Starting phenix.real_space_refine on Sun Aug 24 05:44:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n0d_48781/08_2025/9n0d_48781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n0d_48781/08_2025/9n0d_48781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n0d_48781/08_2025/9n0d_48781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n0d_48781/08_2025/9n0d_48781.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n0d_48781/08_2025/9n0d_48781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n0d_48781/08_2025/9n0d_48781.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.006 sd= 0.106 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 123 5.16 5 C 10869 2.51 5 N 2820 2.21 5 O 3177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 16989 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 441 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "B" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1517 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 11, 'TRANS': 175} Chain: "C" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1829 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Chain: "D" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 796 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 Chain: "F" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 441 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "G" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1517 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 11, 'TRANS': 175} Chain: "H" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1829 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Chain: "I" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 796 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 Chain: "K" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 441 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "L" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1517 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 11, 'TRANS': 175} Chain: "M" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1829 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Chain: "N" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 796 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "O" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" 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: "M" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.99, per 1000 atoms: 0.23 Number of scatterers: 16989 At special positions: 0 Unit cell: (133.63, 124.5, 180.94, 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 123 16.00 O 3177 8.00 N 2820 7.00 C 10869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS C 469 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 271 " - pdb=" SG CYS C 284 " distance=2.04 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 356 " - pdb=" SG CYS C 377 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS H 469 " distance=2.03 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 226 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 164 " distance=2.03 Simple disulfide: pdb=" SG CYS G 207 " - pdb=" SG CYS G 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 271 " - pdb=" SG CYS H 284 " distance=2.04 Simple disulfide: pdb=" SG CYS H 293 " - pdb=" SG CYS H 302 " distance=2.03 Simple disulfide: pdb=" SG CYS H 356 " - pdb=" SG CYS H 377 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 87 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 57 " - pdb=" SG CYS M 469 " distance=2.03 Simple disulfide: pdb=" SG CYS L 92 " - pdb=" SG CYS L 226 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 164 " distance=2.03 Simple disulfide: pdb=" SG CYS L 207 " - pdb=" SG CYS L 213 " distance=2.03 Simple disulfide: pdb=" SG CYS M 271 " - pdb=" SG CYS M 284 " distance=2.04 Simple disulfide: pdb=" SG CYS M 293 " - pdb=" SG CYS M 302 " distance=2.03 Simple disulfide: pdb=" SG CYS M 356 " - pdb=" SG CYS M 377 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 87 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 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=3, symmetry=0 Links applied BETA1-4 " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " NAG-ASN " NAG B 301 " - " ASN B 95 " " NAG B 302 " - " ASN B 166 " " NAG C 501 " - " ASN C 365 " " NAG C 502 " - " ASN C 382 " " NAG C 503 " - " ASN C 387 " " NAG G 301 " - " ASN G 95 " " NAG G 302 " - " ASN G 166 " " NAG H 501 " - " ASN H 365 " " NAG H 502 " - " ASN H 382 " " NAG H 503 " - " ASN H 387 " " NAG L 301 " - " ASN L 95 " " NAG L 302 " - " ASN L 166 " " NAG M 501 " - " ASN M 365 " " NAG M 502 " - " ASN M 382 " " NAG M 503 " - " ASN M 387 " " NAG R 1 " - " ASN B 178 " " NAG W 1 " - " ASN G 178 " " NAG Y 1 " - " ASN C 357 " " NAG b 1 " - " ASN L 178 " " NAG h 1 " - " ASN H 357 " " NAG n 1 " - " ASN M 357 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 891.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3876 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 33 sheets defined 33.8% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 removed outlier: 3.905A pdb=" N SER A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) Proline residue: A 12 - end of helix Processing helix chain 'A' and resid 17 through 42 Processing helix chain 'A' and resid 42 through 53 Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.633A pdb=" N ILE B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 230 through 240 Processing helix chain 'C' and resid 273 through 277 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 292 through 295 removed outlier: 4.424A pdb=" N LEU C 295 " --> pdb=" O LYS C 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 292 through 295' Processing helix chain 'C' and resid 299 through 321 Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 338 through 351 removed outlier: 3.546A pdb=" N MET C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 391 through 416 removed outlier: 4.285A pdb=" N TRP C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU C 397 " --> pdb=" O ASN C 393 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 414 " --> pdb=" O GLU C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 443 removed outlier: 3.519A pdb=" N VAL C 423 " --> pdb=" O PRO C 419 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY C 443 " --> pdb=" O LEU C 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 3 through 15 Proline residue: F 12 - end of helix Processing helix chain 'F' and resid 17 through 42 Processing helix chain 'F' and resid 42 through 53 Processing helix chain 'G' and resid 77 through 84 Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'G' and resid 138 through 153 removed outlier: 3.633A pdb=" N ILE G 142 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 200 Processing helix chain 'G' and resid 230 through 240 Processing helix chain 'H' and resid 273 through 277 Processing helix chain 'H' and resid 286 through 291 Processing helix chain 'H' and resid 292 through 295 removed outlier: 4.424A pdb=" N LEU H 295 " --> pdb=" O LYS H 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 292 through 295' Processing helix chain 'H' and resid 299 through 321 Processing helix chain 'H' and resid 329 through 337 Processing helix chain 'H' and resid 338 through 351 removed outlier: 3.545A pdb=" N MET H 351 " --> pdb=" O ILE H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 390 Processing helix chain 'H' and resid 391 through 416 removed outlier: 4.285A pdb=" N TRP H 395 " --> pdb=" O PHE H 391 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE H 396 " --> pdb=" O ARG H 392 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU H 397 " --> pdb=" O ASN H 393 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG H 414 " --> pdb=" O GLU H 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 419 through 443 removed outlier: 3.519A pdb=" N VAL H 423 " --> pdb=" O PRO H 419 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY H 443 " --> pdb=" O LEU H 439 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 3 through 15 Proline residue: K 12 - end of helix Processing helix chain 'K' and resid 17 through 42 Processing helix chain 'K' and resid 42 through 53 Processing helix chain 'L' and resid 77 through 84 Processing helix chain 'L' and resid 130 through 135 Processing helix chain 'L' and resid 138 through 153 removed outlier: 3.633A pdb=" N ILE L 142 " --> pdb=" O SER L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 200 Processing helix chain 'L' and resid 230 through 240 Processing helix chain 'M' and resid 273 through 277 Processing helix chain 'M' and resid 286 through 291 Processing helix chain 'M' and resid 292 through 295 removed outlier: 4.424A pdb=" N LEU M 295 " --> pdb=" O LYS M 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 292 through 295' Processing helix chain 'M' and resid 299 through 321 Processing helix chain 'M' and resid 329 through 337 Processing helix chain 'M' and resid 338 through 351 removed outlier: 3.546A pdb=" N MET M 351 " --> pdb=" O ILE M 347 " (cutoff:3.500A) Processing helix chain 'M' and resid 387 through 390 Processing helix chain 'M' and resid 391 through 416 removed outlier: 4.285A pdb=" N TRP M 395 " --> pdb=" O PHE M 391 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE M 396 " --> pdb=" O ARG M 392 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU M 397 " --> pdb=" O ASN M 393 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG M 414 " --> pdb=" O GLU M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 419 through 443 removed outlier: 3.519A pdb=" N VAL M 423 " --> pdb=" O PRO M 419 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY M 443 " --> pdb=" O LEU M 439 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 65 Processing helix chain 'O' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 62 through 64 removed outlier: 3.581A pdb=" N THR B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 94 removed outlier: 3.623A pdb=" N GLN B 176 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 163 " --> pdb=" O GLN B 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 271 through 272 Processing sheet with id=AA4, first strand: chain 'C' and resid 380 through 381 Processing sheet with id=AA5, first strand: chain 'C' and resid 447 through 450 Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 13 removed outlier: 5.830A pdb=" N MET D 11 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP D 34 " --> pdb=" O TRP D 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13 removed outlier: 5.830A pdb=" N MET D 11 " --> pdb=" O GLU D 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.222A pdb=" N GLY E 10 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET E 34 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG E 44 " --> pdb=" O THR E 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.222A pdb=" N GLY E 10 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N CYS E 96 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP E 112 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 17 through 22 Processing sheet with id=AB3, first strand: chain 'G' and resid 62 through 64 removed outlier: 3.582A pdb=" N THR G 68 " --> pdb=" O ILE G 64 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 90 through 94 removed outlier: 3.623A pdb=" N GLN G 176 " --> pdb=" O LEU G 163 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 163 " --> pdb=" O GLN G 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 271 through 272 Processing sheet with id=AB6, first strand: chain 'H' and resid 380 through 381 Processing sheet with id=AB7, first strand: chain 'H' and resid 447 through 450 Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.830A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP I 34 " --> pdb=" O TRP I 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.830A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.222A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG J 44 " --> pdb=" O THR J 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.222A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N CYS J 96 " --> pdb=" O TRP J 112 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP J 112 " --> pdb=" O CYS J 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 17 through 22 Processing sheet with id=AC5, first strand: chain 'L' and resid 62 through 64 removed outlier: 3.581A pdb=" N THR L 68 " --> pdb=" O ILE L 64 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 90 through 94 removed outlier: 3.623A pdb=" N GLN L 176 " --> pdb=" O LEU L 163 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU L 163 " --> pdb=" O GLN L 176 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 271 through 272 Processing sheet with id=AC8, first strand: chain 'M' and resid 380 through 381 Processing sheet with id=AC9, first strand: chain 'M' and resid 447 through 450 Processing sheet with id=AD1, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'N' and resid 10 through 13 removed outlier: 5.829A pdb=" N MET N 11 " --> pdb=" O GLU N 104 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP N 34 " --> pdb=" O TRP N 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 10 through 13 removed outlier: 5.829A pdb=" N MET N 11 " --> pdb=" O GLU N 104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.223A pdb=" N GLY O 10 " --> pdb=" O THR O 119 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET O 34 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG O 44 " --> pdb=" O THR O 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.223A pdb=" N GLY O 10 " --> pdb=" O THR O 119 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N CYS O 96 " --> pdb=" O TRP O 112 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TRP O 112 " --> pdb=" O CYS O 96 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 17 through 22 792 hydrogen bonds defined for protein. 2061 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 1.79 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: 5229 1.34 - 1.46: 4376 1.46 - 1.58: 7621 1.58 - 1.70: 0 1.70 - 1.82: 183 Bond restraints: 17409 Sorted by residual: bond pdb=" CB ASP J 42 " pdb=" CG ASP J 42 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.21e+00 bond pdb=" CB ASP E 42 " pdb=" CG ASP E 42 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.20e+00 bond pdb=" CB ASP O 42 " pdb=" CG ASP O 42 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.18e+00 bond pdb=" CA ASP J 42 " pdb=" CB ASP J 42 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.66e-02 3.63e+03 1.00e+00 bond pdb=" CA ASP E 42 " pdb=" CB ASP E 42 " ideal model delta sigma weight residual 1.528 1.545 -0.016 1.66e-02 3.63e+03 9.70e-01 ... (remaining 17404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.45: 23466 4.45 - 8.90: 87 8.90 - 13.35: 3 13.35 - 17.81: 6 17.81 - 22.26: 3 Bond angle restraints: 23565 Sorted by residual: angle pdb=" C ALA G 106 " pdb=" CA ALA G 106 " pdb=" CB ALA G 106 " ideal model delta sigma weight residual 109.70 87.44 22.26 1.81e+00 3.05e-01 1.51e+02 angle pdb=" C ALA L 106 " pdb=" CA ALA L 106 " pdb=" CB ALA L 106 " ideal model delta sigma weight residual 109.70 87.46 22.24 1.81e+00 3.05e-01 1.51e+02 angle pdb=" C ALA B 106 " pdb=" CA ALA B 106 " pdb=" CB ALA B 106 " ideal model delta sigma weight residual 109.70 87.46 22.24 1.81e+00 3.05e-01 1.51e+02 angle pdb=" N ALA L 106 " pdb=" CA ALA L 106 " pdb=" C ALA L 106 " ideal model delta sigma weight residual 108.76 91.00 17.76 1.69e+00 3.50e-01 1.10e+02 angle pdb=" N ALA B 106 " pdb=" CA ALA B 106 " pdb=" C ALA B 106 " ideal model delta sigma weight residual 108.76 91.00 17.76 1.69e+00 3.50e-01 1.10e+02 ... (remaining 23560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.88: 8556 13.88 - 27.76: 1261 27.76 - 41.63: 659 41.63 - 55.51: 231 55.51 - 69.39: 60 Dihedral angle restraints: 10767 sinusoidal: 4743 harmonic: 6024 Sorted by residual: dihedral pdb=" C ALA G 106 " pdb=" N ALA G 106 " pdb=" CA ALA G 106 " pdb=" CB ALA G 106 " ideal model delta harmonic sigma weight residual -122.60 -87.65 -34.95 0 2.50e+00 1.60e-01 1.95e+02 dihedral pdb=" C ALA L 106 " pdb=" N ALA L 106 " pdb=" CA ALA L 106 " pdb=" CB ALA L 106 " ideal model delta harmonic sigma weight residual -122.60 -87.66 -34.94 0 2.50e+00 1.60e-01 1.95e+02 dihedral pdb=" C ALA B 106 " pdb=" N ALA B 106 " pdb=" CA ALA B 106 " pdb=" CB ALA B 106 " ideal model delta harmonic sigma weight residual -122.60 -87.67 -34.93 0 2.50e+00 1.60e-01 1.95e+02 ... (remaining 10764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 2643 0.145 - 0.289: 6 0.289 - 0.434: 3 0.434 - 0.578: 0 0.578 - 0.723: 6 Chirality restraints: 2658 Sorted by residual: chirality pdb=" CA ALA B 106 " pdb=" N ALA B 106 " pdb=" C ALA B 106 " pdb=" CB ALA B 106 " both_signs ideal model delta sigma weight residual False 2.48 3.21 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ALA G 106 " pdb=" N ALA G 106 " pdb=" C ALA G 106 " pdb=" CB ALA G 106 " both_signs ideal model delta sigma weight residual False 2.48 3.21 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA ALA L 106 " pdb=" N ALA L 106 " pdb=" C ALA L 106 " pdb=" CB ALA L 106 " both_signs ideal model delta sigma weight residual False 2.48 3.21 -0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 2655 not shown) Planarity restraints: 2946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 28 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.86e+00 pdb=" C SER E 28 " 0.038 2.00e-02 2.50e+03 pdb=" O SER E 28 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE E 29 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER O 28 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C SER O 28 " 0.038 2.00e-02 2.50e+03 pdb=" O SER O 28 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE O 29 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER J 28 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C SER J 28 " 0.038 2.00e-02 2.50e+03 pdb=" O SER J 28 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE J 29 " -0.013 2.00e-02 2.50e+03 ... (remaining 2943 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1172 2.73 - 3.27: 16562 3.27 - 3.82: 27834 3.82 - 4.36: 30117 4.36 - 4.90: 53568 Nonbonded interactions: 129253 Sorted by model distance: nonbonded pdb=" O VAL I 29 " pdb=" OH TYR I 70 " model vdw 2.190 3.040 nonbonded pdb=" O VAL D 29 " pdb=" OH TYR D 70 " model vdw 2.190 3.040 nonbonded pdb=" O VAL N 29 " pdb=" OH TYR N 70 " model vdw 2.191 3.040 nonbonded pdb=" O SER F 41 " pdb=" NH2 ARG H 483 " model vdw 2.198 3.120 nonbonded pdb=" O SER A 41 " pdb=" NH2 ARG C 483 " model vdw 2.198 3.120 ... (remaining 129248 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'R' selection = chain 'W' selection = chain 'Y' selection = chain 'b' selection = chain 'h' selection = chain 'n' } 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: 5.060 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.360 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 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 : 0.003 0.089 17472 Z= 0.180 Angle : 0.790 22.257 23718 Z= 0.415 Chirality : 0.053 0.723 2658 Planarity : 0.004 0.041 2925 Dihedral : 17.503 69.387 6810 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.85 % Allowed : 32.56 % Favored : 62.59 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 10.00 % 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: -0.03 (0.19), residues: 2037 helix: 1.55 (0.21), residues: 573 sheet: 0.06 (0.25), residues: 411 loop : -0.94 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 60 TYR 0.008 0.001 TYR O 111 PHE 0.011 0.001 PHE E 68 TRP 0.014 0.001 TRP C 275 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00287 (17409) covalent geometry : angle 0.77589 (23565) SS BOND : bond 0.00438 ( 27) SS BOND : angle 0.87926 ( 54) hydrogen bonds : bond 0.12422 ( 774) hydrogen bonds : angle 6.30080 ( 2061) Misc. bond : bond 0.08907 ( 3) link_BETA1-4 : bond 0.00630 ( 12) link_BETA1-4 : angle 1.88731 ( 36) link_NAG-ASN : bond 0.00437 ( 21) link_NAG-ASN : angle 2.63351 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 316 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 LYS cc_start: 0.8209 (mttt) cc_final: 0.8004 (mmtp) REVERT: B 158 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7724 (pp) REVERT: C 304 MET cc_start: 0.6334 (mmm) cc_final: 0.6121 (mmm) REVERT: C 406 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6210 (tmm) REVERT: C 482 ARG cc_start: 0.6238 (mtt180) cc_final: 0.5727 (mmp-170) REVERT: D 1 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: D 32 MET cc_start: 0.7481 (ttm) cc_final: 0.7136 (ttt) REVERT: E 82 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8080 (tp40) REVERT: E 109 MET cc_start: 0.7791 (mtt) cc_final: 0.7577 (mtp) REVERT: E 112 TRP cc_start: 0.7963 (m-10) cc_final: 0.6958 (m100) REVERT: G 213 CYS cc_start: 0.6540 (OUTLIER) cc_final: 0.6313 (t) REVERT: H 304 MET cc_start: 0.6370 (mmm) cc_final: 0.6104 (mmm) REVERT: H 406 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6271 (tmm) REVERT: H 482 ARG cc_start: 0.6193 (mtt180) cc_final: 0.5755 (mmp-170) REVERT: I 1 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: I 32 MET cc_start: 0.7400 (ttm) cc_final: 0.6956 (ttt) REVERT: I 104 GLU cc_start: 0.7234 (mp0) cc_final: 0.6837 (mp0) REVERT: L 229 ASP cc_start: 0.7807 (p0) cc_final: 0.7562 (p0) REVERT: M 304 MET cc_start: 0.6434 (mmm) cc_final: 0.6082 (mmm) REVERT: M 406 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6229 (tmm) REVERT: M 482 ARG cc_start: 0.6129 (mtt180) cc_final: 0.5696 (tpm170) REVERT: N 1 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: N 32 MET cc_start: 0.7470 (ttm) cc_final: 0.7080 (ttt) REVERT: O 53 ARG cc_start: 0.7379 (ttp-170) cc_final: 0.6999 (ttp-170) outliers start: 88 outliers final: 66 residues processed: 367 average time/residue: 0.0962 time to fit residues: 56.8586 Evaluate side-chains 362 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 288 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 180 SER Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 311 ASN Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 318 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 390 ASP Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain I residue 1 GLN Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 122 TYR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 213 CYS Chi-restraints excluded: chain L residue 226 CYS Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 299 SER Chi-restraints excluded: chain M residue 317 THR Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 390 ASP Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 429 SER Chi-restraints excluded: chain M residue 430 THR Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 74 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.0670 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN C 327 ASN C 366 HIS D 6 GLN D 91 ASN E 39 GLN E 77 ASN E 82 GLN ** G 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 GLN H 327 ASN H 366 HIS I 6 GLN I 91 ASN J 39 GLN J 77 ASN ** L 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 GLN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 230 HIS L 244 GLN M 327 ASN M 366 HIS N 6 GLN N 91 ASN O 39 GLN O 77 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.178594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.146459 restraints weight = 24972.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.149426 restraints weight = 18058.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.151549 restraints weight = 14516.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.153059 restraints weight = 12448.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.154024 restraints weight = 11137.466| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17472 Z= 0.158 Angle : 0.661 7.487 23718 Z= 0.333 Chirality : 0.043 0.335 2658 Planarity : 0.004 0.044 2925 Dihedral : 7.804 57.324 3067 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 7.71 % Allowed : 29.42 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.04 (0.19), residues: 2037 helix: 1.57 (0.21), residues: 576 sheet: 0.14 (0.25), residues: 405 loop : -1.02 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 460 TYR 0.013 0.001 TYR L 157 PHE 0.016 0.002 PHE B 175 TRP 0.018 0.001 TRP M 275 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00354 (17409) covalent geometry : angle 0.63664 (23565) SS BOND : bond 0.00868 ( 27) SS BOND : angle 1.04876 ( 54) hydrogen bonds : bond 0.04655 ( 774) hydrogen bonds : angle 5.46309 ( 2061) Misc. bond : bond 0.00223 ( 3) link_BETA1-4 : bond 0.00666 ( 12) link_BETA1-4 : angle 2.03161 ( 36) link_NAG-ASN : bond 0.00385 ( 21) link_NAG-ASN : angle 3.07109 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 305 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4397 (OUTLIER) cc_final: 0.4181 (mp) REVERT: B 96 LYS cc_start: 0.8348 (mttt) cc_final: 0.8103 (mmtp) REVERT: B 150 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.6961 (m-40) REVERT: B 158 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7439 (pp) REVERT: B 159 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8025 (m-30) REVERT: C 304 MET cc_start: 0.6444 (mmm) cc_final: 0.6237 (mmm) REVERT: C 406 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6178 (tmm) REVERT: D 78 GLU cc_start: 0.7425 (mp0) cc_final: 0.7111 (mp0) REVERT: D 103 LEU cc_start: 0.8725 (tt) cc_final: 0.8478 (tp) REVERT: E 60 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7427 (m90) REVERT: F 43 LEU cc_start: 0.4321 (OUTLIER) cc_final: 0.3999 (mp) REVERT: G 150 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7049 (m-40) REVERT: G 199 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8046 (mp) REVERT: H 304 MET cc_start: 0.6428 (mmm) cc_final: 0.6215 (mmm) REVERT: H 406 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.6477 (tmm) REVERT: I 104 GLU cc_start: 0.7282 (mp0) cc_final: 0.7071 (mp0) REVERT: J 35 SER cc_start: 0.9350 (p) cc_final: 0.9074 (p) REVERT: K 43 LEU cc_start: 0.4386 (OUTLIER) cc_final: 0.4078 (mp) REVERT: L 150 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7098 (m-40) REVERT: L 199 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7699 (mp) REVERT: M 304 MET cc_start: 0.6452 (mmm) cc_final: 0.6113 (mmm) REVERT: M 406 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6298 (tmm) REVERT: O 35 SER cc_start: 0.9386 (p) cc_final: 0.9128 (p) REVERT: O 60 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7872 (m90) REVERT: O 102 TYR cc_start: 0.8147 (m-10) cc_final: 0.7929 (m-10) outliers start: 140 outliers final: 82 residues processed: 415 average time/residue: 0.0904 time to fit residues: 61.3946 Evaluate side-chains 390 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 293 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 46 TRP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 46 TRP Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain J residue 60 HIS Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 71 GLN Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 122 TYR Chi-restraints excluded: chain L residue 150 ASN Chi-restraints excluded: chain L residue 158 LEU Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 174 ILE Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 226 CYS Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain M residue 299 SER Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 464 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 91 ASN Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 60 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 43 optimal weight: 30.0000 chunk 48 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 177 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS C 327 ASN D 91 ASN ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 HIS H 327 ASN I 91 ASN L 71 GLN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN O 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.178276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.146446 restraints weight = 25256.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.149644 restraints weight = 17843.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.151843 restraints weight = 14089.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.153425 restraints weight = 11966.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.154337 restraints weight = 10622.765| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17472 Z= 0.128 Angle : 0.631 9.190 23718 Z= 0.315 Chirality : 0.042 0.315 2658 Planarity : 0.004 0.043 2925 Dihedral : 6.972 58.723 2996 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 7.44 % Allowed : 29.75 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.03 (0.19), residues: 2037 helix: 1.64 (0.21), residues: 576 sheet: 0.14 (0.25), residues: 405 loop : -1.05 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.010 0.001 TYR G 157 PHE 0.016 0.001 PHE B 175 TRP 0.020 0.001 TRP H 275 HIS 0.003 0.001 HIS L 230 Details of bonding type rmsd covalent geometry : bond 0.00278 (17409) covalent geometry : angle 0.60806 (23565) SS BOND : bond 0.00537 ( 27) SS BOND : angle 0.77518 ( 54) hydrogen bonds : bond 0.04366 ( 774) hydrogen bonds : angle 5.22775 ( 2061) Misc. bond : bond 0.00014 ( 3) link_BETA1-4 : bond 0.00708 ( 12) link_BETA1-4 : angle 1.97762 ( 36) link_NAG-ASN : bond 0.00423 ( 21) link_NAG-ASN : angle 2.97783 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 305 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4441 (OUTLIER) cc_final: 0.4170 (mp) REVERT: B 96 LYS cc_start: 0.8313 (mttt) cc_final: 0.8097 (mmtp) REVERT: B 150 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.6963 (m-40) REVERT: B 159 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: C 336 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7693 (mp) REVERT: C 406 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6194 (tmm) REVERT: E 60 HIS cc_start: 0.8090 (OUTLIER) cc_final: 0.7350 (m90) REVERT: F 43 LEU cc_start: 0.4360 (OUTLIER) cc_final: 0.4049 (mp) REVERT: G 150 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7038 (m-40) REVERT: G 199 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7985 (mp) REVERT: H 304 MET cc_start: 0.6325 (mmm) cc_final: 0.6110 (mmm) REVERT: H 406 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6501 (tmm) REVERT: I 104 GLU cc_start: 0.7353 (mp0) cc_final: 0.7090 (mp0) REVERT: K 43 LEU cc_start: 0.4331 (OUTLIER) cc_final: 0.4018 (mp) REVERT: L 150 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7133 (m-40) REVERT: L 199 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7647 (mp) REVERT: M 304 MET cc_start: 0.6413 (mmm) cc_final: 0.6192 (mmm) REVERT: M 336 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7716 (mp) REVERT: M 406 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6277 (tmm) REVERT: O 35 SER cc_start: 0.9399 (p) cc_final: 0.9113 (p) REVERT: O 53 ARG cc_start: 0.7283 (ttp-170) cc_final: 0.7030 (ttp-170) REVERT: O 60 HIS cc_start: 0.8055 (OUTLIER) cc_final: 0.7784 (m90) outliers start: 135 outliers final: 81 residues processed: 403 average time/residue: 0.1006 time to fit residues: 66.5686 Evaluate side-chains 387 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 290 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 46 TRP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 46 TRP Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 60 HIS Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 71 GLN Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 122 TYR Chi-restraints excluded: chain L residue 150 ASN Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 158 LEU Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 369 SER Chi-restraints excluded: chain M residue 403 ILE Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 430 THR Chi-restraints excluded: chain M residue 464 LEU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 91 ASN Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 114 optimal weight: 0.0000 chunk 94 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN E 39 GLN G 71 GLN ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 ASN J 39 GLN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.176155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.144152 restraints weight = 25332.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.147203 restraints weight = 18022.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.149376 restraints weight = 14367.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150720 restraints weight = 12267.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.151896 restraints weight = 11010.907| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17472 Z= 0.157 Angle : 0.654 7.635 23718 Z= 0.325 Chirality : 0.043 0.332 2658 Planarity : 0.004 0.042 2925 Dihedral : 6.862 58.742 2984 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 8.43 % Allowed : 28.76 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.17 (0.19), residues: 2037 helix: 1.53 (0.21), residues: 576 sheet: 0.14 (0.26), residues: 399 loop : -1.17 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 90 TYR 0.017 0.001 TYR D 31 PHE 0.017 0.002 PHE B 175 TRP 0.023 0.001 TRP M 275 HIS 0.004 0.001 HIS G 230 Details of bonding type rmsd covalent geometry : bond 0.00357 (17409) covalent geometry : angle 0.63050 (23565) SS BOND : bond 0.00415 ( 27) SS BOND : angle 0.97300 ( 54) hydrogen bonds : bond 0.04511 ( 774) hydrogen bonds : angle 5.20577 ( 2061) Misc. bond : bond 0.00008 ( 3) link_BETA1-4 : bond 0.00647 ( 12) link_BETA1-4 : angle 1.98483 ( 36) link_NAG-ASN : bond 0.00352 ( 21) link_NAG-ASN : angle 3.06407 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 291 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4465 (OUTLIER) cc_final: 0.4181 (mp) REVERT: B 150 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.6967 (m-40) REVERT: B 159 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: C 336 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7704 (mp) REVERT: C 406 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6154 (tmm) REVERT: E 60 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7374 (m90) REVERT: F 43 LEU cc_start: 0.4301 (OUTLIER) cc_final: 0.4011 (mp) REVERT: G 150 ASN cc_start: 0.7874 (OUTLIER) cc_final: 0.7212 (m-40) REVERT: G 199 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8017 (mp) REVERT: H 336 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7647 (mp) REVERT: H 406 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6487 (tmm) REVERT: I 104 GLU cc_start: 0.7374 (mp0) cc_final: 0.7141 (mp0) REVERT: K 43 LEU cc_start: 0.4381 (OUTLIER) cc_final: 0.4102 (mp) REVERT: L 150 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7212 (m-40) REVERT: L 199 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7748 (mp) REVERT: M 304 MET cc_start: 0.6429 (mmm) cc_final: 0.6140 (mmm) REVERT: M 336 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7750 (mp) REVERT: M 406 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6296 (tmm) REVERT: N 81 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.7111 (t0) REVERT: O 35 SER cc_start: 0.9472 (p) cc_final: 0.9189 (p) REVERT: O 60 HIS cc_start: 0.8077 (OUTLIER) cc_final: 0.7802 (m90) outliers start: 153 outliers final: 106 residues processed: 392 average time/residue: 0.0922 time to fit residues: 60.0865 Evaluate side-chains 410 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 286 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 46 TRP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 311 ASN Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain H residue 464 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 46 TRP Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 60 HIS Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 71 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 122 TYR Chi-restraints excluded: chain L residue 132 MET Chi-restraints excluded: chain L residue 150 ASN Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 226 CYS Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 403 ILE Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 430 THR Chi-restraints excluded: chain M residue 464 LEU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 89 GLU Chi-restraints excluded: chain O residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 60.6315 > 50: distance: 18 - 23: 6.434 distance: 23 - 24: 3.970 distance: 24 - 25: 13.650 distance: 24 - 27: 8.392 distance: 25 - 26: 19.649 distance: 25 - 28: 8.720 distance: 26 - 44: 15.629 distance: 28 - 29: 5.125 distance: 29 - 30: 10.726 distance: 30 - 31: 9.849 distance: 30 - 36: 4.949 distance: 31 - 50: 39.191 distance: 33 - 34: 7.473 distance: 33 - 35: 5.289 distance: 36 - 37: 13.236 distance: 37 - 38: 7.252 distance: 37 - 40: 6.216 distance: 38 - 39: 9.287 distance: 38 - 44: 14.023 distance: 39 - 64: 12.699 distance: 40 - 41: 11.325 distance: 41 - 42: 8.376 distance: 42 - 43: 5.634 distance: 44 - 45: 11.021 distance: 45 - 46: 15.720 distance: 45 - 48: 6.823 distance: 46 - 47: 14.111 distance: 46 - 50: 12.037 distance: 48 - 49: 6.828 distance: 50 - 51: 12.756 distance: 51 - 52: 12.230 distance: 51 - 54: 10.651 distance: 52 - 53: 27.896 distance: 52 - 64: 40.383 distance: 54 - 55: 15.624 distance: 55 - 56: 9.990 distance: 55 - 57: 15.294 distance: 56 - 58: 13.985 distance: 57 - 59: 14.582 distance: 57 - 60: 18.800 distance: 58 - 59: 4.928 distance: 59 - 61: 12.038 distance: 60 - 62: 12.490 distance: 61 - 63: 18.056 distance: 62 - 63: 16.553 distance: 64 - 65: 17.942 distance: 65 - 66: 38.932 distance: 65 - 68: 11.259 distance: 66 - 67: 8.864 distance: 66 - 70: 21.618 distance: 68 - 69: 28.750 distance: 69 - 145: 22.446 distance: 70 - 71: 36.713 distance: 71 - 72: 29.840 distance: 71 - 74: 9.803 distance: 72 - 76: 31.342 distance: 74 - 75: 19.504 distance: 76 - 77: 11.743 distance: 77 - 78: 4.737 distance: 77 - 80: 11.091 distance: 78 - 85: 6.570 distance: 80 - 81: 14.614 distance: 81 - 82: 20.748 distance: 82 - 83: 25.340 distance: 83 - 84: 10.100 distance: 85 - 86: 26.413 distance: 86 - 87: 27.070 distance: 86 - 89: 22.645 distance: 87 - 88: 20.414 distance: 87 - 91: 17.167 distance: 89 - 90: 4.605 distance: 91 - 92: 6.406 distance: 92 - 95: 20.584 distance: 93 - 94: 3.988 distance: 93 - 99: 3.628 distance: 94 - 123: 3.017 distance: 95 - 96: 6.875 distance: 96 - 97: 16.782 distance: 96 - 98: 17.655