight residual 114.56 108.10 6.46 1.27e+00 6.20e-01 2.59e+01 angle pdb=" O ALA E 397 " pdb=" C ALA E 397 " pdb=" N ASP E 398 " ideal model delta sigma weight residual 123.27 129.19 -5.92 1.17e+00 7.31e-01 2.56e+01 angle pdb=" CA ALA E 397 " pdb=" C ALA E 397 " pdb=" N ASP E 398 " ideal model delta sigma weight residual 116.45 110.39 6.06 1.23e+00 6.61e-01 2.43e+01 ... (remaining 9005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 3425 17.73 - 35.45: 357 35.45 - 53.18: 74 53.18 - 70.91: 12 70.91 - 88.64: 10 Dihedral angle restraints: 3878 sinusoidal: 1552 harmonic: 2326 Sorted by residual: dihedral pdb=" CA GLU A 145 " pdb=" C GLU A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta harmonic sigma weight residual -180.00 -130.48 -49.52 0 5.00e+00 4.00e-02 9.81e+01 dihedral pdb=" CA VAL A 581 " pdb=" C VAL A 581 " pdb=" N LYS A 582 " pdb=" CA LYS A 582 " ideal model delta harmonic sigma weight residual 180.00 150.16 29.84 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA CYS E 361 " pdb=" C CYS E 361 " pdb=" N VAL E 362 " pdb=" CA VAL E 362 " ideal model delta harmonic sigma weight residual 180.00 151.67 28.33 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 3875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 523 0.036 - 0.072: 311 0.072 - 0.108: 84 0.108 - 0.144: 22 0.144 - 0.180: 4 Chirality restraints: 944 Sorted by residual: chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CA PRO E 337 " pdb=" N PRO E 337 " pdb=" C PRO E 337 " pdb=" CB PRO E 337 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA ILE E 434 " pdb=" N ILE E 434 " pdb=" C ILE E 434 " pdb=" CB ILE E 434 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 941 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO A 146 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 453 " 0.021 2.00e-02 2.50e+03 1.68e-02 5.68e+00 pdb=" CG TYR E 453 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR E 453 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR E 453 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 453 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 453 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 453 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 453 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 388 " -0.039 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A 389 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " -0.031 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 138 2.64 - 3.21: 6520 3.21 - 3.77: 9963 3.77 - 4.34: 13424 4.34 - 4.90: 21531 Nonbonded interactions: 51576 Sorted by model distance: nonbonded pdb=" OH TYR A 41 " pdb=" O THR E 500 " model vdw 2.080 3.040 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.113 3.040 nonbonded pdb=" OH TYR A 535 " pdb=" O SER A 538 " model vdw 2.117 3.040 nonbonded pdb=" O ILE E 418 " pdb=" N ASP E 420 " model vdw 2.122 3.120 nonbonded pdb=" OH TYR A 535 " pdb=" O LYS A 541 " model vdw 2.156 3.040 ... (remaining 51571 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.480 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.008 0.221 6637 Z= 0.439 Angle : 0.889 11.185 9025 Z= 0.523 Chirality : 0.048 0.180 944 Planarity : 0.006 0.069 1167 Dihedral : 15.409 88.637 2379 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.21 % Favored : 86.66 % Rotamer: Outliers : 0.29 % Allowed : 6.83 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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 are not related in a simple way. whole: -4.54 (0.24), residues: 788 helix: -2.30 (0.21), residues: 373 sheet: -3.02 (0.68), residues: 44 loop : -3.82 (0.27), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 454 TYR 0.041 0.002 TYR E 453 PHE 0.028 0.003 PHE A 390 TRP 0.028 0.002 TRP A 302 HIS 0.006 0.002 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00848 / 0.44 ( 6631) covalent geometry : angle 0.88154 / 0.52 ( 9010) SS BOND : bond 0.00350 / 0.17 ( 3) SS BOND : angle 2.12552 / 1.06 ( 6) hydrogen bonds : bond 0.16363 / 10.63 ( 270) hydrogen bonds : angle 7.44417 / 5.37 ( 788) link_NAG-ASN : bond 0.00919 / 0.48 ( 3) link_NAG-ASN : angle 3.36865 / 1.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 HIS cc_start: 0.8167 (p-80) cc_final: 0.7876 (p90) REVERT: A 297 MET cc_start: 0.6037 (ptt) cc_final: 0.5796 (ptp) REVERT: A 454 TYR cc_start: 0.7576 (t80) cc_final: 0.7248 (t80) REVERT: E 346 ARG cc_start: 0.7135 (ttm110) cc_final: 0.5726 (ptt180) REVERT: E 356 LYS cc_start: 0.8944 (tttm) cc_final: 0.8681 (ttmt) REVERT: E 357 ARG cc_start: 0.8591 (ttt90) cc_final: 0.6565 (mtt180) REVERT: E 424 LYS cc_start: 0.8907 (tptp) cc_final: 0.8506 (tttp) REVERT: E 451 TYR cc_start: 0.8043 (m-80) cc_final: 0.7096 (m-80) REVERT: E 462 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8407 (mtpp) REVERT: E 465 GLU cc_start: 0.6059 (tp30) cc_final: 0.5740 (tp30) REVERT: E 466 ARG cc_start: 0.8503 (ttm110) cc_final: 0.8212 (ttm110) REVERT: E 467 ASP cc_start: 0.7996 (t0) cc_final: 0.7492 (t70) REVERT: E 508 TYR cc_start: 0.8344 (m-80) cc_final: 0.7998 (m-80) outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.0970 time to fit residues: 12.3601 Evaluate side-chains 77 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN A 33 ASN A 34 GLN A 134 ASN A 195 ASN A 388 GLN A 522 GLN A 599 ASN E 460 ASN E 487 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.140464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111332 restraints weight = 20491.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115310 restraints weight = 13857.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.115444 restraints weight = 9470.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.116417 restraints weight = 5886.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.117504 restraints weight = 5151.493| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6637 Z= 0.173 Angle : 0.692 8.297 9025 Z= 0.353 Chirality : 0.045 0.221 944 Planarity : 0.006 0.062 1167 Dihedral : 5.869 57.922 869 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.53 % Favored : 90.34 % Rotamer: Outliers : 1.60 % Allowed : 10.90 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -2.99 (0.27), residues: 788 helix: -0.74 (0.25), residues: 370 sheet: -2.80 (0.63), residues: 50 loop : -3.26 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 408 TYR 0.018 0.002 TYR E 453 PHE 0.018 0.002 PHE A 390 TRP 0.023 0.002 TRP A 163 HIS 0.004 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 6631) covalent geometry : angle 0.68570 / 0.35 ( 9010) SS BOND : bond 0.00148 / 0.07 ( 3) SS BOND : angle 1.87731 / 0.94 ( 6) hydrogen bonds : bond 0.05028 / 3.21 ( 270) hydrogen bonds : angle 5.41938 / 3.94 ( 788) link_NAG-ASN : bond 0.00608 / 0.31 ( 3) link_NAG-ASN : angle 2.54700 / 1.35 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8176 (ttp-110) cc_final: 0.7941 (ttp-170) REVERT: A 265 HIS cc_start: 0.8049 (p-80) cc_final: 0.7656 (p90) REVERT: A 383 MET cc_start: 0.8729 (ttt) cc_final: 0.8427 (ttt) REVERT: A 557 MET cc_start: 0.8875 (tmm) cc_final: 0.8638 (tmm) REVERT: E 347 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6200 (m-80) REVERT: E 357 ARG cc_start: 0.8554 (ttt90) cc_final: 0.6488 (mtt180) REVERT: E 424 LYS cc_start: 0.8875 (tptp) cc_final: 0.8452 (tttp) REVERT: E 451 TYR cc_start: 0.8019 (m-80) cc_final: 0.6962 (m-80) REVERT: E 462 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8392 (mtpp) REVERT: E 467 ASP cc_start: 0.7698 (t0) cc_final: 0.7102 (t70) REVERT: E 495 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.8078 (p90) REVERT: E 508 TYR cc_start: 0.8294 (m-80) cc_final: 0.7851 (m-80) outliers start: 10 outliers final: 6 residues processed: 100 average time/residue: 0.0903 time to fit residues: 11.7103 Evaluate side-chains 88 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.140840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.110669 restraints weight = 13392.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111757 restraints weight = 7254.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.112524 restraints weight = 6152.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.112950 restraints weight = 5063.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113525 restraints weight = 4582.317| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6637 Z= 0.181 Angle : 0.685 8.090 9025 Z= 0.346 Chirality : 0.044 0.213 944 Planarity : 0.005 0.059 1167 Dihedral : 5.698 57.190 869 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.15 % Favored : 90.72 % Rotamer: Outliers : 1.60 % Allowed : 13.66 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -2.23 (0.29), residues: 788 helix: -0.11 (0.27), residues: 368 sheet: -2.33 (0.67), residues: 50 loop : -2.87 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 408 TYR 0.018 0.002 TYR E 495 PHE 0.020 0.002 PHE A 390 TRP 0.020 0.001 TRP A 163 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 6631) covalent geometry : angle 0.67899 / 0.34 ( 9010) SS BOND : bond 0.00274 / 0.13 ( 3) SS BOND : angle 1.65248 / 0.83 ( 6) hydrogen bonds : bond 0.04833 / 3.16 ( 270) hydrogen bonds : angle 5.16176 / 3.77 ( 788) link_NAG-ASN : bond 0.00565 / 0.29 ( 3) link_NAG-ASN : angle 2.64215 / 1.40 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.265 Fit side-chains REVERT: A 139 GLN cc_start: 0.6621 (mm-40) cc_final: 0.6359 (pp30) REVERT: A 265 HIS cc_start: 0.7917 (p-80) cc_final: 0.7468 (p90) REVERT: A 267 LEU cc_start: 0.8460 (mt) cc_final: 0.7781 (mt) REVERT: E 347 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: E 356 LYS cc_start: 0.8784 (tttt) cc_final: 0.7756 (mmtt) REVERT: E 357 ARG cc_start: 0.8607 (ttt90) cc_final: 0.6524 (mtt180) REVERT: E 424 LYS cc_start: 0.8750 (tptp) cc_final: 0.8458 (tttp) REVERT: E 451 TYR cc_start: 0.7934 (m-80) cc_final: 0.7028 (m-80) REVERT: E 462 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8417 (mtpp) REVERT: E 467 ASP cc_start: 0.7926 (t0) cc_final: 0.7553 (t0) REVERT: E 495 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.8161 (p90) REVERT: E 508 TYR cc_start: 0.8542 (m-80) cc_final: 0.8210 (m-80) outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 0.0814 time to fit residues: 9.9711 Evaluate side-chains 88 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 41 optimal weight: 0.0070 chunk 77 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.145024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.113979 restraints weight = 14391.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116134 restraints weight = 7573.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.117052 restraints weight = 5902.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.117135 restraints weight = 4896.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.117748 restraints weight = 4418.547| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6637 Z= 0.129 Angle : 0.627 7.247 9025 Z= 0.314 Chirality : 0.042 0.203 944 Planarity : 0.005 0.057 1167 Dihedral : 5.370 56.512 869 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.77 % Favored : 91.11 % Rotamer: Outliers : 2.18 % Allowed : 13.95 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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 are not related in a simple way. whole: -1.66 (0.30), residues: 788 helix: 0.31 (0.27), residues: 371 sheet: -2.03 (0.67), residues: 46 loop : -2.54 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 408 TYR 0.015 0.001 TYR A 385 PHE 0.014 0.002 PHE A 390 TRP 0.020 0.001 TRP A 163 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 6631) covalent geometry : angle 0.62136 / 0.31 ( 9010) SS BOND : bond 0.00207 / 0.11 ( 3) SS BOND : angle 1.85191 / 0.95 ( 6) hydrogen bonds : bond 0.04126 / 2.71 ( 270) hydrogen bonds : angle 4.85504 / 3.55 ( 788) link_NAG-ASN : bond 0.00397 / 0.20 ( 3) link_NAG-ASN : angle 2.20547 / 1.17 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6558 (mm-40) cc_final: 0.6263 (pp30) REVERT: A 265 HIS cc_start: 0.8011 (p-80) cc_final: 0.7653 (p90) REVERT: A 270 MET cc_start: 0.5928 (tpp) cc_final: 0.5256 (tpp) REVERT: A 367 ASP cc_start: 0.7456 (m-30) cc_final: 0.6779 (t0) REVERT: A 383 MET cc_start: 0.8699 (ttt) cc_final: 0.8498 (ttt) REVERT: A 402 GLU cc_start: 0.6974 (tp30) cc_final: 0.5672 (mp0) REVERT: A 518 ARG cc_start: 0.8341 (ptt-90) cc_final: 0.7539 (ttp80) REVERT: A 591 LEU cc_start: 0.8254 (tt) cc_final: 0.7928 (tt) REVERT: E 356 LYS cc_start: 0.8638 (tttt) cc_final: 0.7710 (mmtt) REVERT: E 357 ARG cc_start: 0.8592 (ttt90) cc_final: 0.6424 (mtt180) REVERT: E 424 LYS cc_start: 0.8730 (tptp) cc_final: 0.8350 (tttm) REVERT: E 451 TYR cc_start: 0.7803 (m-80) cc_final: 0.6878 (m-80) REVERT: E 462 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8311 (mtpp) REVERT: E 495 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.8113 (p90) REVERT: E 508 TYR cc_start: 0.8451 (m-80) cc_final: 0.8154 (m-80) REVERT: E 516 GLU cc_start: 0.6855 (pm20) cc_final: 0.6541 (pm20) outliers start: 14 outliers final: 9 residues processed: 115 average time/residue: 0.0833 time to fit residues: 12.6393 Evaluate side-chains 97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 0.0040 chunk 72 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.147143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.116689 restraints weight = 13739.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.119042 restraints weight = 7402.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.120050 restraints weight = 5708.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.120127 restraints weight = 4539.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.120297 restraints weight = 4560.720| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6637 Z= 0.125 Angle : 0.637 7.072 9025 Z= 0.317 Chirality : 0.042 0.195 944 Planarity : 0.005 0.055 1167 Dihedral : 5.172 55.703 869 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.26 % Favored : 91.61 % Rotamer: Outliers : 2.18 % Allowed : 15.41 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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 are not related in a simple way. whole: -1.38 (0.30), residues: 788 helix: 0.42 (0.27), residues: 380 sheet: -1.71 (0.69), residues: 46 loop : -2.34 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 466 TYR 0.019 0.001 TYR A 587 PHE 0.013 0.001 PHE A 525 TRP 0.018 0.001 TRP A 163 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 6631) covalent geometry : angle 0.63274 / 0.32 ( 9010) SS BOND : bond 0.00099 / 0.05 ( 3) SS BOND : angle 1.67829 / 0.86 ( 6) hydrogen bonds : bond 0.03926 / 2.58 ( 270) hydrogen bonds : angle 4.78498 / 3.52 ( 788) link_NAG-ASN : bond 0.00373 / 0.19 ( 3) link_NAG-ASN : angle 2.07850 / 1.10 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6560 (mm-40) cc_final: 0.6350 (pp30) REVERT: A 267 LEU cc_start: 0.8223 (mt) cc_final: 0.7597 (mt) REVERT: A 367 ASP cc_start: 0.7511 (m-30) cc_final: 0.7064 (t0) REVERT: A 383 MET cc_start: 0.8688 (ttt) cc_final: 0.8475 (ttt) REVERT: A 401 HIS cc_start: 0.7671 (OUTLIER) cc_final: 0.6739 (m-70) REVERT: A 402 GLU cc_start: 0.7053 (tp30) cc_final: 0.6592 (mp0) REVERT: A 480 MET cc_start: 0.7968 (mtp) cc_final: 0.7554 (mtm) REVERT: A 591 LEU cc_start: 0.8236 (tt) cc_final: 0.7892 (tt) REVERT: E 347 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.6086 (m-80) REVERT: E 356 LYS cc_start: 0.8576 (tttt) cc_final: 0.7760 (mmtt) REVERT: E 357 ARG cc_start: 0.8564 (ttt90) cc_final: 0.6364 (mtt180) REVERT: E 451 TYR cc_start: 0.7826 (m-80) cc_final: 0.6908 (m-80) REVERT: E 462 LYS cc_start: 0.8474 (mtpt) cc_final: 0.8207 (mtpp) REVERT: E 495 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.8110 (p90) REVERT: E 508 TYR cc_start: 0.8383 (m-80) cc_final: 0.8049 (m-80) REVERT: E 515 PHE cc_start: 0.6941 (m-80) cc_final: 0.6741 (m-80) outliers start: 14 outliers final: 7 residues processed: 109 average time/residue: 0.0897 time to fit residues: 12.8368 Evaluate side-chains 96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.143742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.114154 restraints weight = 11239.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.114211 restraints weight = 6762.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115786 restraints weight = 5593.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115730 restraints weight = 4616.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.115827 restraints weight = 4289.725| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6637 Z= 0.168 Angle : 0.663 7.674 9025 Z= 0.329 Chirality : 0.043 0.200 944 Planarity : 0.005 0.054 1167 Dihedral : 5.241 56.115 869 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.64 % Favored : 91.23 % Rotamer: Outliers : 2.47 % Allowed : 16.42 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -1.34 (0.30), residues: 788 helix: 0.41 (0.27), residues: 377 sheet: -1.42 (0.72), residues: 46 loop : -2.27 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 466 TYR 0.020 0.002 TYR A 50 PHE 0.018 0.002 PHE A 390 TRP 0.016 0.001 TRP A 163 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 6631) covalent geometry : angle 0.65813 / 0.33 ( 9010) SS BOND : bond 0.00108 / 0.05 ( 3) SS BOND : angle 1.76816 / 0.90 ( 6) hydrogen bonds : bond 0.04244 / 2.81 ( 270) hydrogen bonds : angle 4.81652 / 3.55 ( 788) link_NAG-ASN : bond 0.00477 / 0.24 ( 3) link_NAG-ASN : angle 2.25405 / 1.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6611 (mm-40) cc_final: 0.6370 (pp30) REVERT: A 148 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7278 (mt) REVERT: A 249 MET cc_start: 0.7792 (tpp) cc_final: 0.7489 (tpp) REVERT: A 267 LEU cc_start: 0.8283 (mt) cc_final: 0.7647 (mt) REVERT: A 367 ASP cc_start: 0.7491 (m-30) cc_final: 0.7078 (t0) REVERT: A 402 GLU cc_start: 0.6825 (tp30) cc_final: 0.6556 (mp0) REVERT: A 480 MET cc_start: 0.7995 (mtp) cc_final: 0.7594 (mtm) REVERT: A 557 MET cc_start: 0.8773 (tmm) cc_final: 0.8536 (tmm) REVERT: E 347 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6201 (m-80) REVERT: E 356 LYS cc_start: 0.8592 (tttt) cc_final: 0.7667 (mmtt) REVERT: E 357 ARG cc_start: 0.8589 (ttt90) cc_final: 0.6518 (mtt180) REVERT: E 451 TYR cc_start: 0.7895 (m-80) cc_final: 0.7031 (m-80) REVERT: E 462 LYS cc_start: 0.8585 (mtpt) cc_final: 0.8312 (mtpp) REVERT: E 495 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8230 (p90) REVERT: E 508 TYR cc_start: 0.8416 (m-80) cc_final: 0.8068 (m-80) REVERT: E 516 GLU cc_start: 0.6948 (pm20) cc_final: 0.6589 (pm20) outliers start: 16 outliers final: 10 residues processed: 100 average time/residue: 0.0815 time to fit residues: 10.6158 Evaluate side-chains 94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.2609 > 50: distance: 50 - 54: 34.840 distance: 54 - 55: 49.146 distance: 55 - 56: 22.636 distance: 55 - 58: 15.054 distance: 56 - 57: 40.225 distance: 56 - 62: 51.419 distance: 58 - 59: 41.225 distance: 58 - 60: 29.004 distance: 59 - 61: 5.201 distance: 62 - 63: 28.043 distance: 62 - 68: 4.637 distance: 63 - 64: 18.218 distance: 63 - 66: 18.625 distance: 64 - 65: 57.081 distance: 64 - 69: 18.439 distance: 66 - 67: 39.045 distance: 67 - 68: 54.164 distance: 69 - 70: 16.919 distance: 70 - 71: 19.200 distance: 70 - 73: 31.080 distance: 71 - 72: 17.496 distance: 71 - 78: 28.602 distance: 73 - 74: 12.590 distance: 74 - 75: 8.342 distance: 75 - 76: 34.144 distance: 76 - 77: 40.138 distance: 78 - 79: 18.062 distance: 79 - 80: 19.116 distance: 80 - 81: 8.653 distance: 80 - 87: 40.259 distance: 82 - 83: 30.693 distance: 83 - 84: 8.287 distance: 84 - 85: 29.803 distance: 84 - 86: 17.804 distance: 87 - 88: 39.417 distance: 88 - 89: 41.084 distance: 88 - 91: 25.136 distance: 89 - 96: 40.252 distance: 91 - 92: 33.495 distance: 92 - 93: 32.407 distance: 93 - 94: 8.563 distance: 93 - 95: 12.181 distance: 96 - 97: 23.630 distance: 97 - 98: 24.807 distance: 97 - 100: 6.824 distance: 98 - 99: 3.905 distance: 98 - 110: 8.043 distance: 99 - 136: 33.290 distance: 100 - 101: 20.147 distance: 101 - 102: 26.677 distance: 101 - 103: 21.453 distance: 102 - 104: 18.896 distance: 103 - 105: 39.696 distance: 103 - 106: 11.937 distance: 104 - 105: 22.362 distance: 105 - 107: 10.119 distance: 106 - 108: 24.795 distance: 107 - 109: 33.002 distance: 108 - 109: 13.778 distance: 111 - 112: 26.868 distance: 111 - 114: 37.139 distance: 112 - 113: 27.483 distance: 112 - 118: 21.562 distance: 113 - 150: 28.870 distance: 114 - 115: 40.244 distance: 115 - 116: 10.253 distance: 116 - 117: 37.493 distance: 118 - 119: 5.573 distance: 119 - 120: 11.747 distance: 119 - 122: 21.963 distance: 120 - 121: 22.706 distance: 120 - 127: 30.659 distance: 121 - 164: 18.789 distance: 122 - 123: 34.281 distance: 123 - 124: 14.552 distance: 124 - 125: 23.958 distance: 125 - 126: 24.041 distance: 127 - 128: 9.218 distance: 128 - 129: 11.666 distance: 128 - 131: 18.990 distance: 129 - 130: 14.511 distance: 129 - 136: 16.169 distance: 130 - 173: 29.330 distance: 131 - 132: 10.404 distance: 132 - 133: 16.409 distance: 133 - 134: 10.423 distance: 134 - 135: 22.242 distance: 136 - 137: 24.726 distance: 137 - 138: 4.979 distance: 137 - 140: 17.015 distance: 138 - 139: 10.355 distance: 138 - 150: 16.799 distance: 139 - 179: 17.781 distance: 140 - 141: 6.521 distance: 141 - 142: 9.592 distance: 141 - 143: 16.966 distance: 142 - 144: 16.833 distance: 143 - 145: 23.076 distance: 143 - 146: 14.196 distance: 144 - 145: 11.374 distance: 145 - 147: 13.886 distance: 146 - 148: 28.576 distance: 147 - 149: 22.122 distance: 148 - 149: 3.419