Starting phenix.real_space_refine on Thu Jul 2 11:58:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7eja_31157/07_2026/7eja_31157.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eja_31157/07_2026/7eja_31157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7eja_31157/07_2026/7eja_31157.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7eja_31157/07_2026/7eja_31157.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eja_31157/07_2026/7eja_31157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eja_31157/07_2026/7eja_31157.map" model { file = "/net/cci-nas-00/data/ceres_data/7eja_31157/07_2026/7eja_31157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eja_31157/07_2026/7eja_31157.cif" } resolution = 3.6 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= -0.007 sd= 0.192 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5487 2.51 5 N 1458 2.21 5 O 1581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 8584 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1632 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 7, 'PTRANS': 4, 'TRANS': 198} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2541 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2193 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1785 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CZX': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 1.82, per 1000 atoms: 0.21 Number of scatterers: 8584 At special positions: 0 Unit cell: (88.4, 120.7, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1581 8.00 N 1458 7.00 C 5487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 411.2 milliseconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 12 sheets defined 34.7% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.682A pdb=" N ARG A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 4.207A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 removed outlier: 4.170A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 245 through 256 removed outlier: 4.213A pdb=" N MET A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 removed outlier: 4.100A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 329 through 350 removed outlier: 4.482A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.591A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.802A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'R' and resid 47 through 74 Processing helix chain 'R' and resid 83 through 108 removed outlier: 4.473A pdb=" N LEU R 87 " --> pdb=" O GLN R 83 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) Proline residue: R 103 - end of helix Processing helix chain 'R' and resid 120 through 151 Processing helix chain 'R' and resid 152 through 157 Processing helix chain 'R' and resid 158 through 160 No H-bonds generated for 'chain 'R' and resid 158 through 160' Processing helix chain 'R' and resid 161 through 181 Processing helix chain 'R' and resid 208 through 242 removed outlier: 3.683A pdb=" N ILE R 213 " --> pdb=" O LYS R 209 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER R 214 " --> pdb=" O TRP R 210 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ALA R 222 " --> pdb=" O GLY R 218 " (cutoff:3.500A) Proline residue: R 223 - end of helix Processing helix chain 'R' and resid 376 through 411 removed outlier: 3.698A pdb=" N ASN R 382 " --> pdb=" O ARG R 378 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE R 398 " --> pdb=" O VAL R 394 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL R 399 " --> pdb=" O ILE R 395 " (cutoff:3.500A) Proline residue: R 404 - end of helix Processing helix chain 'R' and resid 422 through 443 removed outlier: 3.775A pdb=" N GLY R 430 " --> pdb=" O PHE R 426 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR R 431 " --> pdb=" O PHE R 427 " (cutoff:3.500A) Proline residue: R 438 - end of helix removed outlier: 3.543A pdb=" N TYR R 441 " --> pdb=" O ASN R 437 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 457 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.762A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 189 removed outlier: 3.862A pdb=" N VAL A 186 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 201 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.967A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.931A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.306A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.615A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.679A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.599A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 277 Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.804A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.464A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 134 through 136 removed outlier: 3.847A pdb=" N GLU H 234 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU H 162 " --> pdb=" O TYR H 178 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR H 178 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TRP H 164 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU H 176 " --> pdb=" O TRP H 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 143 through 148 removed outlier: 3.952A pdb=" N PHE H 200 " --> pdb=" O CYS H 147 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 1035 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: 0.93 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1385 1.31 - 1.44: 2457 1.44 - 1.56: 4847 1.56 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 8768 Sorted by residual: bond pdb=" N ILE R 123 " pdb=" CA ILE R 123 " ideal model delta sigma weight residual 1.461 1.396 0.065 1.17e-02 7.31e+03 3.07e+01 bond pdb=" N ASN A 346 " pdb=" CA ASN A 346 " ideal model delta sigma weight residual 1.459 1.400 0.060 1.20e-02 6.94e+03 2.47e+01 bond pdb=" CA TYR R 156 " pdb=" C TYR R 156 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.29e-02 6.01e+03 2.45e+01 bond pdb=" CA ASN A 346 " pdb=" C ASN A 346 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.26e-02 6.30e+03 2.30e+01 bond pdb=" N PRO R 438 " pdb=" CD PRO R 438 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.22e+01 ... (remaining 8763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 11697 2.88 - 5.76: 148 5.76 - 8.64: 27 8.64 - 11.53: 6 11.53 - 14.41: 3 Bond angle restraints: 11881 Sorted by residual: angle pdb=" N ARG R 378 " pdb=" CA ARG R 378 " pdb=" C ARG R 378 " ideal model delta sigma weight residual 111.28 121.19 -9.91 1.09e+00 8.42e-01 8.27e+01 angle pdb=" N LYS A 211 " pdb=" CA LYS A 211 " pdb=" C LYS A 211 " ideal model delta sigma weight residual 111.14 119.75 -8.61 1.08e+00 8.57e-01 6.36e+01 angle pdb=" N HIS A 214 " pdb=" CA HIS A 214 " pdb=" C HIS A 214 " ideal model delta sigma weight residual 111.28 119.83 -8.55 1.09e+00 8.42e-01 6.16e+01 angle pdb=" N LYS R 159 " pdb=" CA LYS R 159 " pdb=" C LYS R 159 " ideal model delta sigma weight residual 113.15 122.41 -9.26 1.19e+00 7.06e-01 6.06e+01 angle pdb=" N CYS R 121 " pdb=" CA CYS R 121 " pdb=" C CYS R 121 " ideal model delta sigma weight residual 112.90 103.56 9.34 1.31e+00 5.83e-01 5.08e+01 ... (remaining 11876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4741 17.69 - 35.39: 349 35.39 - 53.08: 70 53.08 - 70.78: 7 70.78 - 88.47: 7 Dihedral angle restraints: 5174 sinusoidal: 1996 harmonic: 3178 Sorted by residual: dihedral pdb=" N ILE R 123 " pdb=" C ILE R 123 " pdb=" CA ILE R 123 " pdb=" CB ILE R 123 " ideal model delta harmonic sigma weight residual 123.40 109.48 13.92 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" C PHE A 216 " pdb=" N PHE A 216 " pdb=" CA PHE A 216 " pdb=" CB PHE A 216 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" CA ILE G 25 " pdb=" C ILE G 25 " pdb=" N ASP G 26 " pdb=" CA ASP G 26 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 5171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1292 0.110 - 0.219: 39 0.219 - 0.329: 12 0.329 - 0.438: 4 0.438 - 0.548: 2 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CA PHE A 216 " pdb=" N PHE A 216 " pdb=" C PHE A 216 " pdb=" CB PHE A 216 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.51e+00 chirality pdb=" CA GLU A 217 " pdb=" N GLU A 217 " pdb=" C GLU A 217 " pdb=" CB GLU A 217 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA LYS R 159 " pdb=" N LYS R 159 " pdb=" C LYS R 159 " pdb=" CB LYS R 159 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 1346 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 161 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO R 162 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 162 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 162 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 183 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C THR A 183 " -0.034 2.00e-02 2.50e+03 pdb=" O THR A 183 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 184 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 282 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO A 283 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.026 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 68 2.49 - 3.10: 6396 3.10 - 3.70: 13194 3.70 - 4.30: 17548 4.30 - 4.90: 28824 Nonbonded interactions: 66030 Sorted by model distance: nonbonded pdb=" OE1 GLN R 83 " pdb=" NH2 ARG R 160 " model vdw 1.893 3.120 nonbonded pdb=" O PHE A 224 " pdb=" N PHE A 268 " model vdw 1.959 3.120 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.175 3.040 nonbonded pdb=" OG SER H 192 " pdb=" OG1 THR H 203 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.224 3.040 ... (remaining 66025 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.210 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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: 0.020 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.005 0.103 8772 Z= 0.305 Angle : 0.850 14.408 11887 Z= 0.537 Chirality : 0.059 0.548 1349 Planarity : 0.004 0.055 1496 Dihedral : 13.050 88.469 3113 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.11 % Allowed : 0.75 % Favored : 99.14 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.43 (0.26), residues: 1075 helix: 1.20 (0.28), residues: 341 sheet: -0.37 (0.33), residues: 263 loop : -1.32 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 202 TYR 0.013 0.001 TYR R 156 PHE 0.022 0.001 PHE R 398 TRP 0.008 0.001 TRP B 169 HIS 0.004 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.28 ( 8768) covalent geometry : angle 0.84981 / 0.54 (11881) SS BOND : bond 0.00262 / 0.13 ( 3) SS BOND : angle 0.57853 / 0.22 ( 6) hydrogen bonds : bond 0.17853 / 12.34 ( 361) hydrogen bonds : angle 7.31004 / 4.97 ( 1035) Misc. bond : bond 0.10299 / 5.42 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.8918 (mmm160) cc_final: 0.8705 (mmm-85) REVERT: B 36 ASN cc_start: 0.8672 (m-40) cc_final: 0.8362 (p0) REVERT: B 255 LEU cc_start: 0.9382 (pt) cc_final: 0.9117 (mm) REVERT: B 261 LEU cc_start: 0.9371 (mt) cc_final: 0.9168 (mt) REVERT: B 280 LYS cc_start: 0.9349 (tptp) cc_final: 0.9026 (tptp) REVERT: B 292 PHE cc_start: 0.7801 (m-10) cc_final: 0.7482 (m-10) REVERT: G 21 MET cc_start: 0.8107 (mmp) cc_final: 0.7294 (mtm) REVERT: G 32 LYS cc_start: 0.9511 (ptpp) cc_final: 0.9293 (ptmm) REVERT: G 42 GLU cc_start: 0.8135 (tp30) cc_final: 0.7530 (mt-10) REVERT: G 58 GLU cc_start: 0.8998 (mp0) cc_final: 0.8428 (mp0) REVERT: R 53 CYS cc_start: 0.9179 (m) cc_final: 0.8880 (p) REVERT: R 57 LEU cc_start: 0.9416 (tp) cc_final: 0.9184 (tp) REVERT: R 109 GLU cc_start: 0.8887 (tp30) cc_final: 0.8314 (tm-30) REVERT: R 450 ARG cc_start: 0.9489 (mtm110) cc_final: 0.9217 (mtm-85) REVERT: H 46 GLU cc_start: 0.8579 (pt0) cc_final: 0.8189 (pm20) REVERT: H 90 ASP cc_start: 0.8059 (m-30) cc_final: 0.7532 (m-30) REVERT: H 137 VAL cc_start: 0.7359 (m) cc_final: 0.7129 (m) REVERT: H 180 MET cc_start: 0.8772 (ppp) cc_final: 0.8274 (ppp) REVERT: H 210 GLU cc_start: 0.8971 (mp0) cc_final: 0.8577 (mp0) REVERT: H 211 ASP cc_start: 0.7848 (m-30) cc_final: 0.7330 (m-30) REVERT: H 218 MET cc_start: 0.8712 (tmm) cc_final: 0.8146 (tmm) outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.0905 time to fit residues: 28.0479 Evaluate side-chains 152 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 256 ASN A 333 GLN B 266 HIS ** R 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 433 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.091204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.066888 restraints weight = 31853.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068915 restraints weight = 17290.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.070282 restraints weight = 11862.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.071162 restraints weight = 9307.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.071634 restraints weight = 8017.435| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8772 Z= 0.206 Angle : 0.734 10.284 11887 Z= 0.383 Chirality : 0.046 0.183 1349 Planarity : 0.004 0.054 1496 Dihedral : 4.668 19.728 1185 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.15 % Allowed : 12.90 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.33 (0.26), residues: 1075 helix: 1.36 (0.28), residues: 341 sheet: -0.39 (0.32), residues: 275 loop : -1.31 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 168 TYR 0.026 0.002 TYR R 156 PHE 0.028 0.002 PHE R 387 TRP 0.015 0.001 TRP B 169 HIS 0.008 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 ( 8768) covalent geometry : angle 0.73391 / 0.38 (11881) SS BOND : bond 0.00545 / 0.28 ( 3) SS BOND : angle 0.60474 / 0.23 ( 6) hydrogen bonds : bond 0.04725 / 3.09 ( 361) hydrogen bonds : angle 5.13632 / 3.53 ( 1035) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8591 (tm-30) REVERT: A 354 TYR cc_start: 0.8676 (p90) cc_final: 0.8337 (p90) REVERT: B 12 GLU cc_start: 0.9310 (pt0) cc_final: 0.8983 (pm20) REVERT: B 36 ASN cc_start: 0.8616 (m-40) cc_final: 0.8316 (p0) REVERT: B 292 PHE cc_start: 0.8142 (m-10) cc_final: 0.7710 (m-10) REVERT: G 42 GLU cc_start: 0.8190 (tp30) cc_final: 0.7586 (mt-10) REVERT: G 58 GLU cc_start: 0.9089 (mp0) cc_final: 0.8502 (mp0) REVERT: R 53 CYS cc_start: 0.9081 (m) cc_final: 0.8858 (m) REVERT: R 94 ASP cc_start: 0.8252 (t70) cc_final: 0.7465 (t70) REVERT: R 95 ILE cc_start: 0.9703 (mm) cc_final: 0.9489 (mm) REVERT: R 109 GLU cc_start: 0.8831 (tp30) cc_final: 0.8201 (tm-30) REVERT: R 381 GLN cc_start: 0.9020 (pt0) cc_final: 0.8537 (pt0) REVERT: R 446 HIS cc_start: 0.9017 (OUTLIER) cc_final: 0.8643 (t70) REVERT: R 447 ASP cc_start: 0.9341 (p0) cc_final: 0.9117 (p0) REVERT: H 180 MET cc_start: 0.8841 (ppp) cc_final: 0.8384 (ppp) REVERT: H 218 MET cc_start: 0.8603 (tmm) cc_final: 0.8302 (tmm) outliers start: 20 outliers final: 14 residues processed: 192 average time/residue: 0.0943 time to fit residues: 24.8951 Evaluate side-chains 161 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 433 ASN Chi-restraints excluded: chain R residue 446 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 176 GLN ** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.090874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.066933 restraints weight = 31742.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.068984 restraints weight = 17266.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.070345 restraints weight = 11818.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.071137 restraints weight = 9279.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.071773 restraints weight = 8032.893| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8772 Z= 0.193 Angle : 0.736 11.834 11887 Z= 0.376 Chirality : 0.045 0.144 1349 Planarity : 0.004 0.050 1496 Dihedral : 4.658 20.025 1185 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.23 % Allowed : 16.56 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.33 (0.26), residues: 1075 helix: 1.40 (0.28), residues: 340 sheet: -0.36 (0.32), residues: 271 loop : -1.35 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 378 TYR 0.026 0.002 TYR R 409 PHE 0.021 0.001 PHE R 387 TRP 0.011 0.001 TRP B 169 HIS 0.008 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 8768) covalent geometry : angle 0.73558 / 0.38 (11881) SS BOND : bond 0.00429 / 0.22 ( 3) SS BOND : angle 0.65540 / 0.25 ( 6) hydrogen bonds : bond 0.04455 / 2.90 ( 361) hydrogen bonds : angle 4.80231 / 3.29 ( 1035) Misc. bond : bond 0.00076 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8598 (tm-30) REVERT: A 354 TYR cc_start: 0.8718 (p90) cc_final: 0.8302 (p90) REVERT: B 12 GLU cc_start: 0.9303 (pt0) cc_final: 0.8971 (pm20) REVERT: B 36 ASN cc_start: 0.8574 (m-40) cc_final: 0.8274 (p0) REVERT: B 232 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8470 (tt) REVERT: B 292 PHE cc_start: 0.8227 (m-10) cc_final: 0.7830 (m-10) REVERT: G 21 MET cc_start: 0.8428 (mmm) cc_final: 0.7406 (mtm) REVERT: G 38 MET cc_start: 0.6558 (ptp) cc_final: 0.5867 (ptt) REVERT: G 42 GLU cc_start: 0.8188 (tp30) cc_final: 0.7612 (mt-10) REVERT: G 58 GLU cc_start: 0.9142 (mp0) cc_final: 0.8568 (mp0) REVERT: R 49 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7196 (pt) REVERT: R 53 CYS cc_start: 0.9094 (m) cc_final: 0.8882 (m) REVERT: R 94 ASP cc_start: 0.8128 (t70) cc_final: 0.7340 (t70) REVERT: R 109 GLU cc_start: 0.8781 (tp30) cc_final: 0.8174 (tm-30) REVERT: R 446 HIS cc_start: 0.9001 (OUTLIER) cc_final: 0.8672 (t70) REVERT: H 180 MET cc_start: 0.8831 (ppp) cc_final: 0.8382 (ppp) REVERT: H 218 MET cc_start: 0.8650 (tmm) cc_final: 0.8434 (tmm) outliers start: 30 outliers final: 21 residues processed: 182 average time/residue: 0.0931 time to fit residues: 23.6073 Evaluate side-chains 166 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 435 SER Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 454 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN R 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.092833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.068887 restraints weight = 31803.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.070985 restraints weight = 17110.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.072383 restraints weight = 11629.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.073199 restraints weight = 9103.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.073860 restraints weight = 7884.128| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8772 Z= 0.133 Angle : 0.701 11.965 11887 Z= 0.352 Chirality : 0.043 0.155 1349 Planarity : 0.004 0.051 1496 Dihedral : 4.496 20.908 1185 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.90 % Allowed : 17.74 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.18 (0.26), residues: 1075 helix: 1.61 (0.28), residues: 336 sheet: -0.18 (0.34), residues: 250 loop : -1.34 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 168 TYR 0.027 0.001 TYR R 409 PHE 0.022 0.001 PHE R 387 TRP 0.010 0.001 TRP B 169 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 8768) covalent geometry : angle 0.70094 / 0.35 (11881) SS BOND : bond 0.00345 / 0.17 ( 3) SS BOND : angle 0.56592 / 0.23 ( 6) hydrogen bonds : bond 0.03877 / 2.53 ( 361) hydrogen bonds : angle 4.51974 / 3.10 ( 1035) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8636 (tm-30) REVERT: A 354 TYR cc_start: 0.8733 (p90) cc_final: 0.8341 (p90) REVERT: B 12 GLU cc_start: 0.9308 (pt0) cc_final: 0.8965 (pm20) REVERT: B 36 ASN cc_start: 0.8515 (m-40) cc_final: 0.8179 (p0) REVERT: B 292 PHE cc_start: 0.8155 (m-10) cc_final: 0.7749 (m-10) REVERT: G 21 MET cc_start: 0.8570 (mmm) cc_final: 0.7687 (mtm) REVERT: G 38 MET cc_start: 0.6593 (ptp) cc_final: 0.6334 (ptt) REVERT: G 42 GLU cc_start: 0.8123 (tp30) cc_final: 0.7641 (mt-10) REVERT: G 58 GLU cc_start: 0.9134 (mp0) cc_final: 0.8570 (mp0) REVERT: R 53 CYS cc_start: 0.9040 (m) cc_final: 0.8740 (p) REVERT: R 94 ASP cc_start: 0.8117 (t70) cc_final: 0.7272 (t70) REVERT: R 95 ILE cc_start: 0.9672 (mm) cc_final: 0.9405 (mm) REVERT: R 109 GLU cc_start: 0.8638 (tp30) cc_final: 0.8117 (tm-30) REVERT: R 204 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8684 (tm-30) REVERT: R 446 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.8719 (t70) REVERT: H 34 MET cc_start: 0.8576 (tpp) cc_final: 0.8290 (tpp) outliers start: 27 outliers final: 15 residues processed: 179 average time/residue: 0.0904 time to fit residues: 22.5233 Evaluate side-chains 155 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 454 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.092253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.068284 restraints weight = 31429.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.070353 restraints weight = 16895.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.071728 restraints weight = 11512.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072630 restraints weight = 9016.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.073165 restraints weight = 7743.791| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8772 Z= 0.151 Angle : 0.722 12.459 11887 Z= 0.359 Chirality : 0.044 0.242 1349 Planarity : 0.004 0.049 1496 Dihedral : 4.476 22.017 1185 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.80 % Allowed : 19.35 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.19 (0.26), residues: 1075 helix: 1.61 (0.28), residues: 340 sheet: -0.26 (0.33), residues: 260 loop : -1.33 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.016 0.001 TYR R 156 PHE 0.020 0.001 PHE R 387 TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 8768) covalent geometry : angle 0.72213 / 0.36 (11881) SS BOND : bond 0.00303 / 0.15 ( 3) SS BOND : angle 0.62879 / 0.23 ( 6) hydrogen bonds : bond 0.03814 / 2.49 ( 361) hydrogen bonds : angle 4.48928 / 3.08 ( 1035) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8751 (p90) cc_final: 0.8340 (p90) REVERT: B 12 GLU cc_start: 0.9296 (pt0) cc_final: 0.8964 (pm20) REVERT: B 36 ASN cc_start: 0.8503 (m-40) cc_final: 0.8189 (p0) REVERT: B 130 GLU cc_start: 0.8982 (mp0) cc_final: 0.8698 (mp0) REVERT: B 292 PHE cc_start: 0.8223 (m-10) cc_final: 0.7838 (m-10) REVERT: G 38 MET cc_start: 0.6638 (ptp) cc_final: 0.6391 (ptt) REVERT: G 42 GLU cc_start: 0.8137 (tp30) cc_final: 0.7664 (mt-10) REVERT: G 58 GLU cc_start: 0.9132 (mp0) cc_final: 0.8574 (mp0) REVERT: R 53 CYS cc_start: 0.8987 (m) cc_final: 0.8714 (p) REVERT: R 94 ASP cc_start: 0.8128 (t70) cc_final: 0.7258 (t70) REVERT: R 95 ILE cc_start: 0.9679 (mm) cc_final: 0.9402 (mm) REVERT: R 109 GLU cc_start: 0.8650 (tp30) cc_final: 0.8186 (tm-30) REVERT: H 148 ARG cc_start: 0.8819 (tpp-160) cc_final: 0.8368 (mmm160) REVERT: H 218 MET cc_start: 0.8729 (tmm) cc_final: 0.8471 (ppp) outliers start: 26 outliers final: 17 residues processed: 170 average time/residue: 0.0814 time to fit residues: 19.6344 Evaluate side-chains 156 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 454 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 0.9980 chunk 98 optimal weight: 40.0000 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.093409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.069441 restraints weight = 31388.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071554 restraints weight = 16920.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.072898 restraints weight = 11528.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.073859 restraints weight = 9069.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074362 restraints weight = 7777.435| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8772 Z= 0.127 Angle : 0.729 13.237 11887 Z= 0.356 Chirality : 0.043 0.167 1349 Planarity : 0.004 0.050 1496 Dihedral : 4.398 20.645 1185 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.90 % Allowed : 20.32 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.21 (0.26), residues: 1075 helix: 1.55 (0.29), residues: 342 sheet: -0.27 (0.34), residues: 250 loop : -1.31 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 168 TYR 0.015 0.001 TYR R 156 PHE 0.023 0.001 PHE R 387 TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8768) covalent geometry : angle 0.72891 / 0.36 (11881) SS BOND : bond 0.00254 / 0.13 ( 3) SS BOND : angle 0.46329 / 0.15 ( 6) hydrogen bonds : bond 0.03560 / 2.34 ( 361) hydrogen bonds : angle 4.34359 / 2.99 ( 1035) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8747 (p90) cc_final: 0.8281 (p90) REVERT: B 12 GLU cc_start: 0.9297 (pt0) cc_final: 0.8972 (pm20) REVERT: B 36 ASN cc_start: 0.8561 (m-40) cc_final: 0.8182 (p0) REVERT: B 59 TYR cc_start: 0.8402 (m-80) cc_final: 0.7829 (m-80) REVERT: B 100 VAL cc_start: 0.9319 (t) cc_final: 0.9113 (p) REVERT: B 130 GLU cc_start: 0.8941 (mp0) cc_final: 0.8645 (mp0) REVERT: B 175 GLN cc_start: 0.8289 (mp10) cc_final: 0.8018 (mp10) REVERT: B 220 GLN cc_start: 0.8745 (mp10) cc_final: 0.8527 (mp10) REVERT: B 283 ARG cc_start: 0.7386 (ttt180) cc_final: 0.6826 (ttt90) REVERT: B 292 PHE cc_start: 0.8157 (m-10) cc_final: 0.7765 (m-10) REVERT: G 21 MET cc_start: 0.8372 (mmm) cc_final: 0.7426 (mtm) REVERT: G 24 ASN cc_start: 0.7703 (t0) cc_final: 0.7168 (m-40) REVERT: G 38 MET cc_start: 0.6689 (ptp) cc_final: 0.6003 (ptt) REVERT: G 42 GLU cc_start: 0.8080 (tp30) cc_final: 0.7497 (mt-10) REVERT: G 58 GLU cc_start: 0.9116 (mp0) cc_final: 0.8575 (mp0) REVERT: R 53 CYS cc_start: 0.9010 (m) cc_final: 0.8730 (p) REVERT: R 79 LEU cc_start: 0.8764 (tp) cc_final: 0.8554 (tp) REVERT: R 109 GLU cc_start: 0.8645 (tp30) cc_final: 0.8256 (tm-30) REVERT: R 111 MET cc_start: 0.8518 (mtm) cc_final: 0.8223 (ptp) REVERT: H 34 MET cc_start: 0.8594 (tpp) cc_final: 0.8340 (tpp) REVERT: H 148 ARG cc_start: 0.8832 (tpp-160) cc_final: 0.8392 (mmm160) REVERT: H 160 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8036 (p) REVERT: H 190 ARG cc_start: 0.5931 (OUTLIER) cc_final: 0.5668 (ptm160) REVERT: H 234 GLU cc_start: 0.6690 (pm20) cc_final: 0.6354 (pp20) outliers start: 27 outliers final: 17 residues processed: 186 average time/residue: 0.0843 time to fit residues: 21.3070 Evaluate side-chains 167 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 190 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 56.1194 > 50: distance: 41 - 45: 7.459 distance: 45 - 46: 24.839 distance: 46 - 47: 36.600 distance: 46 - 49: 31.278 distance: 47 - 48: 37.852 distance: 47 - 52: 46.715 distance: 49 - 50: 24.321 distance: 49 - 51: 44.376 distance: 52 - 53: 40.843 distance: 52 - 58: 35.856 distance: 53 - 54: 37.661 distance: 53 - 56: 31.378 distance: 54 - 55: 26.703 distance: 54 - 59: 12.707 distance: 56 - 57: 33.652 distance: 57 - 58: 5.412 distance: 59 - 60: 15.337 distance: 60 - 61: 5.347 distance: 60 - 63: 9.133 distance: 61 - 62: 28.339 distance: 61 - 70: 23.375 distance: 63 - 64: 12.895 distance: 64 - 65: 25.056 distance: 65 - 66: 19.227 distance: 66 - 67: 16.452 distance: 67 - 69: 19.624 distance: 70 - 71: 33.257 distance: 71 - 72: 27.040 distance: 71 - 74: 10.243 distance: 72 - 73: 28.028 distance: 72 - 77: 29.063 distance: 74 - 75: 44.589 distance: 74 - 76: 20.758 distance: 77 - 78: 16.292 distance: 78 - 79: 14.341 distance: 78 - 81: 35.939 distance: 79 - 80: 27.894 distance: 80 - 116: 23.057 distance: 81 - 82: 33.885 distance: 82 - 83: 34.676 distance: 85 - 86: 23.895 distance: 86 - 87: 18.884 distance: 86 - 89: 24.091 distance: 87 - 88: 16.029 distance: 87 - 96: 26.949 distance: 88 - 127: 41.316 distance: 89 - 90: 42.279 distance: 90 - 91: 4.659 distance: 90 - 92: 3.628 distance: 96 - 97: 12.780 distance: 97 - 100: 8.939 distance: 98 - 99: 35.988 distance: 98 - 105: 13.735 distance: 99 - 138: 28.904 distance: 101 - 102: 12.308 distance: 102 - 103: 40.203 distance: 103 - 104: 29.984 distance: 105 - 106: 12.000 distance: 106 - 107: 20.548 distance: 106 - 109: 15.852 distance: 107 - 108: 11.609 distance: 107 - 116: 4.429 distance: 108 - 151: 28.339 distance: 109 - 110: 10.648 distance: 110 - 111: 25.017 distance: 110 - 112: 10.690 distance: 111 - 113: 7.503 distance: 112 - 114: 3.613 distance: 113 - 115: 15.049 distance: 114 - 115: 16.578 distance: 116 - 117: 22.165 distance: 117 - 118: 7.514 distance: 117 - 120: 28.187 distance: 118 - 119: 8.874 distance: 118 - 127: 14.533 distance: 120 - 121: 16.013 distance: 121 - 122: 29.756 distance: 121 - 123: 23.043 distance: 122 - 124: 11.748 distance: 123 - 125: 13.413 distance: 124 - 126: 28.392 distance: 125 - 126: 28.586 distance: 127 - 128: 16.891 distance: 128 - 129: 15.631 distance: 128 - 131: 15.020 distance: 129 - 130: 21.555 distance: 129 - 138: 6.782 distance: 131 - 132: 6.399 distance: 132 - 133: 8.263 distance: 132 - 134: 8.645 distance: 134 - 136: 12.358 distance: 135 - 137: 18.019 distance: 136 - 137: 10.987