Starting phenix.real_space_refine on Sun Aug 24 08:47:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oeg_20020/08_2025/6oeg_20020_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oeg_20020/08_2025/6oeg_20020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6oeg_20020/08_2025/6oeg_20020_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oeg_20020/08_2025/6oeg_20020_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oeg_20020/08_2025/6oeg_20020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oeg_20020/08_2025/6oeg_20020.map" } resolution = 3.8 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 70 5.16 5 C 11872 2.51 5 N 3206 2.21 5 O 3416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 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: 18564 Number of models: 1 Model: "" Number of chains: 1 Chain: "N" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Restraints were copied for chains: O, P, Q, R, S, T, U, V, W, X, Y, Z, a Time building chain proxies: 1.67, per 1000 atoms: 0.09 Number of scatterers: 18564 At special positions: 0 Unit cell: (188.6, 188.6, 123, 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 70 16.00 O 3416 8.00 N 3206 7.00 C 11872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 677.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4340 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 28 sheets defined 27.2% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'N' and resid 351 through 356 Processing helix chain 'N' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE N 363 " --> pdb=" O ASN N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 460 through 464 removed outlier: 3.504A pdb=" N GLY N 463 " --> pdb=" O THR N 460 " (cutoff:3.500A) Processing helix chain 'O' and resid 351 through 356 Processing helix chain 'O' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE O 363 " --> pdb=" O ASN O 359 " (cutoff:3.500A) Processing helix chain 'O' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY O 463 " --> pdb=" O THR O 460 " (cutoff:3.500A) Processing helix chain 'P' and resid 351 through 356 Processing helix chain 'P' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE P 363 " --> pdb=" O ASN P 359 " (cutoff:3.500A) Processing helix chain 'P' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY P 463 " --> pdb=" O THR P 460 " (cutoff:3.500A) Processing helix chain 'Q' and resid 351 through 356 Processing helix chain 'Q' and resid 359 through 391 removed outlier: 3.870A pdb=" N ILE Q 363 " --> pdb=" O ASN Q 359 " (cutoff:3.500A) Processing helix chain 'Q' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY Q 463 " --> pdb=" O THR Q 460 " (cutoff:3.500A) Processing helix chain 'R' and resid 351 through 356 Processing helix chain 'R' and resid 359 through 391 removed outlier: 3.870A pdb=" N ILE R 363 " --> pdb=" O ASN R 359 " (cutoff:3.500A) Processing helix chain 'R' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY R 463 " --> pdb=" O THR R 460 " (cutoff:3.500A) Processing helix chain 'S' and resid 351 through 356 Processing helix chain 'S' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE S 363 " --> pdb=" O ASN S 359 " (cutoff:3.500A) Processing helix chain 'S' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY S 463 " --> pdb=" O THR S 460 " (cutoff:3.500A) Processing helix chain 'T' and resid 351 through 356 Processing helix chain 'T' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE T 363 " --> pdb=" O ASN T 359 " (cutoff:3.500A) Processing helix chain 'T' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY T 463 " --> pdb=" O THR T 460 " (cutoff:3.500A) Processing helix chain 'U' and resid 351 through 356 Processing helix chain 'U' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE U 363 " --> pdb=" O ASN U 359 " (cutoff:3.500A) Processing helix chain 'U' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY U 463 " --> pdb=" O THR U 460 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 356 Processing helix chain 'V' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE V 363 " --> pdb=" O ASN V 359 " (cutoff:3.500A) Processing helix chain 'V' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY V 463 " --> pdb=" O THR V 460 " (cutoff:3.500A) Processing helix chain 'W' and resid 351 through 356 Processing helix chain 'W' and resid 359 through 391 removed outlier: 3.870A pdb=" N ILE W 363 " --> pdb=" O ASN W 359 " (cutoff:3.500A) Processing helix chain 'W' and resid 460 through 464 removed outlier: 3.504A pdb=" N GLY W 463 " --> pdb=" O THR W 460 " (cutoff:3.500A) Processing helix chain 'X' and resid 351 through 356 Processing helix chain 'X' and resid 359 through 391 removed outlier: 3.870A pdb=" N ILE X 363 " --> pdb=" O ASN X 359 " (cutoff:3.500A) Processing helix chain 'X' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY X 463 " --> pdb=" O THR X 460 " (cutoff:3.500A) Processing helix chain 'Y' and resid 351 through 356 Processing helix chain 'Y' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE Y 363 " --> pdb=" O ASN Y 359 " (cutoff:3.500A) Processing helix chain 'Y' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY Y 463 " --> pdb=" O THR Y 460 " (cutoff:3.500A) Processing helix chain 'Z' and resid 351 through 356 Processing helix chain 'Z' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE Z 363 " --> pdb=" O ASN Z 359 " (cutoff:3.500A) Processing helix chain 'Z' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY Z 463 " --> pdb=" O THR Z 460 " (cutoff:3.500A) Processing helix chain 'a' and resid 351 through 356 Processing helix chain 'a' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE a 363 " --> pdb=" O ASN a 359 " (cutoff:3.500A) Processing helix chain 'a' and resid 460 through 464 removed outlier: 3.504A pdb=" N GLY a 463 " --> pdb=" O THR a 460 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS N 475 " --> pdb=" O VAL N 442 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 420 through 421 Processing sheet with id=AA3, first strand: chain 'O' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS O 475 " --> pdb=" O VAL O 442 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 420 through 421 Processing sheet with id=AA5, first strand: chain 'P' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS P 475 " --> pdb=" O VAL P 442 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 420 through 421 Processing sheet with id=AA7, first strand: chain 'Q' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS Q 475 " --> pdb=" O VAL Q 442 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 420 through 421 Processing sheet with id=AA9, first strand: chain 'R' and resid 403 through 407 removed outlier: 5.188A pdb=" N LYS R 475 " --> pdb=" O VAL R 442 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 420 through 421 Processing sheet with id=AB2, first strand: chain 'S' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS S 475 " --> pdb=" O VAL S 442 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 420 through 421 Processing sheet with id=AB4, first strand: chain 'T' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS T 475 " --> pdb=" O VAL T 442 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 420 through 421 Processing sheet with id=AB6, first strand: chain 'U' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS U 475 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 420 through 421 Processing sheet with id=AB8, first strand: chain 'V' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS V 475 " --> pdb=" O VAL V 442 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'V' and resid 420 through 421 Processing sheet with id=AC1, first strand: chain 'W' and resid 403 through 407 removed outlier: 5.188A pdb=" N LYS W 475 " --> pdb=" O VAL W 442 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'W' and resid 420 through 421 Processing sheet with id=AC3, first strand: chain 'X' and resid 403 through 407 removed outlier: 5.188A pdb=" N LYS X 475 " --> pdb=" O VAL X 442 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 420 through 421 Processing sheet with id=AC5, first strand: chain 'Y' and resid 403 through 407 removed outlier: 5.188A pdb=" N LYS Y 475 " --> pdb=" O VAL Y 442 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Y' and resid 420 through 421 Processing sheet with id=AC7, first strand: chain 'Z' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS Z 475 " --> pdb=" O VAL Z 442 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Z' and resid 420 through 421 Processing sheet with id=AC9, first strand: chain 'a' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS a 475 " --> pdb=" O VAL a 442 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'a' and resid 420 through 421 784 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.86 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: 5739 1.34 - 1.45: 3274 1.45 - 1.57: 9775 1.57 - 1.69: 14 1.69 - 1.81: 140 Bond restraints: 18942 Sorted by residual: bond pdb=" CB GLU X 418 " pdb=" CG GLU X 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.30e+00 bond pdb=" CB GLU W 418 " pdb=" CG GLU W 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.25e+00 bond pdb=" CB GLU Y 418 " pdb=" CG GLU Y 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.23e+00 bond pdb=" CB GLU R 418 " pdb=" CG GLU R 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.21e+00 bond pdb=" CB GLU a 418 " pdb=" CG GLU a 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.18e+00 ... (remaining 18937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 24528 2.42 - 4.84: 835 4.84 - 7.26: 131 7.26 - 9.68: 14 9.68 - 12.10: 28 Bond angle restraints: 25536 Sorted by residual: angle pdb=" CB GLU P 418 " pdb=" CG GLU P 418 " pdb=" CD GLU P 418 " ideal model delta sigma weight residual 112.60 123.51 -10.91 1.70e+00 3.46e-01 4.12e+01 angle pdb=" CB GLU Q 418 " pdb=" CG GLU Q 418 " pdb=" CD GLU Q 418 " ideal model delta sigma weight residual 112.60 123.51 -10.91 1.70e+00 3.46e-01 4.12e+01 angle pdb=" CB GLU a 418 " pdb=" CG GLU a 418 " pdb=" CD GLU a 418 " ideal model delta sigma weight residual 112.60 123.50 -10.90 1.70e+00 3.46e-01 4.11e+01 angle pdb=" CB GLU S 418 " pdb=" CG GLU S 418 " pdb=" CD GLU S 418 " ideal model delta sigma weight residual 112.60 123.49 -10.89 1.70e+00 3.46e-01 4.11e+01 angle pdb=" CB GLU T 418 " pdb=" CG GLU T 418 " pdb=" CD GLU T 418 " ideal model delta sigma weight residual 112.60 123.49 -10.89 1.70e+00 3.46e-01 4.10e+01 ... (remaining 25531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 10766 17.54 - 35.07: 672 35.07 - 52.61: 224 52.61 - 70.15: 28 70.15 - 87.68: 14 Dihedral angle restraints: 11704 sinusoidal: 4970 harmonic: 6734 Sorted by residual: dihedral pdb=" CA ILE V 479 " pdb=" C ILE V 479 " pdb=" N LYS V 480 " pdb=" CA LYS V 480 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ILE T 479 " pdb=" C ILE T 479 " pdb=" N LYS T 480 " pdb=" CA LYS T 480 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ILE R 479 " pdb=" C ILE R 479 " pdb=" N LYS R 480 " pdb=" CA LYS R 480 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 11701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1640 0.050 - 0.100: 827 0.100 - 0.150: 249 0.150 - 0.200: 14 0.200 - 0.250: 14 Chirality restraints: 2744 Sorted by residual: chirality pdb=" CB ILE Q 503 " pdb=" CA ILE Q 503 " pdb=" CG1 ILE Q 503 " pdb=" CG2 ILE Q 503 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE W 503 " pdb=" CA ILE W 503 " pdb=" CG1 ILE W 503 " pdb=" CG2 ILE W 503 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE T 503 " pdb=" CA ILE T 503 " pdb=" CG1 ILE T 503 " pdb=" CG2 ILE T 503 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2741 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE P 376 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C ILE P 376 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE P 376 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU P 377 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE V 376 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C ILE V 376 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE V 376 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU V 377 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE Y 376 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C ILE Y 376 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE Y 376 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU Y 377 " 0.012 2.00e-02 2.50e+03 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 6587 2.88 - 3.38: 17093 3.38 - 3.89: 29490 3.89 - 4.39: 31340 4.39 - 4.90: 53217 Nonbonded interactions: 137727 Sorted by model distance: nonbonded pdb=" O MET T 355 " pdb=" OG SER T 358 " model vdw 2.370 3.040 nonbonded pdb=" O MET Y 355 " pdb=" OG SER Y 358 " model vdw 2.370 3.040 nonbonded pdb=" O MET S 355 " pdb=" OG SER S 358 " model vdw 2.370 3.040 nonbonded pdb=" O MET U 355 " pdb=" OG SER U 358 " model vdw 2.370 3.040 nonbonded pdb=" O MET a 355 " pdb=" OG SER a 358 " model vdw 2.370 3.040 ... (remaining 137722 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: 0.07 Found NCS groups: ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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: 9.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.670 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 0.075 18942 Z= 0.354 Angle : 1.117 12.097 25536 Z= 0.623 Chirality : 0.061 0.250 2744 Planarity : 0.008 0.052 3304 Dihedral : 13.456 87.684 7364 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 5.56 % Allowed : 4.17 % Favored : 90.28 % 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: -4.92 (0.12), residues: 2240 helix: -2.82 (0.17), residues: 560 sheet: -2.75 (0.17), residues: 434 loop : -3.81 (0.12), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 399 TYR 0.018 0.003 TYR R 467 PHE 0.022 0.004 PHE X 420 TRP 0.015 0.004 TRP U 466 HIS 0.002 0.001 HIS P 389 Details of bonding type rmsd covalent geometry : bond 0.00772 (18942) covalent geometry : angle 1.11676 (25536) hydrogen bonds : bond 0.11041 ( 784) hydrogen bonds : angle 6.73162 ( 2142) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 841 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 373 GLN cc_start: 0.8631 (tp40) cc_final: 0.8379 (tp40) REVERT: N 379 GLN cc_start: 0.8787 (tt0) cc_final: 0.8450 (tm-30) REVERT: N 384 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: N 404 TYR cc_start: 0.8339 (m-10) cc_final: 0.4589 (t80) REVERT: N 405 GLN cc_start: 0.8704 (pt0) cc_final: 0.8190 (pt0) REVERT: N 415 MET cc_start: 0.8081 (ttm) cc_final: 0.7830 (ttm) REVERT: N 449 SER cc_start: 0.8969 (t) cc_final: 0.8694 (p) REVERT: N 450 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.6226 (ptp) REVERT: O 379 GLN cc_start: 0.8903 (tt0) cc_final: 0.8442 (tm-30) REVERT: O 404 TYR cc_start: 0.8148 (m-10) cc_final: 0.5684 (t80) REVERT: O 405 GLN cc_start: 0.8791 (pt0) cc_final: 0.8442 (pt0) REVERT: O 415 MET cc_start: 0.7742 (ttm) cc_final: 0.7415 (ttm) REVERT: O 450 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.6721 (ptp) REVERT: P 364 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8477 (t0) REVERT: P 367 LYS cc_start: 0.8501 (ptmt) cc_final: 0.8267 (pttm) REVERT: P 379 GLN cc_start: 0.8753 (tt0) cc_final: 0.7994 (tm-30) REVERT: P 387 TYR cc_start: 0.8924 (t80) cc_final: 0.8713 (t80) REVERT: P 404 TYR cc_start: 0.8104 (m-10) cc_final: 0.5385 (t80) REVERT: P 415 MET cc_start: 0.7759 (ttm) cc_final: 0.7540 (ttm) REVERT: P 450 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6715 (ttt) REVERT: P 456 ASP cc_start: 0.8783 (t0) cc_final: 0.8511 (t0) REVERT: P 464 LEU cc_start: 0.9307 (mp) cc_final: 0.9013 (mm) REVERT: Q 383 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7566 (mt) REVERT: Q 404 TYR cc_start: 0.8737 (m-10) cc_final: 0.5699 (t80) REVERT: Q 421 ASP cc_start: 0.8568 (p0) cc_final: 0.8155 (p0) REVERT: Q 427 TYR cc_start: 0.8761 (m-80) cc_final: 0.8455 (m-80) REVERT: Q 452 ASP cc_start: 0.7911 (p0) cc_final: 0.7663 (p0) REVERT: R 481 ASP cc_start: 0.7718 (p0) cc_final: 0.7492 (p0) REVERT: S 383 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7176 (mt) REVERT: S 384 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: S 404 TYR cc_start: 0.8072 (m-10) cc_final: 0.5835 (t80) REVERT: S 422 ASP cc_start: 0.8663 (p0) cc_final: 0.8398 (p0) REVERT: S 450 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7053 (ptp) REVERT: S 452 ASP cc_start: 0.8033 (p0) cc_final: 0.7795 (p0) REVERT: S 478 LEU cc_start: 0.9318 (mp) cc_final: 0.9082 (mp) REVERT: T 364 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7924 (t0) REVERT: T 379 GLN cc_start: 0.8477 (tt0) cc_final: 0.7663 (tm-30) REVERT: T 404 TYR cc_start: 0.7904 (m-10) cc_final: 0.5477 (t80) REVERT: T 405 GLN cc_start: 0.8588 (pt0) cc_final: 0.8064 (pt0) REVERT: T 456 ASP cc_start: 0.8828 (t0) cc_final: 0.8407 (t0) REVERT: U 367 LYS cc_start: 0.8713 (ptmt) cc_final: 0.8473 (pttm) REVERT: U 379 GLN cc_start: 0.9016 (tt0) cc_final: 0.8175 (tm-30) REVERT: U 404 TYR cc_start: 0.8317 (m-10) cc_final: 0.4864 (t80) REVERT: U 414 ILE cc_start: 0.9539 (tp) cc_final: 0.9337 (tt) REVERT: U 415 MET cc_start: 0.8070 (ttm) cc_final: 0.7854 (ttm) REVERT: U 434 THR cc_start: 0.8577 (t) cc_final: 0.8370 (t) REVERT: U 449 SER cc_start: 0.9326 (t) cc_final: 0.9046 (m) REVERT: U 450 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.6711 (ptp) REVERT: V 366 GLU cc_start: 0.8517 (pp20) cc_final: 0.8298 (tm-30) REVERT: V 408 GLU cc_start: 0.6183 (mm-30) cc_final: 0.5901 (mm-30) REVERT: V 411 SER cc_start: 0.9173 (m) cc_final: 0.8943 (m) REVERT: V 450 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.6105 (ptp) REVERT: W 379 GLN cc_start: 0.8973 (tt0) cc_final: 0.8207 (tm-30) REVERT: W 417 SER cc_start: 0.9016 (t) cc_final: 0.8815 (t) REVERT: W 450 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.6810 (ptp) REVERT: X 384 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: X 404 TYR cc_start: 0.8106 (m-10) cc_final: 0.5678 (t80) REVERT: X 414 ILE cc_start: 0.9140 (tp) cc_final: 0.8921 (tp) REVERT: X 421 ASP cc_start: 0.8751 (p0) cc_final: 0.8300 (p0) REVERT: X 427 TYR cc_start: 0.8788 (m-80) cc_final: 0.8500 (m-80) REVERT: X 450 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.5807 (ptp) REVERT: X 501 TYR cc_start: 0.7631 (t80) cc_final: 0.7379 (t80) REVERT: Y 364 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8192 (t0) REVERT: Y 372 LYS cc_start: 0.9185 (pptt) cc_final: 0.8913 (mmmt) REVERT: Y 377 LEU cc_start: 0.8759 (tp) cc_final: 0.8549 (tp) REVERT: Y 379 GLN cc_start: 0.8839 (tt0) cc_final: 0.8475 (tm-30) REVERT: Y 384 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: Y 387 TYR cc_start: 0.8999 (t80) cc_final: 0.8746 (t80) REVERT: Y 404 TYR cc_start: 0.8002 (m-10) cc_final: 0.5194 (t80) REVERT: Y 415 MET cc_start: 0.7784 (ttm) cc_final: 0.7512 (ttm) REVERT: Y 421 ASP cc_start: 0.8712 (p0) cc_final: 0.8351 (p0) REVERT: Y 456 ASP cc_start: 0.8886 (t0) cc_final: 0.8683 (t0) REVERT: Z 367 LYS cc_start: 0.8653 (ptmt) cc_final: 0.8203 (pttm) REVERT: Z 372 LYS cc_start: 0.8987 (pptt) cc_final: 0.8621 (mtpt) REVERT: Z 379 GLN cc_start: 0.8790 (tt0) cc_final: 0.8401 (tm-30) REVERT: Z 404 TYR cc_start: 0.8258 (m-10) cc_final: 0.5767 (t80) REVERT: Z 405 GLN cc_start: 0.8755 (pt0) cc_final: 0.8456 (pt0) REVERT: Z 415 MET cc_start: 0.7918 (ttm) cc_final: 0.7684 (ttm) REVERT: Z 432 ASN cc_start: 0.9259 (p0) cc_final: 0.9020 (p0) REVERT: Z 450 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.6712 (ptp) REVERT: Z 456 ASP cc_start: 0.8909 (t0) cc_final: 0.8624 (t0) REVERT: a 371 GLU cc_start: 0.8587 (tp30) cc_final: 0.8357 (tp30) REVERT: a 381 LYS cc_start: 0.8701 (tppt) cc_final: 0.8438 (ttmm) REVERT: a 421 ASP cc_start: 0.8677 (p0) cc_final: 0.8359 (p0) REVERT: a 432 ASN cc_start: 0.9075 (p0) cc_final: 0.8872 (p0) REVERT: a 449 SER cc_start: 0.9223 (t) cc_final: 0.8662 (m) REVERT: a 450 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6481 (ptp) outliers start: 112 outliers final: 30 residues processed: 856 average time/residue: 0.1274 time to fit residues: 161.4311 Evaluate side-chains 684 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 635 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain N residue 384 GLU Chi-restraints excluded: chain N residue 450 MET Chi-restraints excluded: chain N residue 509 LEU Chi-restraints excluded: chain O residue 383 LEU Chi-restraints excluded: chain O residue 384 GLU Chi-restraints excluded: chain O residue 450 MET Chi-restraints excluded: chain O residue 509 LEU Chi-restraints excluded: chain P residue 364 ASN Chi-restraints excluded: chain P residue 384 GLU Chi-restraints excluded: chain P residue 418 GLU Chi-restraints excluded: chain P residue 450 MET Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain Q residue 383 LEU Chi-restraints excluded: chain Q residue 384 GLU Chi-restraints excluded: chain Q residue 509 LEU Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain S residue 383 LEU Chi-restraints excluded: chain S residue 384 GLU Chi-restraints excluded: chain S residue 450 MET Chi-restraints excluded: chain S residue 509 LEU Chi-restraints excluded: chain T residue 364 ASN Chi-restraints excluded: chain T residue 383 LEU Chi-restraints excluded: chain T residue 384 GLU Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 450 MET Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain V residue 418 GLU Chi-restraints excluded: chain V residue 450 MET Chi-restraints excluded: chain V residue 509 LEU Chi-restraints excluded: chain W residue 383 LEU Chi-restraints excluded: chain W residue 418 GLU Chi-restraints excluded: chain W residue 450 MET Chi-restraints excluded: chain W residue 509 LEU Chi-restraints excluded: chain X residue 384 GLU Chi-restraints excluded: chain X residue 418 GLU Chi-restraints excluded: chain X residue 450 MET Chi-restraints excluded: chain X residue 509 LEU Chi-restraints excluded: chain Y residue 364 ASN Chi-restraints excluded: chain Y residue 384 GLU Chi-restraints excluded: chain Y residue 418 GLU Chi-restraints excluded: chain Y residue 509 LEU Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 450 MET Chi-restraints excluded: chain Z residue 509 LEU Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 450 MET Chi-restraints excluded: chain a residue 509 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 52.789 > 50: distance: 14 - 50: 31.361 distance: 17 - 47: 8.073 distance: 34 - 39: 5.615 distance: 39 - 40: 15.255 distance: 40 - 41: 12.808 distance: 40 - 43: 18.622 distance: 41 - 42: 28.808 distance: 41 - 47: 18.759 distance: 43 - 44: 5.623 distance: 44 - 45: 35.824 distance: 44 - 46: 11.921 distance: 47 - 48: 19.151 distance: 48 - 49: 15.214 distance: 48 - 51: 26.433 distance: 49 - 50: 18.707 distance: 49 - 53: 10.615 distance: 51 - 52: 24.462 distance: 53 - 54: 6.918 distance: 54 - 55: 7.814 distance: 54 - 57: 14.525 distance: 55 - 56: 6.550 distance: 55 - 61: 7.912 distance: 57 - 58: 35.256 distance: 58 - 59: 43.458 distance: 59 - 60: 23.495 distance: 61 - 62: 14.073 distance: 62 - 63: 12.352 distance: 62 - 65: 7.962 distance: 63 - 64: 16.032 distance: 63 - 68: 8.474 distance: 65 - 66: 18.908 distance: 65 - 67: 7.365 distance: 68 - 69: 9.048 distance: 69 - 70: 16.993 distance: 69 - 72: 12.172 distance: 70 - 71: 21.959 distance: 70 - 76: 12.337 distance: 72 - 73: 20.844 distance: 73 - 74: 5.171 distance: 73 - 75: 15.671 distance: 76 - 77: 3.308 distance: 77 - 78: 7.017 distance: 77 - 80: 26.230 distance: 78 - 79: 10.860 distance: 78 - 81: 9.843 distance: 81 - 82: 10.767 distance: 81 - 148: 20.169 distance: 82 - 83: 15.323 distance: 82 - 85: 15.349 distance: 83 - 84: 23.841 distance: 83 - 86: 18.446 distance: 84 - 145: 27.761 distance: 86 - 87: 17.946 distance: 87 - 88: 10.592 distance: 87 - 90: 17.046 distance: 88 - 89: 36.608 distance: 88 - 94: 10.587 distance: 90 - 91: 19.124 distance: 90 - 92: 35.628 distance: 91 - 93: 23.722 distance: 94 - 95: 3.489 distance: 95 - 96: 11.047 distance: 95 - 98: 12.164 distance: 96 - 97: 14.078 distance: 96 - 102: 19.154 distance: 98 - 99: 11.748 distance: 99 - 100: 7.518 distance: 99 - 101: 20.849 distance: 102 - 103: 25.875 distance: 102 - 108: 20.031 distance: 103 - 104: 17.112 distance: 103 - 106: 18.855 distance: 104 - 105: 11.948 distance: 104 - 109: 6.386 distance: 106 - 107: 36.465 distance: 107 - 108: 29.244