Starting phenix.real_space_refine on Fri Aug 22 22:20:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tnx_41428/08_2025/8tnx_41428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tnx_41428/08_2025/8tnx_41428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tnx_41428/08_2025/8tnx_41428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tnx_41428/08_2025/8tnx_41428.map" model { file = "/net/cci-nas-00/data/ceres_data/8tnx_41428/08_2025/8tnx_41428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tnx_41428/08_2025/8tnx_41428.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 42 5.16 5 C 5414 2.51 5 N 1352 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 8272 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4130 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 19, 'TRANS': 556} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 6, 'ARG:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 176 Chain: "B" Number of atoms: 4130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4130 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 19, 'TRANS': 556} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 6, 'ARG:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 176 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'OXL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'OXL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.16, per 1000 atoms: 0.26 Number of scatterers: 8272 At special positions: 0 Unit cell: (113.162, 96.642, 95.816, 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 42 16.00 O 1464 8.00 N 1352 7.00 C 5414 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: 0.58 Conformation dependent library (CDL) restraints added in 602.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 68.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 94 through 102 Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 110 through 134 removed outlier: 3.625A pdb=" N LEU A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 136 through 155 removed outlier: 3.795A pdb=" N GLY A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 184 Processing helix chain 'A' and resid 213 through 239 removed outlier: 3.626A pdb=" N ILE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 removed outlier: 3.889A pdb=" N VAL A 244 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 273 removed outlier: 3.708A pdb=" N SER A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.579A pdb=" N THR A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 301 through 316 Processing helix chain 'A' and resid 336 through 348 Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 378 through 396 removed outlier: 4.809A pdb=" N VAL A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 408 removed outlier: 4.038A pdb=" N LEU A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 425 through 426 No H-bonds generated for 'chain 'A' and resid 425 through 426' Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.962A pdb=" N HIS A 432 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 removed outlier: 3.710A pdb=" N LYS A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 469 removed outlier: 3.787A pdb=" N VAL A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.704A pdb=" N PHE A 475 " --> pdb=" O ALA A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'A' and resid 526 through 547 removed outlier: 3.597A pdb=" N GLY A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 605 through 614 Processing helix chain 'A' and resid 660 through 678 removed outlier: 3.553A pdb=" N ILE A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 711 through 724 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 94 through 102 Proline residue: B 100 - end of helix Processing helix chain 'B' and resid 110 through 134 removed outlier: 3.625A pdb=" N LEU B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 136 through 155 removed outlier: 3.795A pdb=" N GLY B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 184 Processing helix chain 'B' and resid 213 through 239 removed outlier: 3.626A pdb=" N ILE B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 248 removed outlier: 3.889A pdb=" N VAL B 244 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 273 removed outlier: 3.708A pdb=" N SER B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 Processing helix chain 'B' and resid 297 through 300 removed outlier: 3.579A pdb=" N THR B 300 " --> pdb=" O ILE B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 301 through 316 Processing helix chain 'B' and resid 336 through 348 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 378 through 396 removed outlier: 4.809A pdb=" N VAL B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 408 removed outlier: 4.038A pdb=" N LEU B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 425 through 426 No H-bonds generated for 'chain 'B' and resid 425 through 426' Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.962A pdb=" N HIS B 432 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.710A pdb=" N LYS B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 469 removed outlier: 3.787A pdb=" N VAL B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.704A pdb=" N PHE B 475 " --> pdb=" O ALA B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 500 through 508 Processing helix chain 'B' and resid 508 through 525 Processing helix chain 'B' and resid 526 through 547 removed outlier: 3.596A pdb=" N GLY B 534 " --> pdb=" O GLY B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 605 through 614 Processing helix chain 'B' and resid 660 through 678 removed outlier: 3.553A pdb=" N ILE B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'B' and resid 711 through 724 Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 563 through 565 removed outlier: 4.633A pdb=" N ILE A 580 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N LEU A 556 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 13.480A pdb=" N ILE A 578 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE A 583 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N PHE A 709 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 683 " --> pdb=" O PHE A 709 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 163 Processing sheet with id=AA4, first strand: chain 'B' and resid 563 through 565 removed outlier: 4.633A pdb=" N ILE B 580 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N LEU B 556 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 13.480A pdb=" N ILE B 578 " --> pdb=" O LEU B 556 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE B 583 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N PHE B 709 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 683 " --> pdb=" O PHE B 709 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1554 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1287 1.32 - 1.44: 2271 1.44 - 1.57: 4824 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 8442 Sorted by residual: bond pdb=" CA SER A 254 " pdb=" CB SER A 254 " ideal model delta sigma weight residual 1.536 1.441 0.095 1.46e-02 4.69e+03 4.27e+01 bond pdb=" CA SER B 254 " pdb=" CB SER B 254 " ideal model delta sigma weight residual 1.536 1.441 0.095 1.46e-02 4.69e+03 4.27e+01 bond pdb=" CA SER B 126 " pdb=" CB SER B 126 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.58e-02 4.01e+03 2.50e+01 bond pdb=" CA SER A 126 " pdb=" CB SER A 126 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.58e-02 4.01e+03 2.50e+01 bond pdb=" N ILE A 160 " pdb=" CA ILE A 160 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.17e-02 7.31e+03 1.37e+01 ... (remaining 8437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 11063 2.24 - 4.48: 413 4.48 - 6.72: 48 6.72 - 8.96: 6 8.96 - 11.20: 8 Bond angle restraints: 11538 Sorted by residual: angle pdb=" N ALA B 441 " pdb=" CA ALA B 441 " pdb=" C ALA B 441 " ideal model delta sigma weight residual 114.39 103.19 11.20 1.45e+00 4.76e-01 5.97e+01 angle pdb=" N ALA A 441 " pdb=" CA ALA A 441 " pdb=" C ALA A 441 " ideal model delta sigma weight residual 114.39 103.19 11.20 1.45e+00 4.76e-01 5.97e+01 angle pdb=" N THR A 443 " pdb=" CA THR A 443 " pdb=" C THR A 443 " ideal model delta sigma weight residual 113.28 103.96 9.32 1.22e+00 6.72e-01 5.83e+01 angle pdb=" N THR B 443 " pdb=" CA THR B 443 " pdb=" C THR B 443 " ideal model delta sigma weight residual 113.28 103.96 9.32 1.22e+00 6.72e-01 5.83e+01 angle pdb=" N LEU A 440 " pdb=" CA LEU A 440 " pdb=" C LEU A 440 " ideal model delta sigma weight residual 113.40 102.81 10.59 1.47e+00 4.63e-01 5.19e+01 ... (remaining 11533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 4238 16.32 - 32.64: 460 32.64 - 48.96: 144 48.96 - 65.28: 36 65.28 - 81.61: 12 Dihedral angle restraints: 4890 sinusoidal: 1552 harmonic: 3338 Sorted by residual: dihedral pdb=" CD ARG A 58 " pdb=" NE ARG A 58 " pdb=" CZ ARG A 58 " pdb=" NH1 ARG A 58 " ideal model delta sinusoidal sigma weight residual 0.00 71.94 -71.94 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CD ARG B 58 " pdb=" NE ARG B 58 " pdb=" CZ ARG B 58 " pdb=" NH1 ARG B 58 " ideal model delta sinusoidal sigma weight residual 0.00 71.94 -71.94 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" N LEU A 468 " pdb=" CA LEU A 468 " pdb=" CB LEU A 468 " pdb=" CG LEU A 468 " ideal model delta sinusoidal sigma weight residual -60.00 -119.18 59.18 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 965 0.044 - 0.088: 269 0.088 - 0.132: 139 0.132 - 0.176: 48 0.176 - 0.220: 21 Chirality restraints: 1442 Sorted by residual: chirality pdb=" CA LEU B 491 " pdb=" N LEU B 491 " pdb=" C LEU B 491 " pdb=" CB LEU B 491 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LEU A 491 " pdb=" N LEU A 491 " pdb=" C LEU A 491 " pdb=" CB LEU A 491 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LEU A 444 " pdb=" N LEU A 444 " pdb=" C LEU A 444 " pdb=" CB LEU A 444 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1439 not shown) Planarity restraints: 1420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 58 " -1.042 9.50e-02 1.11e+02 4.67e-01 1.32e+02 pdb=" NE ARG B 58 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG B 58 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 58 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 58 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 58 " 1.042 9.50e-02 1.11e+02 4.67e-01 1.32e+02 pdb=" NE ARG A 58 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 58 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 58 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 58 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 159 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C HIS B 159 " 0.055 2.00e-02 2.50e+03 pdb=" O HIS B 159 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE B 160 " -0.019 2.00e-02 2.50e+03 ... (remaining 1417 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2277 2.80 - 3.33: 8170 3.33 - 3.85: 13985 3.85 - 4.38: 15915 4.38 - 4.90: 27421 Nonbonded interactions: 67768 Sorted by model distance: nonbonded pdb=" O MET B 220 " pdb=" OG1 THR B 224 " model vdw 2.278 3.040 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 224 " model vdw 2.278 3.040 nonbonded pdb=" O LEU A 122 " pdb=" OG SER A 126 " model vdw 2.296 3.040 nonbonded pdb=" O LEU B 122 " pdb=" OG SER B 126 " model vdw 2.296 3.040 nonbonded pdb=" O SER B 126 " pdb=" OG SER B 130 " model vdw 2.329 3.040 ... (remaining 67763 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.750 Find NCS groups from input model: 0.080 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:1.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 : 0.007 0.095 8442 Z= 0.466 Angle : 0.901 11.203 11538 Z= 0.645 Chirality : 0.058 0.220 1442 Planarity : 0.018 0.467 1420 Dihedral : 16.340 81.606 2734 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.83 % Favored : 96.82 % Rotamer: Outliers : 4.12 % Allowed : 25.62 % Favored : 70.25 % 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: 0.06 (0.24), residues: 1132 helix: 0.35 (0.19), residues: 754 sheet: 1.76 (0.72), residues: 50 loop : -0.73 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 178 TYR 0.015 0.001 TYR B 588 PHE 0.013 0.001 PHE B 434 TRP 0.005 0.001 TRP B 376 HIS 0.003 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00664 ( 8442) covalent geometry : angle 0.90106 (11538) hydrogen bonds : bond 0.18141 ( 538) hydrogen bonds : angle 6.65252 ( 1554) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.337 Fit side-chains REVERT: A 238 PHE cc_start: 0.7371 (t80) cc_final: 0.7099 (t80) REVERT: A 239 PHE cc_start: 0.6150 (m-80) cc_final: 0.5927 (m-10) REVERT: A 270 LYS cc_start: 0.7068 (mtmt) cc_final: 0.6532 (ttpp) REVERT: A 489 VAL cc_start: 0.8078 (t) cc_final: 0.7871 (t) REVERT: A 490 ASN cc_start: 0.7544 (m110) cc_final: 0.7319 (m-40) REVERT: A 716 MET cc_start: 0.7895 (mmm) cc_final: 0.7635 (mmm) REVERT: B 238 PHE cc_start: 0.7370 (t80) cc_final: 0.7101 (t80) REVERT: B 239 PHE cc_start: 0.6147 (m-80) cc_final: 0.5928 (m-10) REVERT: B 270 LYS cc_start: 0.7064 (mtmt) cc_final: 0.6530 (ttpp) REVERT: B 489 VAL cc_start: 0.8076 (t) cc_final: 0.7868 (t) REVERT: B 490 ASN cc_start: 0.7539 (m110) cc_final: 0.7315 (m-40) REVERT: B 716 MET cc_start: 0.7896 (mmm) cc_final: 0.7634 (mmm) outliers start: 33 outliers final: 13 residues processed: 176 average time/residue: 0.0871 time to fit residues: 22.0852 Evaluate side-chains 124 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 538 SER 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: 54.2462 > 50: distance: 18 - 117: 13.671 distance: 21 - 130: 4.888 distance: 33 - 133: 12.608 distance: 36 - 146: 3.117 distance: 80 - 102: 6.139 distance: 97 - 102: 7.884 distance: 102 - 103: 9.967 distance: 103 - 104: 4.822 distance: 104 - 105: 16.058 distance: 104 - 106: 5.498 distance: 106 - 107: 18.350 distance: 107 - 108: 28.729 distance: 107 - 110: 6.813 distance: 108 - 109: 6.551 distance: 108 - 114: 5.827 distance: 110 - 111: 23.433 distance: 110 - 112: 20.097 distance: 111 - 113: 4.165 distance: 114 - 115: 30.484 distance: 115 - 116: 12.723 distance: 115 - 118: 26.519 distance: 116 - 117: 20.544 distance: 116 - 123: 4.419 distance: 118 - 119: 8.948 distance: 119 - 120: 10.940 distance: 120 - 121: 21.714 distance: 120 - 122: 10.689 distance: 123 - 124: 19.732 distance: 124 - 125: 11.300 distance: 124 - 127: 10.717 distance: 125 - 126: 29.879 distance: 125 - 130: 12.506 distance: 127 - 128: 24.190 distance: 127 - 129: 17.260 distance: 130 - 131: 7.412 distance: 131 - 132: 5.022 distance: 131 - 134: 11.621 distance: 132 - 133: 9.791 distance: 132 - 138: 9.575 distance: 134 - 135: 12.137 distance: 135 - 136: 14.581 distance: 135 - 137: 32.224 distance: 138 - 139: 9.193 distance: 139 - 140: 12.060 distance: 139 - 142: 3.122 distance: 140 - 141: 6.150 distance: 140 - 146: 15.276 distance: 142 - 143: 6.858 distance: 143 - 144: 25.530 distance: 143 - 145: 16.619 distance: 146 - 147: 7.694 distance: 147 - 148: 3.141 distance: 147 - 150: 10.996 distance: 148 - 149: 9.201 distance: 148 - 151: 9.071 distance: 151 - 152: 12.446 distance: 152 - 153: 7.007 distance: 152 - 155: 5.554 distance: 153 - 154: 3.831 distance: 153 - 160: 4.106 distance: 155 - 156: 6.234 distance: 156 - 157: 5.492 distance: 157 - 158: 7.432 distance: 157 - 159: 6.536 distance: 160 - 161: 5.109 distance: 161 - 162: 6.648 distance: 161 - 164: 6.523 distance: 162 - 163: 7.640 distance: 162 - 166: 8.318 distance: 164 - 165: 13.666 distance: 166 - 167: 4.649 distance: 167 - 168: 3.643 distance: 167 - 170: 5.765 distance: 168 - 169: 8.863 distance: 168 - 174: 3.569 distance: 169 - 195: 5.717 distance: 170 - 171: 9.258 distance: 171 - 173: 15.077 distance: 247 - 252: 3.010