Starting phenix.real_space_refine on Fri Jul 3 12:42:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgf_50399/07_2026/9fgf_50399.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgf_50399/07_2026/9fgf_50399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fgf_50399/07_2026/9fgf_50399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgf_50399/07_2026/9fgf_50399.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgf_50399/07_2026/9fgf_50399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgf_50399/07_2026/9fgf_50399.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 78 5.16 5 Cl 3 4.86 5 C 9332 2.51 5 N 2303 2.21 5 O 2637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14359 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2801 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 345, 2793 Classifications: {'peptide': 345} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 330} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 345, 2793 Classifications: {'peptide': 345} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 330} Chain breaks: 1 bond proxies already assigned to first conformer: 2855 Chain: "B" Number of atoms: 2751 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2742 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 334, 2742 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 bond proxies already assigned to first conformer: 2804 Chain: "C" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2720 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 343, 2780 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 343, 2780 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 bond proxies already assigned to first conformer: 2842 Chain: "E" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2740 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "e" 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: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 1, 'PIO': 1, 'R16': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 1, 'PIO': 1, 'R16': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.84, per 1000 atoms: 0.34 Number of scatterers: 14359 At special positions: 0 Unit cell: (96.408, 99.704, 136.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 78 16.00 P 6 15.00 O 2637 8.00 N 2303 7.00 C 9332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 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 ALPHA1-2 " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " ALPHA1-3 " BMA F 3 " - " MAN F 6 " " MAN F 4 " - " MAN F 5 " " BMA G 3 " - " MAN G 6 " " MAN G 4 " - " MAN G 5 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 8 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 9 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG C 502 " - " ASN C 208 " " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN E 149 " " NAG a 1 " - " ASN A 111 " " NAG b 1 " - " ASN B 80 " " NAG d 1 " - " ASN D 111 " " NAG e 1 " - " ASN E 80 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 899.9 milliseconds 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3214 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 40.0% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 73 through 76 removed outlier: 3.748A pdb=" N LYS A 76 " --> pdb=" O GLU A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.426A pdb=" N ASP A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.716A pdb=" N SER A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 251 through 277 removed outlier: 3.800A pdb=" N SER A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.518A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 415 removed outlier: 3.824A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Proline residue: A 401 - end of helix removed outlier: 3.612A pdb=" N TYR A 415 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.513A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 237 removed outlier: 3.654A pdb=" N SER B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 246 through 272 Processing helix chain 'B' and resid 279 through 308 removed outlier: 3.574A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 447 removed outlier: 3.779A pdb=" N ILE B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 27 through 36 removed outlier: 3.563A pdb=" N LEU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 99 through 103 removed outlier: 4.014A pdb=" N MET C 102 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.596A pdb=" N ILE C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 252 Processing helix chain 'C' and resid 253 through 256 Processing helix chain 'C' and resid 261 through 280 Processing helix chain 'C' and resid 281 through 283 No H-bonds generated for 'chain 'C' and resid 281 through 283' Processing helix chain 'C' and resid 294 through 322 Processing helix chain 'C' and resid 409 through 436 removed outlier: 3.853A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.657A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.620A pdb=" N ASP D 145 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.662A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 277 removed outlier: 3.599A pdb=" N LEU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 310 removed outlier: 3.550A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 417 removed outlier: 3.993A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix removed outlier: 3.611A pdb=" N ASN D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 21 Processing helix chain 'E' and resid 70 through 73 removed outlier: 3.591A pdb=" N ALA E 73 " --> pdb=" O LYS E 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 73' Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 218 through 225 removed outlier: 3.534A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 237 removed outlier: 3.540A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 246 through 272 Processing helix chain 'E' and resid 279 through 308 removed outlier: 3.586A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 446 removed outlier: 3.702A pdb=" N ASP E 424 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 54 removed outlier: 6.547A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU A 59 " --> pdb=" O PRO A 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 71 current: chain 'A' and resid 126 through 138 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.333A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 51 removed outlier: 9.632A pdb=" N GLY B 39 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ARG B 68 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASN B 41 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TYR B 66 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ASP B 43 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLN B 64 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA B 45 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N TYR B 62 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE B 47 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR B 60 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 58 " --> pdb=" O MET B 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 68 current: chain 'B' and resid 123 through 135 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.135A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 51 through 66 removed outlier: 9.498A pdb=" N HIS C 54 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TYR C 83 " --> pdb=" O HIS C 54 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ASP C 56 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR C 81 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N TYR C 58 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA C 79 " --> pdb=" O TYR C 58 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASN C 60 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N PHE C 77 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE C 62 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP C 75 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR C 73 " --> pdb=" O PRO C 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 83 current: chain 'C' and resid 138 through 150 Processing sheet with id=AA6, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.568A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 39 through 49 current: chain 'D' and resid 59 through 71 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 71 current: chain 'D' and resid 126 through 138 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 99 through 101 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 99 through 101 current: chain 'D' and resid 208 through 221 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 36 through 51 removed outlier: 8.389A pdb=" N VAL E 38 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ARG E 68 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N MET E 40 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TYR E 66 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE E 42 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLN E 64 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE E 44 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR E 62 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL E 50 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP E 56 " --> pdb=" O VAL E 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 56 through 68 current: chain 'E' and resid 123 through 135 Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.104A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) 529 hydrogen bonds defined for protein. 1505 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: 2.39 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2250 1.32 - 1.45: 4300 1.45 - 1.57: 8022 1.57 - 1.69: 8 1.69 - 1.81: 135 Bond restraints: 14715 Sorted by residual: bond pdb=" O4 PIO A 502 " pdb=" P4 PIO A 502 " ideal model delta sigma weight residual 1.710 1.595 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" O4 PIO D 502 " pdb=" P4 PIO D 502 " ideal model delta sigma weight residual 1.710 1.596 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" O5 PIO D 502 " pdb=" P5 PIO D 502 " ideal model delta sigma weight residual 1.699 1.611 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" O5 PIO A 502 " pdb=" P5 PIO A 502 " ideal model delta sigma weight residual 1.699 1.613 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" O13 PIO D 502 " pdb=" P1 PIO D 502 " ideal model delta sigma weight residual 1.651 1.590 0.061 2.00e-02 2.50e+03 9.30e+00 ... (remaining 14710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 19692 2.10 - 4.20: 245 4.20 - 6.30: 38 6.30 - 8.41: 2 8.41 - 10.51: 2 Bond angle restraints: 19979 Sorted by residual: angle pdb=" C4 PIO A 502 " pdb=" O4 PIO A 502 " pdb=" P4 PIO A 502 " ideal model delta sigma weight residual 121.90 132.41 -10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C4 PIO D 502 " pdb=" O4 PIO D 502 " pdb=" P4 PIO D 502 " ideal model delta sigma weight residual 121.90 131.74 -9.84 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C VAL E 109 " pdb=" N THR E 110 " pdb=" CA THR E 110 " ideal model delta sigma weight residual 121.70 127.44 -5.74 1.80e+00 3.09e-01 1.02e+01 angle pdb=" C MET A 112 " pdb=" N THR A 113 " pdb=" CA THR A 113 " ideal model delta sigma weight residual 121.70 127.33 -5.63 1.80e+00 3.09e-01 9.79e+00 angle pdb=" C VAL B 109 " pdb=" N THR B 110 " pdb=" CA THR B 110 " ideal model delta sigma weight residual 121.70 127.05 -5.35 1.80e+00 3.09e-01 8.83e+00 ... (remaining 19974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.49: 8689 21.49 - 42.97: 261 42.97 - 64.46: 31 64.46 - 85.94: 33 85.94 - 107.43: 16 Dihedral angle restraints: 9030 sinusoidal: 4037 harmonic: 4993 Sorted by residual: dihedral pdb=" CA GLY B 170 " pdb=" C GLY B 170 " pdb=" N GLY B 171 " pdb=" CA GLY B 171 " ideal model delta harmonic sigma weight residual -180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" O4 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.72 107.43 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C3 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sinusoidal sigma weight residual 47.62 -58.02 105.64 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 9027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1953 0.053 - 0.105: 331 0.105 - 0.158: 52 0.158 - 0.210: 3 0.210 - 0.263: 3 Chirality restraints: 2342 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C5 BMA d 3 " pdb=" C4 BMA d 3 " pdb=" C6 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2339 not shown) Planarity restraints: 2412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 275 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 276 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 277 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO D 278 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 278 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 278 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 310 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO B 311 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 311 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 311 " -0.020 5.00e-02 4.00e+02 ... (remaining 2409 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1258 2.74 - 3.28: 13944 3.28 - 3.82: 24914 3.82 - 4.36: 31249 4.36 - 4.90: 51598 Nonbonded interactions: 122963 Sorted by model distance: nonbonded pdb=" O7 NAG a 2 " pdb=" O4 MAN a 9 " model vdw 2.206 3.040 nonbonded pdb=" O LYS C 184 " pdb=" O6 NAG C 502 " model vdw 2.229 3.040 nonbonded pdb=" NH1 ARG C 284 " pdb=" O VAL C 290 " model vdw 2.238 3.120 nonbonded pdb=" OG SER D 390 " pdb=" O11 PIO D 502 " model vdw 2.280 3.040 nonbonded pdb=" OG1 THR E 202 " pdb=" OH TYR E 205 " model vdw 2.281 3.040 ... (remaining 122958 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' and (resid 13 through 66 or resid 68 through 320 or resid 384 through \ 504)) selection = (chain 'D' and (resid 13 through 66 or resid 68 through 504)) } ncs_group { reference = (chain 'B' and (resid 10 through 65 or resid 67 through 312 or resid 419 through \ 3101)) selection = (chain 'E' and (resid 10 through 65 or resid 67 through 3201)) } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'b' selection = chain 'e' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.090 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 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 : 0.004 0.115 14751 Z= 0.190 Angle : 0.572 10.507 20082 Z= 0.257 Chirality : 0.042 0.263 2342 Planarity : 0.003 0.037 2405 Dihedral : 12.532 107.430 5801 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.59 % Allowed : 3.09 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.31 % 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 are not related in a simple way. whole: 0.38 (0.21), residues: 1669 helix: 0.52 (0.21), residues: 572 sheet: 0.42 (0.26), residues: 442 loop : 0.10 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 194 TYR 0.015 0.001 TYR E 277 PHE 0.012 0.001 PHE C 113 TRP 0.006 0.001 TRP B 426 HIS 0.002 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (14715) covalent geometry : angle 0.56314 / 0.25 (19979) SS BOND : bond 0.00197 / 0.09 ( 5) SS BOND : angle 0.34534 / 0.20 ( 10) hydrogen bonds : bond 0.21803 / 14.62 ( 529) hydrogen bonds : angle 7.27325 / 4.86 ( 1505) link_ALPHA1-2 : bond 0.00474 / 0.24 ( 2) link_ALPHA1-2 : angle 1.41252 / 0.75 ( 6) link_ALPHA1-3 : bond 0.00496 / 0.29 ( 7) link_ALPHA1-3 : angle 1.03181 / 0.66 ( 21) link_ALPHA1-6 : bond 0.00502 / 0.24 ( 5) link_ALPHA1-6 : angle 1.60430 / 0.82 ( 15) link_BETA1-4 : bond 0.00451 / 0.23 ( 10) link_BETA1-4 : angle 1.84921 / 1.32 ( 30) link_NAG-ASN : bond 0.00167 / 0.08 ( 7) link_NAG-ASN : angle 1.72575 / 1.17 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 239 time to evaluate : 0.589 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 246 average time/residue: 0.7684 time to fit residues: 203.5666 Evaluate side-chains 134 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 287 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN B 65 GLN B 85 ASN C 200 GLN C 239 GLN D 102 HIS D 229 GLN D 242 GLN E 64 GLN E 113 ASN E 217 ASN E 265 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.085810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.065778 restraints weight = 45797.482| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.29 r_work: 0.2583 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14751 Z= 0.182 Angle : 0.598 10.109 20082 Z= 0.304 Chirality : 0.044 0.175 2342 Planarity : 0.005 0.053 2405 Dihedral : 10.055 86.548 2605 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.12 % Allowed : 10.59 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.31 % 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 are not related in a simple way. whole: 0.85 (0.21), residues: 1669 helix: 1.46 (0.21), residues: 571 sheet: 0.35 (0.26), residues: 428 loop : 0.06 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 136 TYR 0.019 0.001 TYR B 299 PHE 0.017 0.001 PHE A 304 TRP 0.011 0.001 TRP B 426 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (14715) covalent geometry : angle 0.58674 / 0.30 (19979) SS BOND : bond 0.00478 / 0.24 ( 5) SS BOND : angle 0.73593 / 0.45 ( 10) hydrogen bonds : bond 0.04403 / 2.97 ( 529) hydrogen bonds : angle 4.68969 / 3.21 ( 1505) link_ALPHA1-2 : bond 0.00412 / 0.21 ( 2) link_ALPHA1-2 : angle 1.72194 / 0.88 ( 6) link_ALPHA1-3 : bond 0.00707 / 0.38 ( 7) link_ALPHA1-3 : angle 1.89330 / 1.15 ( 21) link_ALPHA1-6 : bond 0.00571 / 0.29 ( 5) link_ALPHA1-6 : angle 1.82969 / 1.06 ( 15) link_BETA1-4 : bond 0.00289 / 0.17 ( 10) link_BETA1-4 : angle 1.81505 / 1.29 ( 30) link_NAG-ASN : bond 0.00281 / 0.14 ( 7) link_NAG-ASN : angle 1.67018 / 1.16 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.579 Fit side-chains REVERT: B 49 MET cc_start: 0.7411 (tmt) cc_final: 0.7103 (tmt) REVERT: C 71 GLU cc_start: 0.8891 (pt0) cc_final: 0.8685 (pt0) REVERT: C 85 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8234 (mpp-170) REVERT: C 150 GLU cc_start: 0.8781 (pp20) cc_final: 0.8248 (pp20) REVERT: C 178 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8504 (mm-30) REVERT: C 223 MET cc_start: 0.9102 (mmp) cc_final: 0.8780 (mmp) REVERT: C 254 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8075 (t) REVERT: C 409 LYS cc_start: 0.7493 (mmmt) cc_final: 0.7280 (mtpt) REVERT: D 17 ARG cc_start: 0.8343 (mtm110) cc_final: 0.7924 (ptm-80) REVERT: D 190 GLN cc_start: 0.8874 (pm20) cc_final: 0.8224 (pm20) outliers start: 17 outliers final: 6 residues processed: 143 average time/residue: 0.7120 time to fit residues: 110.7455 Evaluate side-chains 133 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 162 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 22 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN D 229 GLN D 242 GLN E 243 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.083860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.063564 restraints weight = 50470.619| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.43 r_work: 0.2536 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14751 Z= 0.196 Angle : 0.570 10.024 20082 Z= 0.286 Chirality : 0.044 0.248 2342 Planarity : 0.004 0.051 2405 Dihedral : 9.138 74.320 2605 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.51 % Allowed : 10.86 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.31 % 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 are not related in a simple way. whole: 0.96 (0.21), residues: 1669 helix: 1.78 (0.21), residues: 568 sheet: 0.33 (0.26), residues: 391 loop : -0.02 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 85 TYR 0.029 0.002 TYR B 299 PHE 0.024 0.002 PHE A 15 TRP 0.011 0.001 TRP B 426 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (14715) covalent geometry : angle 0.55884 / 0.28 (19979) SS BOND : bond 0.00602 / 0.35 ( 5) SS BOND : angle 0.96471 / 0.60 ( 10) hydrogen bonds : bond 0.04645 / 3.10 ( 529) hydrogen bonds : angle 4.44255 / 3.04 ( 1505) link_ALPHA1-2 : bond 0.00484 / 0.24 ( 2) link_ALPHA1-2 : angle 1.77708 / 0.91 ( 6) link_ALPHA1-3 : bond 0.00777 / 0.43 ( 7) link_ALPHA1-3 : angle 1.80846 / 1.08 ( 21) link_ALPHA1-6 : bond 0.00716 / 0.36 ( 5) link_ALPHA1-6 : angle 1.74556 / 1.01 ( 15) link_BETA1-4 : bond 0.00348 / 0.18 ( 10) link_BETA1-4 : angle 1.61495 / 1.09 ( 30) link_NAG-ASN : bond 0.00275 / 0.13 ( 7) link_NAG-ASN : angle 1.59965 / 1.09 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.576 Fit side-chains REVERT: B 49 MET cc_start: 0.7475 (tmt) cc_final: 0.6979 (tmt) REVERT: B 283 MET cc_start: 0.8929 (mmm) cc_final: 0.8685 (mmm) REVERT: C 85 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8294 (mpp-170) REVERT: C 150 GLU cc_start: 0.8860 (pp20) cc_final: 0.8384 (pp20) REVERT: C 178 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8700 (mm-30) REVERT: C 233 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8190 (ttt) REVERT: C 254 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8302 (t) REVERT: D 59 GLU cc_start: 0.8453 (pt0) cc_final: 0.8231 (tt0) REVERT: D 190 GLN cc_start: 0.8975 (pm20) cc_final: 0.8392 (pm20) REVERT: E 205 TYR cc_start: 0.8356 (m-80) cc_final: 0.8134 (m-80) outliers start: 23 outliers final: 3 residues processed: 153 average time/residue: 0.7433 time to fit residues: 123.1456 Evaluate side-chains 131 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 160 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.084554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.064769 restraints weight = 42187.966| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.17 r_work: 0.2564 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14751 Z= 0.146 Angle : 0.540 10.525 20082 Z= 0.268 Chirality : 0.043 0.243 2342 Planarity : 0.004 0.052 2405 Dihedral : 8.487 66.875 2605 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.32 % Allowed : 12.11 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.31 % 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 are not related in a simple way. whole: 1.10 (0.21), residues: 1669 helix: 2.00 (0.21), residues: 567 sheet: 0.33 (0.26), residues: 390 loop : 0.01 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 17 TYR 0.020 0.001 TYR E 299 PHE 0.014 0.001 PHE D 304 TRP 0.011 0.001 TRP B 426 HIS 0.003 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (14715) covalent geometry : angle 0.52939 / 0.27 (19979) SS BOND : bond 0.00413 / 0.24 ( 5) SS BOND : angle 0.74579 / 0.47 ( 10) hydrogen bonds : bond 0.03684 / 2.49 ( 529) hydrogen bonds : angle 4.27317 / 2.94 ( 1505) link_ALPHA1-2 : bond 0.00527 / 0.26 ( 2) link_ALPHA1-2 : angle 1.72740 / 0.89 ( 6) link_ALPHA1-3 : bond 0.00878 / 0.47 ( 7) link_ALPHA1-3 : angle 1.86792 / 1.11 ( 21) link_ALPHA1-6 : bond 0.01014 / 0.51 ( 5) link_ALPHA1-6 : angle 1.76111 / 1.02 ( 15) link_BETA1-4 : bond 0.00355 / 0.19 ( 10) link_BETA1-4 : angle 1.59097 / 1.10 ( 30) link_NAG-ASN : bond 0.00182 / 0.09 ( 7) link_NAG-ASN : angle 1.48999 / 1.03 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.433 Fit side-chains REVERT: A 21 ARG cc_start: 0.8554 (mmp-170) cc_final: 0.8226 (mmp-170) REVERT: A 89 LEU cc_start: 0.8799 (tp) cc_final: 0.8568 (tm) REVERT: A 190 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8666 (pm20) REVERT: B 49 MET cc_start: 0.7458 (tmt) cc_final: 0.6983 (tmt) REVERT: B 223 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8771 (tm) REVERT: B 245 ASP cc_start: 0.8721 (t0) cc_final: 0.8385 (t0) REVERT: C 71 GLU cc_start: 0.8887 (pt0) cc_final: 0.8608 (pt0) REVERT: C 85 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8221 (mpp-170) REVERT: C 150 GLU cc_start: 0.8834 (pp20) cc_final: 0.8200 (pp20) REVERT: C 178 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8698 (mm-30) REVERT: C 223 MET cc_start: 0.9108 (mmp) cc_final: 0.8771 (mmp) REVERT: C 233 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.8040 (ttt) REVERT: C 254 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8305 (t) REVERT: D 59 GLU cc_start: 0.8514 (pt0) cc_final: 0.8307 (tt0) REVERT: D 89 LEU cc_start: 0.9351 (tp) cc_final: 0.9151 (tm) REVERT: D 190 GLN cc_start: 0.9000 (pm20) cc_final: 0.8436 (pm20) REVERT: E 205 TYR cc_start: 0.8366 (m-80) cc_final: 0.8112 (m-80) outliers start: 20 outliers final: 4 residues processed: 162 average time/residue: 0.7502 time to fit residues: 130.4251 Evaluate side-chains 140 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 114 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 46 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.085848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.066797 restraints weight = 38530.258| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.96 r_work: 0.2590 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14751 Z= 0.122 Angle : 0.523 10.948 20082 Z= 0.257 Chirality : 0.042 0.254 2342 Planarity : 0.004 0.052 2405 Dihedral : 8.031 62.969 2605 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.99 % Allowed : 12.89 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.31 % 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 are not related in a simple way. whole: 1.23 (0.21), residues: 1669 helix: 2.10 (0.21), residues: 570 sheet: 0.42 (0.27), residues: 382 loop : 0.07 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 17 TYR 0.025 0.001 TYR B 244 PHE 0.027 0.001 PHE A 15 TRP 0.011 0.001 TRP B 426 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (14715) covalent geometry : angle 0.51174 / 0.25 (19979) SS BOND : bond 0.00447 / 0.23 ( 5) SS BOND : angle 0.70009 / 0.43 ( 10) hydrogen bonds : bond 0.03505 / 2.36 ( 529) hydrogen bonds : angle 4.16559 / 2.86 ( 1505) link_ALPHA1-2 : bond 0.00562 / 0.28 ( 2) link_ALPHA1-2 : angle 1.74784 / 0.89 ( 6) link_ALPHA1-3 : bond 0.00943 / 0.51 ( 7) link_ALPHA1-3 : angle 1.83105 / 1.09 ( 21) link_ALPHA1-6 : bond 0.01029 / 0.53 ( 5) link_ALPHA1-6 : angle 1.70237 / 0.98 ( 15) link_BETA1-4 : bond 0.00396 / 0.20 ( 10) link_BETA1-4 : angle 1.54948 / 1.06 ( 30) link_NAG-ASN : bond 0.00145 / 0.08 ( 7) link_NAG-ASN : angle 1.41711 / 0.98 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.593 Fit side-chains REVERT: A 89 LEU cc_start: 0.8783 (tp) cc_final: 0.8583 (tm) REVERT: B 49 MET cc_start: 0.7434 (tmt) cc_final: 0.7027 (tmt) REVERT: B 223 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8749 (tm) REVERT: C 71 GLU cc_start: 0.8837 (pt0) cc_final: 0.8593 (pt0) REVERT: C 85 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8189 (mpp-170) REVERT: C 178 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8723 (mm-30) REVERT: C 223 MET cc_start: 0.9076 (mmp) cc_final: 0.8757 (mmp) REVERT: C 254 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8323 (t) REVERT: D 59 GLU cc_start: 0.8479 (pt0) cc_final: 0.8232 (tt0) REVERT: D 190 GLN cc_start: 0.8965 (pm20) cc_final: 0.8380 (pm20) REVERT: E 205 TYR cc_start: 0.8374 (m-80) cc_final: 0.8103 (m-80) outliers start: 15 outliers final: 4 residues processed: 143 average time/residue: 0.7394 time to fit residues: 114.6449 Evaluate side-chains 135 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.1223 > 50: distance: 158 - 163: 14.809 distance: 163 - 164: 18.692 distance: 164 - 165: 41.014 distance: 164 - 167: 44.547 distance: 165 - 166: 10.012 distance: 165 - 173: 32.447 distance: 167 - 168: 41.076 distance: 168 - 169: 59.574 distance: 168 - 170: 57.320 distance: 169 - 171: 50.988 distance: 170 - 172: 50.836 distance: 171 - 172: 63.122 distance: 173 - 174: 34.770 distance: 173 - 179: 31.029 distance: 174 - 177: 18.660 distance: 175 - 180: 30.332 distance: 177 - 178: 20.157 distance: 178 - 179: 4.856 distance: 180 - 181: 21.446 distance: 181 - 182: 15.596 distance: 181 - 184: 15.241 distance: 182 - 183: 3.984 distance: 182 - 188: 36.542 distance: 184 - 185: 28.300 distance: 185 - 186: 19.960 distance: 185 - 187: 22.210 distance: 188 - 189: 6.860 distance: 189 - 190: 32.251 distance: 190 - 191: 7.005 distance: 190 - 192: 31.728 distance: 192 - 193: 20.791 distance: 193 - 194: 6.414 distance: 193 - 196: 43.133 distance: 194 - 195: 37.763 distance: 194 - 199: 45.124 distance: 196 - 197: 40.961 distance: 196 - 198: 7.714 distance: 199 - 200: 31.045 distance: 200 - 201: 27.152 distance: 200 - 203: 29.493 distance: 201 - 202: 43.926 distance: 201 - 206: 39.380 distance: 203 - 204: 7.103 distance: 203 - 205: 24.844 distance: 206 - 207: 22.515 distance: 207 - 208: 13.221 distance: 207 - 210: 13.400 distance: 208 - 209: 14.812 distance: 208 - 214: 29.588 distance: 210 - 211: 43.968 distance: 211 - 212: 40.590 distance: 211 - 213: 35.380 distance: 214 - 215: 40.596 distance: 215 - 216: 38.388 distance: 215 - 218: 10.308 distance: 216 - 217: 33.230 distance: 216 - 226: 29.668 distance: 218 - 219: 47.318 distance: 219 - 220: 45.200 distance: 219 - 221: 21.054 distance: 220 - 222: 19.770 distance: 221 - 223: 10.162 distance: 222 - 224: 18.656 distance: 223 - 224: 12.970 distance: 224 - 225: 8.717 distance: 226 - 227: 18.007 distance: 227 - 228: 42.625 distance: 228 - 229: 40.417 distance: 228 - 230: 28.989 distance: 230 - 231: 18.936 distance: 231 - 232: 17.145 distance: 231 - 234: 15.905 distance: 232 - 233: 22.564 distance: 232 - 238: 20.398 distance: 234 - 235: 47.768 distance: 235 - 236: 22.421 distance: 235 - 237: 27.626