Starting phenix.real_space_refine on Sat Aug 23 13:53:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nfd_12300/08_2025/7nfd_12300.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nfd_12300/08_2025/7nfd_12300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nfd_12300/08_2025/7nfd_12300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nfd_12300/08_2025/7nfd_12300.map" model { file = "/net/cci-nas-00/data/ceres_data/7nfd_12300/08_2025/7nfd_12300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nfd_12300/08_2025/7nfd_12300.cif" } resolution = 3.51 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= 0.081 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 68 5.16 5 C 7998 2.51 5 N 2040 2.21 5 O 2288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12394 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 926 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 926 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'MIX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.77, per 1000 atoms: 0.22 Number of scatterers: 12394 At special positions: 0 Unit cell: (100.32, 98.34, 147.18, 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 68 16.00 O 2288 8.00 N 2040 7.00 C 7998 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.05 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN A 596 " " NAG H 1 " - " ASN B 596 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 543.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 16 sheets defined 42.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.717A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.543A pdb=" N LYS A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 198 removed outlier: 3.807A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 4.328A pdb=" N LYS A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 Processing helix chain 'A' and resid 289 through 300 removed outlier: 4.559A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 333 through 338 removed outlier: 4.365A pdb=" N VAL A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 333 through 338' Processing helix chain 'A' and resid 339 through 353 removed outlier: 4.347A pdb=" N LYS A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 391 removed outlier: 4.101A pdb=" N VAL A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 413 Processing helix chain 'A' and resid 419 through 440 removed outlier: 4.116A pdb=" N ILE A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 478 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 487 through 498 removed outlier: 3.848A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 528 removed outlier: 4.502A pdb=" N MET A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 551 Processing helix chain 'A' and resid 565 through 571 removed outlier: 3.528A pdb=" N GLN A 569 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.538A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.698A pdb=" N GLN A 617 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 632 removed outlier: 3.645A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.546A pdb=" N MET A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 644 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.669A pdb=" N ASP C 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL C 83 " --> pdb=" O THR C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 83' Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.669A pdb=" N ASP E 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL E 83 " --> pdb=" O THR E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'F' and resid 73 through 76 Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.717A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 removed outlier: 3.542A pdb=" N LYS B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 removed outlier: 3.807A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 4.330A pdb=" N LYS B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 281 Processing helix chain 'B' and resid 289 through 300 removed outlier: 4.558A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 333 through 338 removed outlier: 4.365A pdb=" N VAL B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 333 through 338' Processing helix chain 'B' and resid 339 through 353 removed outlier: 4.346A pdb=" N LYS B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 391 removed outlier: 4.100A pdb=" N VAL B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 413 Processing helix chain 'B' and resid 419 through 440 removed outlier: 4.115A pdb=" N ILE B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 445 removed outlier: 3.742A pdb=" N VAL B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 478 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 487 through 498 removed outlier: 3.848A pdb=" N TYR B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 528 removed outlier: 4.502A pdb=" N MET B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 551 Processing helix chain 'B' and resid 565 through 571 removed outlier: 3.528A pdb=" N GLN B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.540A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 removed outlier: 3.697A pdb=" N GLN B 617 " --> pdb=" O TYR B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 632 removed outlier: 3.645A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 650 removed outlier: 3.546A pdb=" N MET B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 638 " --> pdb=" O ALA B 634 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 644 " --> pdb=" O PHE B 640 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 77 removed outlier: 6.529A pdb=" N ASN A 76 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 239 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 241 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260 removed outlier: 6.089A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 20 through 24 removed outlier: 3.761A pdb=" N TYR C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 45 through 48 removed outlier: 3.946A pdb=" N ARG C 45 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 22 through 23 Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 40 Processing sheet with id=AA8, first strand: chain 'D' and resid 51 through 52 Processing sheet with id=AA9, first strand: chain 'E' and resid 20 through 24 removed outlier: 3.761A pdb=" N TYR E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 48 removed outlier: 3.947A pdb=" N ARG E 45 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 22 through 23 Processing sheet with id=AB3, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AB4, first strand: chain 'F' and resid 51 through 52 Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 40 Processing sheet with id=AB6, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.528A pdb=" N ASN B 76 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 239 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 241 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 258 through 260 removed outlier: 6.089A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1281 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: 1.82 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1934 1.28 - 1.42: 3372 1.42 - 1.55: 7248 1.55 - 1.68: 10 1.68 - 1.81: 106 Bond restraints: 12670 Sorted by residual: bond pdb=" C PHE B 432 " pdb=" O PHE B 432 " ideal model delta sigma weight residual 1.236 1.150 0.085 1.29e-02 6.01e+03 4.38e+01 bond pdb=" C VAL B 546 " pdb=" O VAL B 546 " ideal model delta sigma weight residual 1.237 1.163 0.074 1.19e-02 7.06e+03 3.82e+01 bond pdb=" CA ASN A 436 " pdb=" CB ASN A 436 " ideal model delta sigma weight residual 1.531 1.446 0.085 1.56e-02 4.11e+03 3.00e+01 bond pdb=" C MET B 549 " pdb=" O MET B 549 " ideal model delta sigma weight residual 1.237 1.178 0.058 1.19e-02 7.06e+03 2.41e+01 bond pdb=" C PHE B 432 " pdb=" N LEU B 433 " ideal model delta sigma weight residual 1.334 1.269 0.065 1.41e-02 5.03e+03 2.12e+01 ... (remaining 12665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 16635 2.51 - 5.03: 466 5.03 - 7.54: 43 7.54 - 10.06: 14 10.06 - 12.57: 8 Bond angle restraints: 17166 Sorted by residual: angle pdb=" CA THR A 435 " pdb=" CB THR A 435 " pdb=" OG1 THR A 435 " ideal model delta sigma weight residual 109.60 97.03 12.57 1.50e+00 4.44e-01 7.02e+01 angle pdb=" CA THR A 542 " pdb=" CB THR A 542 " pdb=" OG1 THR A 542 " ideal model delta sigma weight residual 109.60 98.27 11.33 1.50e+00 4.44e-01 5.71e+01 angle pdb=" C ASN B 436 " pdb=" CA ASN B 436 " pdb=" CB ASN B 436 " ideal model delta sigma weight residual 110.79 100.32 10.47 1.68e+00 3.54e-01 3.89e+01 angle pdb=" CA MET B 549 " pdb=" C MET B 549 " pdb=" O MET B 549 " ideal model delta sigma weight residual 120.42 114.19 6.23 1.06e+00 8.90e-01 3.46e+01 angle pdb=" CA THR B 542 " pdb=" CB THR B 542 " pdb=" OG1 THR B 542 " ideal model delta sigma weight residual 109.60 101.46 8.14 1.50e+00 4.44e-01 2.94e+01 ... (remaining 17161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 6896 21.68 - 43.35: 513 43.35 - 65.03: 50 65.03 - 86.71: 29 86.71 - 108.38: 11 Dihedral angle restraints: 7499 sinusoidal: 2963 harmonic: 4536 Sorted by residual: dihedral pdb=" CA LYS A 233 " pdb=" C LYS A 233 " pdb=" N GLN A 234 " pdb=" CA GLN A 234 " ideal model delta harmonic sigma weight residual 180.00 137.29 42.71 0 5.00e+00 4.00e-02 7.29e+01 dihedral pdb=" CA LYS B 233 " pdb=" C LYS B 233 " pdb=" N GLN B 234 " pdb=" CA GLN B 234 " ideal model delta harmonic sigma weight residual 180.00 137.32 42.68 0 5.00e+00 4.00e-02 7.29e+01 dihedral pdb=" CA ASP A 217 " pdb=" C ASP A 217 " pdb=" N SER A 218 " pdb=" CA SER A 218 " ideal model delta harmonic sigma weight residual -180.00 -144.44 -35.56 0 5.00e+00 4.00e-02 5.06e+01 ... (remaining 7496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1617 0.069 - 0.138: 314 0.138 - 0.206: 27 0.206 - 0.275: 1 0.275 - 0.344: 5 Chirality restraints: 1964 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.49e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.33e+01 chirality pdb=" CA PHE B 432 " pdb=" N PHE B 432 " pdb=" C PHE B 432 " pdb=" CB PHE B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 1961 not shown) Planarity restraints: 2135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 442 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C VAL A 442 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL A 442 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 443 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 439 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C PHE B 439 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE B 439 " 0.017 2.00e-02 2.50e+03 pdb=" N SER B 440 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 436 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" CG ASN A 436 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 436 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 436 " 0.015 2.00e-02 2.50e+03 ... (remaining 2132 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 264 2.64 - 3.20: 12492 3.20 - 3.77: 18107 3.77 - 4.33: 25509 4.33 - 4.90: 42508 Nonbonded interactions: 98880 Sorted by model distance: nonbonded pdb=" CD1 TYR A 287 " pdb=" CD1 TYR B 287 " model vdw 2.071 3.640 nonbonded pdb=" NH1 ARG C 61 " pdb=" OD2 ASP C 82 " model vdw 2.082 3.120 nonbonded pdb=" ND2 ASN A 68 " pdb=" NZ LYS A 346 " model vdw 2.186 3.200 nonbonded pdb=" NAV MIX B1201 " pdb=" OAB MIX B1201 " model vdw 2.197 3.120 nonbonded pdb=" NE2 GLN C 89 " pdb=" O GLN C 90 " model vdw 2.199 3.120 ... (remaining 98875 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 35 through 654) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 3.310 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.360 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.009 0.085 12681 Z= 0.440 Angle : 1.336 60.353 17192 Z= 0.637 Chirality : 0.055 0.344 1964 Planarity : 0.005 0.044 2133 Dihedral : 16.114 108.383 4582 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 25.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.92 % Favored : 83.95 % Rotamer: Outliers : 0.37 % Allowed : 0.00 % Favored : 99.63 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.50 (0.16), residues: 1558 helix: -2.76 (0.16), residues: 642 sheet: -3.65 (0.33), residues: 198 loop : -4.56 (0.17), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 246 TYR 0.019 0.002 TYR E 91 PHE 0.035 0.003 PHE B 432 TRP 0.009 0.002 TRP E 92 HIS 0.006 0.002 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00923 (12670) covalent geometry : angle 1.01630 (17166) SS BOND : bond 0.01050 ( 7) SS BOND : angle 2.78388 ( 14) hydrogen bonds : bond 0.16545 ( 444) hydrogen bonds : angle 7.17437 ( 1281) link_BETA1-4 : bond 0.06574 ( 2) link_BETA1-4 : angle 46.07313 ( 6) link_NAG-ASN : bond 0.00630 ( 2) link_NAG-ASN : angle 4.00821 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 280 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.7514 (m-40) cc_final: 0.7071 (p0) REVERT: A 96 ARG cc_start: 0.8339 (mmt-90) cc_final: 0.8073 (tpp80) REVERT: A 127 ASP cc_start: 0.7706 (p0) cc_final: 0.7207 (p0) REVERT: A 465 ARG cc_start: 0.6257 (ptp-110) cc_final: 0.5865 (mmt-90) REVERT: A 481 MET cc_start: 0.7616 (tpt) cc_final: 0.6682 (ttp) REVERT: A 515 MET cc_start: 0.8892 (mmm) cc_final: 0.8611 (mmp) REVERT: C 24 LYS cc_start: 0.8326 (ptpp) cc_final: 0.7835 (mmtt) REVERT: C 69 LYS cc_start: 0.8362 (mttt) cc_final: 0.8116 (mttm) REVERT: C 82 ASP cc_start: 0.8123 (m-30) cc_final: 0.7653 (m-30) REVERT: D 16 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8050 (mt0) REVERT: D 73 ASP cc_start: 0.8158 (t0) cc_final: 0.7858 (t70) REVERT: D 100 TYR cc_start: 0.7881 (t80) cc_final: 0.7400 (t80) REVERT: F 100 TYR cc_start: 0.7442 (t80) cc_final: 0.7101 (t80) REVERT: B 288 ASN cc_start: 0.6996 (t0) cc_final: 0.6474 (p0) REVERT: B 341 PHE cc_start: 0.7027 (m-80) cc_final: 0.6787 (m-80) REVERT: B 407 LEU cc_start: 0.9039 (mt) cc_final: 0.8766 (mt) REVERT: B 451 GLU cc_start: 0.7787 (pt0) cc_final: 0.7455 (pt0) REVERT: B 523 MET cc_start: 0.8741 (ttp) cc_final: 0.8492 (ttt) REVERT: B 585 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7732 (tm-30) outliers start: 5 outliers final: 4 residues processed: 283 average time/residue: 0.1077 time to fit residues: 43.3521 Evaluate side-chains 215 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 542 THR 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: 58.0243 > 50: distance: 21 - 46: 11.043 distance: 28 - 54: 18.126 distance: 33 - 37: 4.647 distance: 34 - 62: 24.502 distance: 37 - 38: 8.869 distance: 38 - 39: 17.621 distance: 38 - 41: 14.000 distance: 39 - 40: 22.937 distance: 39 - 46: 13.226 distance: 40 - 71: 14.109 distance: 41 - 42: 10.507 distance: 42 - 43: 5.719 distance: 43 - 44: 3.449 distance: 43 - 45: 9.411 distance: 46 - 47: 23.948 distance: 47 - 48: 47.431 distance: 47 - 50: 22.242 distance: 48 - 49: 47.550 distance: 48 - 54: 23.792 distance: 49 - 82: 44.775 distance: 50 - 51: 10.964 distance: 51 - 52: 9.444 distance: 51 - 53: 21.206 distance: 54 - 55: 40.031 distance: 55 - 56: 21.048 distance: 55 - 58: 14.891 distance: 56 - 57: 47.416 distance: 56 - 62: 54.687 distance: 57 - 88: 20.669 distance: 58 - 59: 12.598 distance: 59 - 60: 14.054 distance: 59 - 61: 28.126 distance: 62 - 63: 50.451 distance: 63 - 64: 29.883 distance: 63 - 66: 36.287 distance: 64 - 65: 16.890 distance: 64 - 71: 14.965 distance: 65 - 93: 35.877 distance: 66 - 67: 8.281 distance: 67 - 68: 11.926 distance: 68 - 69: 9.881 distance: 68 - 70: 8.451 distance: 71 - 72: 7.060 distance: 72 - 73: 3.902 distance: 72 - 75: 5.520 distance: 73 - 74: 12.023 distance: 73 - 82: 20.535 distance: 75 - 76: 7.883 distance: 76 - 77: 16.176 distance: 76 - 78: 8.693 distance: 77 - 79: 16.206 distance: 78 - 80: 8.103 distance: 79 - 81: 7.276 distance: 80 - 81: 12.019 distance: 82 - 83: 20.348 distance: 83 - 84: 4.145 distance: 83 - 86: 14.745 distance: 84 - 85: 12.433 distance: 84 - 88: 5.597 distance: 86 - 87: 8.340 distance: 88 - 89: 4.604 distance: 89 - 90: 30.039 distance: 89 - 92: 27.364 distance: 90 - 91: 23.077 distance: 90 - 93: 21.770 distance: 93 - 94: 26.808 distance: 94 - 95: 15.338 distance: 94 - 97: 18.682 distance: 95 - 96: 16.513 distance: 95 - 98: 17.025 distance: 98 - 99: 25.171 distance: 99 - 100: 17.378 distance: 99 - 102: 15.308 distance: 100 - 101: 14.042 distance: 100 - 106: 23.495 distance: 102 - 103: 20.868 distance: 103 - 104: 12.057 distance: 103 - 105: 11.498 distance: 106 - 107: 31.527 distance: 107 - 108: 20.108 distance: 107 - 110: 15.292 distance: 108 - 109: 35.319 distance: 108 - 117: 17.630 distance: 110 - 111: 29.374 distance: 111 - 112: 5.315 distance: 112 - 113: 11.925 distance: 113 - 114: 10.691 distance: 114 - 115: 4.018 distance: 114 - 116: 7.807