Starting phenix.real_space_refine on Fri Aug 22 15:39:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dcq_30639/08_2025/7dcq_30639.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dcq_30639/08_2025/7dcq_30639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dcq_30639/08_2025/7dcq_30639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dcq_30639/08_2025/7dcq_30639.map" model { file = "/net/cci-nas-00/data/ceres_data/7dcq_30639/08_2025/7dcq_30639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dcq_30639/08_2025/7dcq_30639.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 3316 2.51 5 N 892 2.21 5 O 956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 5197 Number of models: 1 Model: "" Number of chains: 1 Chain: "x" Number of atoms: 5197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5197 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 619} Time building chain proxies: 1.42, per 1000 atoms: 0.27 Number of scatterers: 5197 At special positions: 0 Unit cell: (80.1625, 88.1125, 81.4875, 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 33 16.00 O 956 8.00 N 892 7.00 C 3316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 195.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1236 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 5 sheets defined 51.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'x' and resid 225 through 227 No H-bonds generated for 'chain 'x' and resid 225 through 227' Processing helix chain 'x' and resid 228 through 239 removed outlier: 3.501A pdb=" N LYS x 238 " --> pdb=" O GLN x 234 " (cutoff:3.500A) Processing helix chain 'x' and resid 251 through 263 removed outlier: 3.500A pdb=" N LEU x 256 " --> pdb=" O LYS x 252 " (cutoff:3.500A) Proline residue: x 257 - end of helix Processing helix chain 'x' and resid 279 through 295 removed outlier: 3.558A pdb=" N ALA x 287 " --> pdb=" O ALA x 283 " (cutoff:3.500A) Processing helix chain 'x' and resid 324 through 329 removed outlier: 3.643A pdb=" N LEU x 328 " --> pdb=" O ASP x 324 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG x 329 " --> pdb=" O GLY x 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 324 through 329' Processing helix chain 'x' and resid 329 through 334 removed outlier: 4.076A pdb=" N THR x 333 " --> pdb=" O ARG x 329 " (cutoff:3.500A) Processing helix chain 'x' and resid 347 through 351 Processing helix chain 'x' and resid 352 through 369 removed outlier: 3.693A pdb=" N ASP x 364 " --> pdb=" O GLY x 360 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE x 365 " --> pdb=" O LEU x 361 " (cutoff:3.500A) Proline residue: x 367 - end of helix Processing helix chain 'x' and resid 382 through 390 removed outlier: 3.598A pdb=" N PHE x 386 " --> pdb=" O ASN x 382 " (cutoff:3.500A) Processing helix chain 'x' and resid 416 through 432 removed outlier: 3.517A pdb=" N ILE x 422 " --> pdb=" O ILE x 418 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR x 423 " --> pdb=" O HIS x 419 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR x 431 " --> pdb=" O GLN x 427 " (cutoff:3.500A) Processing helix chain 'x' and resid 444 through 463 removed outlier: 3.839A pdb=" N ILE x 448 " --> pdb=" O GLY x 444 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU x 449 " --> pdb=" O GLN x 445 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU x 457 " --> pdb=" O THR x 453 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE x 458 " --> pdb=" O LYS x 454 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS x 461 " --> pdb=" O GLU x 457 " (cutoff:3.500A) Processing helix chain 'x' and resid 479 through 487 removed outlier: 3.684A pdb=" N LYS x 485 " --> pdb=" O GLU x 481 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE x 487 " --> pdb=" O GLN x 483 " (cutoff:3.500A) Processing helix chain 'x' and resid 542 through 551 Processing helix chain 'x' and resid 566 through 572 Processing helix chain 'x' and resid 580 through 584 Processing helix chain 'x' and resid 587 through 598 Processing helix chain 'x' and resid 612 through 626 Processing helix chain 'x' and resid 636 through 643 Processing helix chain 'x' and resid 648 through 661 removed outlier: 3.698A pdb=" N ALA x 659 " --> pdb=" O LEU x 655 " (cutoff:3.500A) Processing helix chain 'x' and resid 667 through 680 removed outlier: 3.560A pdb=" N THR x 673 " --> pdb=" O GLU x 669 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS x 679 " --> pdb=" O VAL x 675 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU x 680 " --> pdb=" O SER x 676 " (cutoff:3.500A) Processing helix chain 'x' and resid 681 through 684 Processing helix chain 'x' and resid 688 through 697 removed outlier: 3.587A pdb=" N ALA x 692 " --> pdb=" O GLN x 688 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER x 695 " --> pdb=" O ASP x 691 " (cutoff:3.500A) Processing helix chain 'x' and resid 702 through 717 removed outlier: 3.609A pdb=" N PHE x 711 " --> pdb=" O TYR x 707 " (cutoff:3.500A) Processing helix chain 'x' and resid 720 through 727 removed outlier: 3.936A pdb=" N CYS x 724 " --> pdb=" O SER x 720 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP x 726 " --> pdb=" O SER x 722 " (cutoff:3.500A) Processing helix chain 'x' and resid 730 through 752 Processing helix chain 'x' and resid 752 through 764 removed outlier: 3.544A pdb=" N LYS x 756 " --> pdb=" O GLY x 752 " (cutoff:3.500A) Processing helix chain 'x' and resid 770 through 783 removed outlier: 3.847A pdb=" N ILE x 775 " --> pdb=" O ILE x 771 " (cutoff:3.500A) Processing helix chain 'x' and resid 813 through 821 removed outlier: 3.621A pdb=" N VAL x 817 " --> pdb=" O SER x 813 " (cutoff:3.500A) Processing helix chain 'x' and resid 852 through 859 removed outlier: 3.643A pdb=" N ILE x 856 " --> pdb=" O GLU x 852 " (cutoff:3.500A) Processing helix chain 'x' and resid 859 through 867 removed outlier: 4.837A pdb=" N ASP x 865 " --> pdb=" O GLN x 861 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU x 866 " --> pdb=" O ILE x 862 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'x' and resid 310 through 311 removed outlier: 6.874A pdb=" N GLY x 303 " --> pdb=" O TYR x 321 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N THR x 323 " --> pdb=" O GLY x 303 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLN x 305 " --> pdb=" O THR x 323 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE x 273 " --> pdb=" O LYS x 320 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET x 322 " --> pdb=" O ILE x 273 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE x 275 " --> pdb=" O MET x 322 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLN x 272 " --> pdb=" O SER x 341 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE x 343 " --> pdb=" O GLN x 272 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA x 274 " --> pdb=" O ILE x 343 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE x 345 " --> pdb=" O ALA x 274 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR x 276 " --> pdb=" O ILE x 345 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER x 378 " --> pdb=" O ILE x 244 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'x' and resid 405 through 409 removed outlier: 6.115A pdb=" N ASP x 406 " --> pdb=" O CYS x 561 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ARG x 563 " --> pdb=" O ASP x 406 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N HIS x 408 " --> pdb=" O ARG x 563 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS x 560 " --> pdb=" O ARG x 514 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASP x 437 " --> pdb=" O TYR x 515 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE x 517 " --> pdb=" O ASP x 437 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU x 439 " --> pdb=" O ILE x 517 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE x 438 " --> pdb=" O VAL x 498 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA x 500 " --> pdb=" O ILE x 438 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL x 440 " --> pdb=" O ALA x 500 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN x 468 " --> pdb=" O ARG x 495 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL x 497 " --> pdb=" O GLN x 468 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE x 470 " --> pdb=" O VAL x 497 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU x 499 " --> pdb=" O ILE x 470 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR x 472 " --> pdb=" O LEU x 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'x' and resid 521 through 527 Processing sheet with id=AA4, first strand: chain 'x' and resid 795 through 797 removed outlier: 4.091A pdb=" N TYR x 829 " --> pdb=" O ILE x 849 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'x' and resid 808 through 809 removed outlier: 3.557A pdb=" N GLN x 834 " --> pdb=" O ARG x 844 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 615 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: 0.74 Time building geometry restraints manager: 0.54 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: 1637 1.34 - 1.45: 649 1.45 - 1.57: 2954 1.57 - 1.69: 1 1.69 - 1.81: 53 Bond restraints: 5294 Sorted by residual: bond pdb=" CA ARG x 584 " pdb=" CB ARG x 584 " ideal model delta sigma weight residual 1.531 1.610 -0.079 3.12e-02 1.03e+03 6.42e+00 bond pdb=" N GLN x 412 " pdb=" CA GLN x 412 " ideal model delta sigma weight residual 1.455 1.470 -0.015 7.00e-03 2.04e+04 4.45e+00 bond pdb=" C GLN x 412 " pdb=" N PRO x 413 " ideal model delta sigma weight residual 1.332 1.354 -0.022 1.32e-02 5.74e+03 2.83e+00 bond pdb=" CB ARG x 584 " pdb=" CG ARG x 584 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.72e+00 bond pdb=" CA LEU x 411 " pdb=" C LEU x 411 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.30e-02 5.92e+03 2.56e+00 ... (remaining 5289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 6984 2.57 - 5.14: 143 5.14 - 7.71: 25 7.71 - 10.28: 5 10.28 - 12.86: 2 Bond angle restraints: 7159 Sorted by residual: angle pdb=" N LEU x 411 " pdb=" CA LEU x 411 " pdb=" C LEU x 411 " ideal model delta sigma weight residual 111.28 120.48 -9.20 1.09e+00 8.42e-01 7.12e+01 angle pdb=" N GLU x 414 " pdb=" CA GLU x 414 " pdb=" C GLU x 414 " ideal model delta sigma weight residual 107.62 120.48 -12.86 1.97e+00 2.58e-01 4.26e+01 angle pdb=" C GLN x 412 " pdb=" N PRO x 413 " pdb=" CA PRO x 413 " ideal model delta sigma weight residual 119.76 113.74 6.02 1.00e+00 1.00e+00 3.62e+01 angle pdb=" C THR x 266 " pdb=" N ASP x 267 " pdb=" CA ASP x 267 " ideal model delta sigma weight residual 121.54 131.87 -10.33 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C THR x 838 " pdb=" N SER x 839 " pdb=" CA SER x 839 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 ... (remaining 7154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.73: 3074 14.73 - 29.45: 131 29.45 - 44.18: 52 44.18 - 58.90: 5 58.90 - 73.63: 5 Dihedral angle restraints: 3267 sinusoidal: 1360 harmonic: 1907 Sorted by residual: dihedral pdb=" C ASP x 391 " pdb=" N ASP x 391 " pdb=" CA ASP x 391 " pdb=" CB ASP x 391 " ideal model delta harmonic sigma weight residual -122.60 -134.75 12.15 0 2.50e+00 1.60e-01 2.36e+01 dihedral pdb=" N ASP x 391 " pdb=" C ASP x 391 " pdb=" CA ASP x 391 " pdb=" CB ASP x 391 " ideal model delta harmonic sigma weight residual 122.80 134.26 -11.46 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" CA ILE x 862 " pdb=" C ILE x 862 " pdb=" N PHE x 863 " pdb=" CA PHE x 863 " ideal model delta harmonic sigma weight residual -180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 3264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 737 0.092 - 0.183: 86 0.183 - 0.275: 4 0.275 - 0.366: 4 0.366 - 0.458: 1 Chirality restraints: 832 Sorted by residual: chirality pdb=" CA ASP x 391 " pdb=" N ASP x 391 " pdb=" C ASP x 391 " pdb=" CB ASP x 391 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CB THR x 585 " pdb=" CA THR x 585 " pdb=" OG1 THR x 585 " pdb=" CG2 THR x 585 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA GLU x 414 " pdb=" N GLU x 414 " pdb=" C GLU x 414 " pdb=" CB GLU x 414 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 829 not shown) Planarity restraints: 909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE x 605 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.35e+00 pdb=" N PRO x 606 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO x 606 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO x 606 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU x 434 " 0.047 5.00e-02 4.00e+02 7.19e-02 8.26e+00 pdb=" N PRO x 435 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO x 435 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO x 435 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR x 409 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C TYR x 409 " 0.044 2.00e-02 2.50e+03 pdb=" O TYR x 409 " -0.017 2.00e-02 2.50e+03 pdb=" N THR x 410 " -0.015 2.00e-02 2.50e+03 ... (remaining 906 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1785 2.88 - 3.39: 4953 3.39 - 3.89: 8352 3.89 - 4.40: 9688 4.40 - 4.90: 16503 Nonbonded interactions: 41281 Sorted by model distance: nonbonded pdb=" OE1 GLU x 644 " pdb=" NZ LYS x 750 " model vdw 2.378 3.120 nonbonded pdb=" O LEU x 337 " pdb=" NH1 ARG x 369 " model vdw 2.383 3.120 nonbonded pdb=" OE1 GLN x 834 " pdb=" NH2 ARG x 844 " model vdw 2.386 3.120 nonbonded pdb=" OG1 THR x 266 " pdb=" N ASP x 267 " model vdw 2.397 3.120 nonbonded pdb=" OE2 GLU x 449 " pdb=" OH TYR x 475 " model vdw 2.397 3.040 ... (remaining 41276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.730 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.006 0.079 5294 Z= 0.242 Angle : 0.949 12.856 7159 Z= 0.516 Chirality : 0.061 0.458 832 Planarity : 0.008 0.072 909 Dihedral : 10.613 73.626 2031 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.85 % Allowed : 2.73 % Favored : 96.42 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.49 (0.26), residues: 651 helix: -3.36 (0.17), residues: 277 sheet: -0.46 (0.45), residues: 123 loop : -1.75 (0.34), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG x 289 TYR 0.023 0.003 TYR x 321 PHE 0.028 0.003 PHE x 863 TRP 0.029 0.004 TRP x 723 HIS 0.004 0.001 HIS x 572 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 5294) covalent geometry : angle 0.94898 ( 7159) hydrogen bonds : bond 0.30278 ( 213) hydrogen bonds : angle 8.56197 ( 615) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: x 454 LYS cc_start: 0.7709 (tptp) cc_final: 0.7309 (tttt) REVERT: x 494 CYS cc_start: 0.7814 (m) cc_final: 0.7509 (m) outliers start: 5 outliers final: 1 residues processed: 150 average time/residue: 0.6857 time to fit residues: 106.4365 Evaluate side-chains 79 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 585 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.0170 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 295 ASN x 408 HIS ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 477 ASN x 630 ASN x 725 GLN x 743 GLN x 834 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.152252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.131067 restraints weight = 6899.404| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.21 r_work: 0.3572 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5294 Z= 0.118 Angle : 0.605 7.347 7159 Z= 0.309 Chirality : 0.044 0.186 832 Planarity : 0.006 0.065 909 Dihedral : 4.971 40.366 707 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.39 % Allowed : 14.82 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.30), residues: 651 helix: -0.78 (0.26), residues: 292 sheet: -0.48 (0.45), residues: 121 loop : -1.01 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG x 401 TYR 0.008 0.001 TYR x 832 PHE 0.017 0.002 PHE x 396 TRP 0.015 0.001 TRP x 723 HIS 0.003 0.001 HIS x 429 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 5294) covalent geometry : angle 0.60469 ( 7159) hydrogen bonds : bond 0.03667 ( 213) hydrogen bonds : angle 4.42493 ( 615) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: x 301 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.6833 (mt-10) REVERT: x 305 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: x 320 LYS cc_start: 0.8609 (ptmt) cc_final: 0.8291 (ptpt) REVERT: x 427 GLN cc_start: 0.8035 (tp40) cc_final: 0.7769 (tp40) REVERT: x 454 LYS cc_start: 0.7583 (tptp) cc_final: 0.7104 (tttt) REVERT: x 483 GLN cc_start: 0.7415 (mm110) cc_final: 0.7128 (mm110) REVERT: x 700 VAL cc_start: 0.7080 (t) cc_final: 0.6861 (p) REVERT: x 762 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.7109 (ptm) REVERT: x 763 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7343 (tttp) outliers start: 14 outliers final: 8 residues processed: 108 average time/residue: 0.6354 time to fit residues: 71.3075 Evaluate side-chains 86 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 301 GLU Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 342 CYS Chi-restraints excluded: chain x residue 382 ASN Chi-restraints excluded: chain x residue 443 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 762 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.0270 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 630 ASN x 834 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.150655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129421 restraints weight = 6793.593| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.19 r_work: 0.3548 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5294 Z= 0.114 Angle : 0.556 6.160 7159 Z= 0.281 Chirality : 0.043 0.174 832 Planarity : 0.005 0.057 909 Dihedral : 4.599 35.179 707 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.09 % Allowed : 15.50 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.27 (0.32), residues: 651 helix: 0.43 (0.29), residues: 293 sheet: 0.05 (0.47), residues: 121 loop : -0.95 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG x 401 TYR 0.009 0.001 TYR x 832 PHE 0.014 0.002 PHE x 863 TRP 0.008 0.001 TRP x 723 HIS 0.002 0.001 HIS x 429 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 5294) covalent geometry : angle 0.55605 ( 7159) hydrogen bonds : bond 0.03382 ( 213) hydrogen bonds : angle 4.01333 ( 615) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.208 Fit side-chains REVERT: x 301 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.6771 (mt-10) REVERT: x 305 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: x 320 LYS cc_start: 0.8659 (ptmt) cc_final: 0.8297 (ptpt) REVERT: x 427 GLN cc_start: 0.8017 (tp40) cc_final: 0.7694 (tp-100) REVERT: x 454 LYS cc_start: 0.7760 (tptp) cc_final: 0.7337 (tttt) REVERT: x 483 GLN cc_start: 0.7359 (mm110) cc_final: 0.7159 (mm110) REVERT: x 762 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7101 (ptm) REVERT: x 767 ILE cc_start: 0.6059 (OUTLIER) cc_final: 0.5607 (mt) outliers start: 24 outliers final: 9 residues processed: 101 average time/residue: 0.5868 time to fit residues: 61.7730 Evaluate side-chains 91 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 301 GLU Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 342 CYS Chi-restraints excluded: chain x residue 355 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 685 PHE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 762 MET Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 69.4122 > 50: distance: 13 - 18: 20.899 distance: 18 - 19: 20.737 distance: 18 - 24: 23.864 distance: 19 - 20: 29.002 distance: 19 - 22: 12.900 distance: 20 - 21: 44.529 distance: 20 - 25: 10.975 distance: 22 - 23: 50.036 distance: 23 - 24: 37.533 distance: 25 - 26: 27.143 distance: 26 - 27: 14.904 distance: 26 - 29: 25.309 distance: 27 - 28: 22.498 distance: 27 - 32: 8.457 distance: 29 - 30: 41.598 distance: 29 - 31: 30.409 distance: 32 - 33: 24.210 distance: 33 - 34: 26.082 distance: 33 - 36: 41.155 distance: 34 - 35: 23.589 distance: 34 - 42: 12.128 distance: 36 - 37: 7.089 distance: 37 - 38: 35.393 distance: 37 - 39: 38.072 distance: 38 - 40: 30.243 distance: 39 - 41: 41.559 distance: 40 - 41: 26.249 distance: 42 - 43: 35.906 distance: 43 - 44: 24.725 distance: 43 - 46: 52.337 distance: 44 - 45: 36.955 distance: 44 - 51: 12.277 distance: 46 - 47: 44.652 distance: 47 - 48: 13.348 distance: 48 - 49: 13.713 distance: 48 - 50: 15.647 distance: 51 - 52: 23.210 distance: 52 - 53: 24.067 distance: 52 - 55: 26.912 distance: 53 - 54: 56.748 distance: 53 - 63: 22.100 distance: 54 - 89: 53.946 distance: 55 - 56: 25.482 distance: 56 - 57: 17.053 distance: 56 - 58: 9.861 distance: 57 - 59: 11.466 distance: 58 - 60: 14.974 distance: 59 - 61: 14.242 distance: 60 - 61: 19.965 distance: 61 - 62: 4.028 distance: 63 - 64: 15.720 distance: 64 - 65: 32.982 distance: 64 - 67: 36.789 distance: 65 - 66: 10.856 distance: 65 - 72: 33.738 distance: 66 - 97: 48.651 distance: 67 - 68: 10.244 distance: 68 - 69: 32.804 distance: 69 - 70: 14.519 distance: 70 - 71: 23.809 distance: 72 - 73: 25.134 distance: 73 - 74: 21.690 distance: 73 - 76: 27.927 distance: 74 - 75: 37.718 distance: 74 - 80: 38.462 distance: 75 - 105: 27.604 distance: 76 - 77: 21.715 distance: 77 - 78: 13.595 distance: 77 - 79: 21.365 distance: 80 - 81: 38.982 distance: 81 - 82: 36.192 distance: 81 - 84: 29.495 distance: 82 - 83: 56.056 distance: 82 - 89: 23.793 distance: 83 - 113: 29.354 distance: 84 - 85: 30.705 distance: 85 - 86: 18.642 distance: 86 - 87: 11.590 distance: 86 - 88: 12.106 distance: 90 - 91: 58.800 distance: 90 - 93: 69.412 distance: 91 - 92: 52.852 distance: 91 - 97: 42.039 distance: 92 - 120: 28.120 distance: 93 - 94: 50.070 distance: 94 - 95: 36.321 distance: 94 - 96: 36.089 distance: 97 - 98: 11.825 distance: 98 - 99: 26.445 distance: 98 - 101: 38.414 distance: 99 - 100: 41.488 distance: 99 - 105: 32.171 distance: 100 - 128: 23.714 distance: 101 - 102: 42.585 distance: 102 - 103: 57.120 distance: 102 - 104: 45.789