Starting phenix.real_space_refine on Sat Jun 21 08:19:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7utj_26772/06_2025/7utj_26772.cif Found real_map, /net/cci-nas-00/data/ceres_data/7utj_26772/06_2025/7utj_26772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7utj_26772/06_2025/7utj_26772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7utj_26772/06_2025/7utj_26772.map" model { file = "/net/cci-nas-00/data/ceres_data/7utj_26772/06_2025/7utj_26772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7utj_26772/06_2025/7utj_26772.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.045 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 12 5.49 5 Mg 6 5.21 5 S 216 5.16 5 C 15462 2.51 5 N 4200 2.21 5 O 4695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24591 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "H" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "I" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "K" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "L" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "Z" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 15.07, per 1000 atoms: 0.61 Number of scatterers: 24591 At special positions: 0 Unit cell: (122.831, 101.091, 219.574, 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) S 216 16.00 P 12 15.00 Mg 6 11.99 O 4695 8.00 N 4200 7.00 C 15462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.18 Conformation dependent library (CDL) restraints added in 3.1 seconds 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5892 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 36 sheets defined 57.9% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 127 removed outlier: 3.839A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.531A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.511A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 127 removed outlier: 3.839A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.531A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.511A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 127 removed outlier: 3.840A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.530A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.512A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 127 removed outlier: 3.840A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.530A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.511A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 127 removed outlier: 3.839A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.531A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.512A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'F' and resid 55 through 61 removed outlier: 3.542A pdb=" N LYS F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 92 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 127 removed outlier: 3.839A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.531A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 260 Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 261 through 262 No H-bonds generated for 'chain 'F' and resid 261 through 262' Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 289 through 295 Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.511A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'G' and resid 711 through 731 Processing helix chain 'G' and resid 738 through 766 Processing helix chain 'G' and resid 772 through 804 Processing helix chain 'G' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER G 817 " --> pdb=" O ASP G 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU G 818 " --> pdb=" O SER G 814 " (cutoff:3.500A) Processing helix chain 'G' and resid 848 through 853 Processing helix chain 'H' and resid 711 through 731 Processing helix chain 'H' and resid 738 through 766 Processing helix chain 'H' and resid 772 through 804 Processing helix chain 'H' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER H 817 " --> pdb=" O ASP H 813 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU H 818 " --> pdb=" O SER H 814 " (cutoff:3.500A) Processing helix chain 'H' and resid 848 through 853 Processing helix chain 'I' and resid 711 through 731 Processing helix chain 'I' and resid 738 through 766 Processing helix chain 'I' and resid 772 through 804 Processing helix chain 'I' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER I 817 " --> pdb=" O ASP I 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU I 818 " --> pdb=" O SER I 814 " (cutoff:3.500A) Processing helix chain 'I' and resid 848 through 853 Processing helix chain 'K' and resid 711 through 731 Processing helix chain 'K' and resid 738 through 766 Processing helix chain 'K' and resid 772 through 804 Processing helix chain 'K' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER K 817 " --> pdb=" O ASP K 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU K 818 " --> pdb=" O SER K 814 " (cutoff:3.500A) Processing helix chain 'K' and resid 848 through 853 Processing helix chain 'L' and resid 711 through 731 Processing helix chain 'L' and resid 738 through 766 Processing helix chain 'L' and resid 772 through 804 Processing helix chain 'L' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER L 817 " --> pdb=" O ASP L 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU L 818 " --> pdb=" O SER L 814 " (cutoff:3.500A) Processing helix chain 'L' and resid 848 through 853 Processing helix chain 'Z' and resid 711 through 731 Processing helix chain 'Z' and resid 738 through 766 Processing helix chain 'Z' and resid 772 through 804 Processing helix chain 'Z' and resid 812 through 843 removed outlier: 4.002A pdb=" N SER Z 817 " --> pdb=" O ASP Z 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU Z 818 " --> pdb=" O SER Z 814 " (cutoff:3.500A) Processing helix chain 'Z' and resid 848 through 853 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.552A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 42 removed outlier: 6.041A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.043A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AB3, first strand: chain 'B' and resid 41 through 42 removed outlier: 6.042A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB6, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.043A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB8, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AC2, first strand: chain 'C' and resid 41 through 42 removed outlier: 6.043A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC5, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'D' and resid 41 through 42 Processing sheet with id=AC8, first strand: chain 'D' and resid 41 through 42 removed outlier: 6.042A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AD2, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AD4, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD5, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD6, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD8, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 1478 hydrogen bonds defined for protein. 4068 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: 10.05 Time building geometry restraints manager: 7.36 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: 4558 1.32 - 1.45: 5837 1.45 - 1.57: 14235 1.57 - 1.69: 18 1.69 - 1.82: 372 Bond restraints: 25020 Sorted by residual: bond pdb=" N VAL B 159 " pdb=" CA VAL B 159 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.14e-02 7.69e+03 1.42e+01 bond pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.14e-02 7.69e+03 1.35e+01 bond pdb=" N VAL F 159 " pdb=" CA VAL F 159 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" N VAL E 159 " pdb=" CA VAL E 159 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.14e-02 7.69e+03 1.23e+01 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.458 1.498 -0.041 1.18e-02 7.18e+03 1.20e+01 ... (remaining 25015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 31043 1.42 - 2.85: 2041 2.85 - 4.27: 540 4.27 - 5.70: 138 5.70 - 7.12: 78 Bond angle restraints: 33840 Sorted by residual: angle pdb=" CA LEU Z 790 " pdb=" C LEU Z 790 " pdb=" O LEU Z 790 " ideal model delta sigma weight residual 120.55 115.33 5.22 1.06e+00 8.90e-01 2.43e+01 angle pdb=" N GLN I 789 " pdb=" CA GLN I 789 " pdb=" C GLN I 789 " ideal model delta sigma weight residual 111.28 107.19 4.09 1.09e+00 8.42e-01 1.41e+01 angle pdb=" CA ASP E 157 " pdb=" CB ASP E 157 " pdb=" CG ASP E 157 " ideal model delta sigma weight residual 112.60 116.24 -3.64 1.00e+00 1.00e+00 1.32e+01 angle pdb=" N GLN Z 789 " pdb=" CA GLN Z 789 " pdb=" C GLN Z 789 " ideal model delta sigma weight residual 111.28 107.40 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" N GLN K 789 " pdb=" CA GLN K 789 " pdb=" C GLN K 789 " ideal model delta sigma weight residual 111.28 107.50 3.78 1.09e+00 8.42e-01 1.20e+01 ... (remaining 33835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.20: 14441 27.20 - 54.39: 717 54.39 - 81.59: 124 81.59 - 108.78: 6 108.78 - 135.98: 18 Dihedral angle restraints: 15306 sinusoidal: 6156 harmonic: 9150 Sorted by residual: dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.98 -135.98 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.98 -135.98 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.97 -135.97 1 2.00e+01 2.50e-03 4.13e+01 ... (remaining 15303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2586 0.052 - 0.104: 970 0.104 - 0.156: 203 0.156 - 0.208: 62 0.208 - 0.260: 13 Chirality restraints: 3834 Sorted by residual: chirality pdb=" CA LEU A 153 " pdb=" N LEU A 153 " pdb=" C LEU A 153 " pdb=" CB LEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA LEU D 153 " pdb=" N LEU D 153 " pdb=" C LEU D 153 " pdb=" CB LEU D 153 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU C 153 " pdb=" N LEU C 153 " pdb=" C LEU C 153 " pdb=" CB LEU C 153 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3831 not shown) Planarity restraints: 4290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU Z 790 " -0.022 2.00e-02 2.50e+03 4.57e-02 2.08e+01 pdb=" C LEU Z 790 " 0.079 2.00e-02 2.50e+03 pdb=" O LEU Z 790 " -0.029 2.00e-02 2.50e+03 pdb=" N ASN Z 791 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 156 " -0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C GLY D 156 " 0.079 2.00e-02 2.50e+03 pdb=" O GLY D 156 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP D 157 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 156 " 0.022 2.00e-02 2.50e+03 4.51e-02 2.04e+01 pdb=" C GLY A 156 " -0.078 2.00e-02 2.50e+03 pdb=" O GLY A 156 " 0.029 2.00e-02 2.50e+03 pdb=" N ASP A 157 " 0.027 2.00e-02 2.50e+03 ... (remaining 4287 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 118 2.52 - 3.12: 18285 3.12 - 3.71: 38677 3.71 - 4.31: 59255 4.31 - 4.90: 97350 Nonbonded interactions: 213685 Sorted by model distance: nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 1.927 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 1.955 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 1.957 2.170 nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 1.973 2.170 ... (remaining 213680 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: 0.21 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 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: 0.040 Extract box with map and model: 0.930 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 58.030 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.130 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:14.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 25020 Z= 0.422 Angle : 0.915 7.122 33840 Z= 0.525 Chirality : 0.059 0.260 3834 Planarity : 0.005 0.046 4290 Dihedral : 16.795 135.978 9414 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.88 % Allowed : 4.15 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3102 helix: 0.43 (0.12), residues: 1626 sheet: -0.11 (0.25), residues: 408 loop : -0.34 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP K 859 HIS 0.008 0.002 HIS E 161 PHE 0.007 0.001 PHE B 127 TYR 0.009 0.001 TYR F 53 ARG 0.006 0.001 ARG E 28 Details of bonding type rmsd hydrogen bonds : bond 0.15212 ( 1458) hydrogen bonds : angle 6.35337 ( 4068) covalent geometry : bond 0.00927 (25020) covalent geometry : angle 0.91478 (33840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 432 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7964 (mm110) cc_final: 0.7312 (mm110) REVERT: A 325 MET cc_start: 0.8575 (mmp) cc_final: 0.7939 (mmp) REVERT: B 206 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7759 (ttp-170) REVERT: B 211 ASP cc_start: 0.7587 (t0) cc_final: 0.7337 (t0) REVERT: B 305 MET cc_start: 0.9020 (mmm) cc_final: 0.8503 (mmm) REVERT: B 325 MET cc_start: 0.8799 (mmp) cc_final: 0.8182 (mmp) REVERT: C 82 MET cc_start: 0.8755 (tpt) cc_final: 0.8466 (tpp) REVERT: C 211 ASP cc_start: 0.7858 (t0) cc_final: 0.7596 (t0) REVERT: C 325 MET cc_start: 0.9009 (mmp) cc_final: 0.8751 (mmp) REVERT: D 305 MET cc_start: 0.8913 (mmm) cc_final: 0.8547 (mmm) REVERT: D 326 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.6052 (ptpt) REVERT: E 325 MET cc_start: 0.8817 (mmp) cc_final: 0.8524 (mmp) REVERT: E 326 LYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5637 (ptmm) REVERT: F 12 ASN cc_start: 0.7886 (m110) cc_final: 0.7566 (m110) REVERT: F 47 MET cc_start: 0.6726 (mmm) cc_final: 0.6338 (mmp) REVERT: F 206 ARG cc_start: 0.7488 (ttm170) cc_final: 0.6688 (ttp80) REVERT: F 269 MET cc_start: 0.8846 (mtp) cc_final: 0.8547 (mtm) REVERT: G 717 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6527 (ttmt) REVERT: G 719 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7353 (mtm) REVERT: G 816 MET cc_start: 0.7436 (tpt) cc_final: 0.7187 (tpt) REVERT: G 834 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6838 (tptt) REVERT: H 715 LEU cc_start: 0.7340 (tp) cc_final: 0.7116 (tt) REVERT: I 826 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.7010 (mmm) REVERT: K 721 MET cc_start: 0.6388 (mmp) cc_final: 0.5343 (ptt) REVERT: L 744 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7636 (m) REVERT: L 795 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6486 (tmtt) REVERT: Z 719 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7695 (mtp) REVERT: Z 792 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7797 (mt) outliers start: 103 outliers final: 12 residues processed: 481 average time/residue: 1.6463 time to fit residues: 889.4195 Evaluate side-chains 321 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 299 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 717 LYS Chi-restraints excluded: chain G residue 719 MET Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain G residue 834 LYS Chi-restraints excluded: chain I residue 792 ILE Chi-restraints excluded: chain I residue 826 MET Chi-restraints excluded: chain L residue 744 SER Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 719 MET Chi-restraints excluded: chain Z residue 744 SER Chi-restraints excluded: chain Z residue 792 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.7980 chunk 236 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 283 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN B 314 GLN D 353 GLN E 92 ASN I 824 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.151064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.102297 restraints weight = 25216.646| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.49 r_work: 0.2860 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25020 Z= 0.142 Angle : 0.603 7.827 33840 Z= 0.308 Chirality : 0.043 0.173 3834 Planarity : 0.005 0.042 4290 Dihedral : 10.575 144.294 3516 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.34 % Allowed : 10.18 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 3102 helix: 0.99 (0.12), residues: 1644 sheet: 0.16 (0.24), residues: 402 loop : 0.23 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 859 HIS 0.005 0.001 HIS E 161 PHE 0.011 0.001 PHE G 729 TYR 0.010 0.001 TYR F 294 ARG 0.004 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.05045 ( 1458) hydrogen bonds : angle 4.85212 ( 4068) covalent geometry : bond 0.00302 (25020) covalent geometry : angle 0.60296 (33840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 332 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7993 (mm110) cc_final: 0.7096 (mm110) REVERT: A 314 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8677 (tt0) REVERT: A 325 MET cc_start: 0.8518 (mmp) cc_final: 0.7860 (mmp) REVERT: A 364 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: B 229 THR cc_start: 0.8363 (m) cc_final: 0.8154 (m) REVERT: B 299 MET cc_start: 0.9079 (mtm) cc_final: 0.8820 (mtm) REVERT: B 328 LYS cc_start: 0.8537 (mttt) cc_final: 0.8153 (tttp) REVERT: B 372 ARG cc_start: 0.8272 (ptp90) cc_final: 0.8032 (ptt-90) REVERT: C 72 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: C 206 ARG cc_start: 0.8329 (ttp80) cc_final: 0.7923 (ttp-110) REVERT: C 246 GLN cc_start: 0.9005 (mt0) cc_final: 0.8689 (mt0) REVERT: C 328 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8326 (tttp) REVERT: C 372 ARG cc_start: 0.8656 (ptp-170) cc_final: 0.8231 (ptt180) REVERT: D 57 GLU cc_start: 0.7867 (tt0) cc_final: 0.7623 (mm-30) REVERT: D 121 GLN cc_start: 0.8837 (tt0) cc_final: 0.8577 (tt0) REVERT: D 305 MET cc_start: 0.9200 (mmm) cc_final: 0.8829 (mmm) REVERT: D 326 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6964 (tppp) REVERT: D 328 LYS cc_start: 0.8571 (tttp) cc_final: 0.8220 (tmtt) REVERT: E 84 LYS cc_start: 0.8557 (mttp) cc_final: 0.8183 (mtpm) REVERT: E 314 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: E 325 MET cc_start: 0.8846 (mmp) cc_final: 0.8508 (mmp) REVERT: E 355 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8016 (mtt) REVERT: F 47 MET cc_start: 0.6966 (mmm) cc_final: 0.6568 (mmp) REVERT: F 125 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7563 (mt-10) REVERT: F 206 ARG cc_start: 0.7603 (ttm170) cc_final: 0.7057 (ttp80) REVERT: F 269 MET cc_start: 0.9177 (mtp) cc_final: 0.8862 (mtm) REVERT: G 816 MET cc_start: 0.7624 (tpt) cc_final: 0.6978 (tpt) REVERT: G 834 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.5974 (tptt) REVERT: H 715 LEU cc_start: 0.6436 (tp) cc_final: 0.5996 (tp) REVERT: H 719 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6465 (mtp) REVERT: H 756 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.6870 (tpp) REVERT: I 826 MET cc_start: 0.6857 (tpt) cc_final: 0.6501 (mmm) REVERT: K 721 MET cc_start: 0.6082 (mmp) cc_final: 0.4962 (ptt) REVERT: L 773 LYS cc_start: 0.5363 (ptmt) cc_final: 0.4896 (ptpp) REVERT: L 795 LYS cc_start: 0.5894 (OUTLIER) cc_final: 0.5348 (tmtt) REVERT: Z 719 MET cc_start: 0.7459 (mtm) cc_final: 0.7251 (mtp) REVERT: Z 721 MET cc_start: 0.5971 (tpp) cc_final: 0.5739 (tpt) REVERT: Z 792 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.7060 (mt) outliers start: 62 outliers final: 14 residues processed: 366 average time/residue: 1.6633 time to fit residues: 684.3530 Evaluate side-chains 321 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 295 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain G residue 834 LYS Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain H residue 719 MET Chi-restraints excluded: chain H residue 756 MET Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 792 ILE Chi-restraints excluded: chain Z residue 840 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.8913 > 50: distance: 52 - 131: 3.569 distance: 61 - 66: 4.222 distance: 66 - 113: 12.473 distance: 67 - 68: 5.071 distance: 67 - 70: 3.208 distance: 68 - 69: 5.097 distance: 69 - 110: 5.942 distance: 70 - 71: 5.688 distance: 71 - 72: 6.413 distance: 71 - 73: 4.497 distance: 74 - 75: 5.247 distance: 74 - 229: 4.127 distance: 75 - 76: 8.907 distance: 75 - 78: 11.063 distance: 76 - 77: 6.512 distance: 76 - 80: 7.437 distance: 78 - 79: 5.412 distance: 81 - 82: 16.826 distance: 82 - 83: 23.457 distance: 82 - 84: 15.714 distance: 84 - 85: 7.575 distance: 85 - 86: 17.293 distance: 85 - 88: 16.629 distance: 86 - 87: 19.920 distance: 86 - 92: 21.401 distance: 88 - 89: 13.684 distance: 89 - 90: 14.140 distance: 89 - 91: 9.641 distance: 92 - 93: 10.662 distance: 93 - 94: 14.873 distance: 94 - 95: 12.580 distance: 94 - 96: 13.673 distance: 96 - 97: 9.405 distance: 97 - 98: 5.960 distance: 97 - 100: 11.830 distance: 98 - 99: 7.836 distance: 98 - 103: 3.806 distance: 100 - 101: 7.751 distance: 100 - 102: 3.582 distance: 103 - 104: 3.209 distance: 103 - 177: 6.872 distance: 104 - 105: 3.373 distance: 105 - 110: 5.445 distance: 106 - 174: 8.448 distance: 107 - 108: 5.922 distance: 107 - 109: 6.407 distance: 110 - 111: 3.218 distance: 111 - 114: 5.550 distance: 112 - 113: 4.645 distance: 112 - 120: 6.350 distance: 114 - 115: 6.095 distance: 115 - 116: 6.032 distance: 115 - 117: 6.193 distance: 118 - 119: 6.523 distance: 120 - 160: 8.097 distance: 122 - 123: 4.685 distance: 122 - 128: 3.431 distance: 123 - 157: 4.820 distance: 124 - 125: 4.021 distance: 125 - 127: 4.515 distance: 128 - 129: 3.250 distance: 129 - 130: 4.180 distance: 129 - 132: 4.058 distance: 132 - 134: 4.062