Starting phenix.real_space_refine on Fri Aug 22 22:40:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k41_9911/08_2025/6k41_9911.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k41_9911/08_2025/6k41_9911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6k41_9911/08_2025/6k41_9911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k41_9911/08_2025/6k41_9911.map" model { file = "/net/cci-nas-00/data/ceres_data/6k41_9911/08_2025/6k41_9911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k41_9911/08_2025/6k41_9911.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 55 5.16 5 C 5384 2.51 5 N 1435 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8430 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain breaks: 3 Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2559 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "R" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1952 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain breaks: 5 Chain: "H" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1793 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: 1.64, per 1000 atoms: 0.19 Number of scatterers: 8430 At special positions: 0 Unit cell: (109.1, 110.191, 119.464, 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 55 16.00 O 1556 8.00 N 1435 7.00 C 5384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 164 " 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=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 347.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 36.5% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.536A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.341A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.514A pdb=" N GLU A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 9 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.560A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 12 through 39 Processing helix chain 'R' and resid 48 through 74 removed outlier: 3.734A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) Proline residue: R 67 - end of helix Processing helix chain 'R' and resid 86 through 116 Processing helix chain 'R' and resid 116 through 122 removed outlier: 3.680A pdb=" N SER R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 145 Processing helix chain 'R' and resid 171 through 181 removed outlier: 3.630A pdb=" N ALA R 175 " --> pdb=" O TRP R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 203 Processing helix chain 'R' and resid 362 through 393 removed outlier: 3.538A pdb=" N LYS R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE R 380 " --> pdb=" O VAL R 376 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL R 381 " --> pdb=" O ILE R 377 " (cutoff:3.500A) Proline residue: R 386 - end of helix Processing helix chain 'R' and resid 406 through 428 removed outlier: 3.802A pdb=" N TYR R 416 " --> pdb=" O PHE R 412 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN R 418 " --> pdb=" O ILE R 414 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 430 through 442 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.508A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.850A 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 191 removed outlier: 6.304A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.507A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.871A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.785A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.660A 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: 3.739A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.845A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.298A 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: 3.648A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.591A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.785A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.219A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 128 through 129 removed outlier: 3.765A pdb=" N ALA H 199 " --> pdb=" O SER H 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 134 through 137 removed outlier: 3.826A pdb=" N GLU H 234 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 137 " --> pdb=" O GLU H 234 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY H 213 " --> pdb=" O LEU H 233 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP H 164 " --> pdb=" O LEU H 176 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2170 1.33 - 1.45: 1760 1.45 - 1.57: 4598 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 8603 Sorted by residual: bond pdb=" C09 CZX R 501 " pdb=" C12 CZX R 501 " ideal model delta sigma weight residual 1.385 1.523 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C11 CZX R 501 " pdb=" C12 CZX R 501 " ideal model delta sigma weight residual 1.386 1.522 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C08 CZX R 501 " pdb=" C11 CZX R 501 " ideal model delta sigma weight residual 1.392 1.526 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C04 CZX R 501 " pdb=" C09 CZX R 501 " ideal model delta sigma weight residual 1.393 1.521 -0.128 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C04 CZX R 501 " pdb=" C05 CZX R 501 " ideal model delta sigma weight residual 1.403 1.531 -0.128 2.00e-02 2.50e+03 4.08e+01 ... (remaining 8598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 11397 3.08 - 6.16: 226 6.16 - 9.24: 20 9.24 - 12.32: 3 12.32 - 15.40: 4 Bond angle restraints: 11650 Sorted by residual: angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 113.71 107.35 6.36 9.50e-01 1.11e+00 4.49e+01 angle pdb=" N LEU R 145 " pdb=" CA LEU R 145 " pdb=" C LEU R 145 " ideal model delta sigma weight residual 109.81 122.76 -12.95 2.21e+00 2.05e-01 3.44e+01 angle pdb=" N PRO R 146 " pdb=" CA PRO R 146 " pdb=" C PRO R 146 " ideal model delta sigma weight residual 110.70 116.69 -5.99 1.22e+00 6.72e-01 2.41e+01 angle pdb=" C ARG H 179 " pdb=" N MET H 180 " pdb=" CA MET H 180 " ideal model delta sigma weight residual 121.54 129.81 -8.27 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C THR A 296 " pdb=" N TYR A 297 " pdb=" CA TYR A 297 " ideal model delta sigma weight residual 120.54 126.25 -5.71 1.35e+00 5.49e-01 1.79e+01 ... (remaining 11645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 4822 16.48 - 32.95: 219 32.95 - 49.43: 41 49.43 - 65.90: 2 65.90 - 82.38: 6 Dihedral angle restraints: 5090 sinusoidal: 1972 harmonic: 3118 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 164 " pdb=" CB CYS R 164 " ideal model delta sinusoidal sigma weight residual -86.00 -168.38 82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CA SER B 281 " pdb=" C SER B 281 " pdb=" N GLY B 282 " pdb=" CA GLY B 282 " ideal model delta harmonic sigma weight residual 180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ARG R 116 " pdb=" C ARG R 116 " pdb=" N ALA R 117 " pdb=" CA ALA R 117 " ideal model delta harmonic sigma weight residual -180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 5087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1142 0.087 - 0.174: 169 0.174 - 0.260: 13 0.260 - 0.347: 3 0.347 - 0.434: 1 Chirality restraints: 1328 Sorted by residual: chirality pdb=" CB VAL B 71 " pdb=" CA VAL B 71 " pdb=" CG1 VAL B 71 " pdb=" CG2 VAL B 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CG LEU G 50 " pdb=" CB LEU G 50 " pdb=" CD1 LEU G 50 " pdb=" CD2 LEU G 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB VAL A 219 " pdb=" CA VAL A 219 " pdb=" CG1 VAL A 219 " pdb=" CG2 VAL A 219 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 1325 not shown) Planarity restraints: 1467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 62 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C ALA R 62 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA R 62 " -0.018 2.00e-02 2.50e+03 pdb=" N THR R 63 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 111 " 0.019 2.00e-02 2.50e+03 1.72e-02 7.43e+00 pdb=" CG TRP H 111 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP H 111 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP H 111 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP H 111 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 111 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 111 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 111 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 111 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 111 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 50 " -0.019 2.00e-02 2.50e+03 1.94e-02 6.60e+00 pdb=" CG PHE R 50 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE R 50 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE R 50 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE R 50 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE R 50 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE R 50 " -0.001 2.00e-02 2.50e+03 ... (remaining 1464 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 304 2.71 - 3.26: 7545 3.26 - 3.81: 13439 3.81 - 4.35: 17722 4.35 - 4.90: 29880 Nonbonded interactions: 68890 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.166 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.189 3.040 nonbonded pdb=" OG SER R 69 " pdb=" OH TYR R 88 " model vdw 2.220 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.243 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR H 163 " model vdw 2.244 3.040 ... (remaining 68885 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 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: 5.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 0.138 8606 Z= 0.377 Angle : 1.066 15.404 11656 Z= 0.572 Chirality : 0.062 0.434 1328 Planarity : 0.007 0.062 1467 Dihedral : 10.212 74.612 3065 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.44 % Allowed : 3.40 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.22), residues: 1049 helix: -1.40 (0.22), residues: 365 sheet: -0.89 (0.30), residues: 277 loop : -2.54 (0.25), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 15 TYR 0.030 0.004 TYR B 59 PHE 0.044 0.004 PHE R 50 TRP 0.044 0.004 TRP H 111 HIS 0.014 0.004 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00869 ( 8603) covalent geometry : angle 1.06502 (11650) SS BOND : bond 0.00187 ( 3) SS BOND : angle 2.45330 ( 6) hydrogen bonds : bond 0.16711 ( 412) hydrogen bonds : angle 6.82047 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 208 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7554 (m-30) cc_final: 0.7321 (m-30) REVERT: A 193 LYS cc_start: 0.7468 (mtpm) cc_final: 0.7179 (mmpt) REVERT: A 210 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7678 (mmtm) REVERT: A 328 ASP cc_start: 0.7295 (m-30) cc_final: 0.6547 (m-30) REVERT: A 332 ILE cc_start: 0.8282 (mp) cc_final: 0.8001 (mt) REVERT: B 207 SER cc_start: 0.8695 (p) cc_final: 0.8379 (m) REVERT: G 19 LEU cc_start: 0.8030 (mt) cc_final: 0.7745 (mp) REVERT: R 72 ASN cc_start: 0.6408 (t0) cc_final: 0.6057 (t0) REVERT: R 201 ARG cc_start: 0.6969 (ttp-170) cc_final: 0.6739 (tmm160) REVERT: R 407 LEU cc_start: 0.6761 (mt) cc_final: 0.6501 (mm) REVERT: H 3 GLN cc_start: 0.7505 (mt0) cc_final: 0.7304 (mm-40) outliers start: 4 outliers final: 2 residues processed: 212 average time/residue: 0.4857 time to fit residues: 108.7397 Evaluate side-chains 135 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.0010 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 214 HIS A 257 ASN B 32 GLN B 239 ASN B 293 ASN R 30 ASN H 167 GLN H 171 GLN H 219 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.167183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.153304 restraints weight = 8937.155| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 0.73 r_work: 0.3464 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8606 Z= 0.112 Angle : 0.554 8.164 11656 Z= 0.298 Chirality : 0.042 0.144 1328 Planarity : 0.004 0.045 1467 Dihedral : 5.138 41.462 1173 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.61 % Allowed : 10.62 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.25), residues: 1049 helix: 1.16 (0.27), residues: 354 sheet: -0.49 (0.30), residues: 290 loop : -1.97 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 209 TYR 0.021 0.002 TYR B 105 PHE 0.037 0.001 PHE R 369 TRP 0.016 0.001 TRP B 297 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8603) covalent geometry : angle 0.55367 (11650) SS BOND : bond 0.00217 ( 3) SS BOND : angle 0.77741 ( 6) hydrogen bonds : bond 0.04055 ( 412) hydrogen bonds : angle 4.70469 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.233 Fit side-chains REVERT: A 33 ASP cc_start: 0.7910 (m-30) cc_final: 0.7655 (m-30) REVERT: A 277 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6749 (mm-30) REVERT: A 308 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: A 328 ASP cc_start: 0.7172 (m-30) cc_final: 0.6500 (m-30) REVERT: B 212 ASP cc_start: 0.7731 (t0) cc_final: 0.7493 (t0) REVERT: B 234 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8172 (t80) REVERT: R 39 THR cc_start: 0.8569 (p) cc_final: 0.8335 (t) REVERT: R 187 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8324 (mt) REVERT: R 377 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7860 (tp) REVERT: R 428 ILE cc_start: 0.8360 (tt) cc_final: 0.8143 (tp) outliers start: 33 outliers final: 9 residues processed: 168 average time/residue: 0.4801 time to fit residues: 85.2832 Evaluate side-chains 148 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 377 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 143 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 100 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 0.0970 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.0670 chunk 17 optimal weight: 0.0270 chunk 95 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN R 30 ASN H 130 GLN H 167 GLN H 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.167574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.157199 restraints weight = 8793.319| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 0.53 r_work: 0.3505 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8606 Z= 0.103 Angle : 0.521 8.127 11656 Z= 0.278 Chirality : 0.041 0.143 1328 Planarity : 0.004 0.048 1467 Dihedral : 4.662 38.889 1173 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.74 % Allowed : 14.57 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.26), residues: 1049 helix: 2.01 (0.28), residues: 353 sheet: -0.27 (0.30), residues: 293 loop : -1.70 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 209 TYR 0.016 0.001 TYR B 105 PHE 0.033 0.001 PHE R 369 TRP 0.011 0.001 TRP B 297 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 8603) covalent geometry : angle 0.52113 (11650) SS BOND : bond 0.00290 ( 3) SS BOND : angle 0.79727 ( 6) hydrogen bonds : bond 0.03663 ( 412) hydrogen bonds : angle 4.36057 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7987 (mtmt) REVERT: A 33 ASP cc_start: 0.7744 (m-30) cc_final: 0.7530 (m-30) REVERT: A 277 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6530 (mm-30) REVERT: A 279 ILE cc_start: 0.6839 (tp) cc_final: 0.6638 (tp) REVERT: A 308 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8335 (m-80) REVERT: A 328 ASP cc_start: 0.7135 (m-30) cc_final: 0.6400 (m-30) REVERT: B 234 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7992 (t80) REVERT: R 187 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8260 (mt) REVERT: R 377 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7820 (tp) REVERT: H 3 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7885 (mt0) outliers start: 25 outliers final: 8 residues processed: 152 average time/residue: 0.5017 time to fit residues: 80.8366 Evaluate side-chains 141 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 377 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 162 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 4.9990 chunk 62 optimal weight: 0.0370 chunk 47 optimal weight: 0.0050 chunk 10 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.6274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.164236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.154756 restraints weight = 8929.035| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 0.67 r_work: 0.3490 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8606 Z= 0.108 Angle : 0.521 7.822 11656 Z= 0.277 Chirality : 0.041 0.143 1328 Planarity : 0.004 0.039 1467 Dihedral : 4.551 40.421 1172 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.72 % Allowed : 13.91 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.26), residues: 1049 helix: 2.30 (0.28), residues: 353 sheet: -0.04 (0.30), residues: 285 loop : -1.45 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 209 TYR 0.013 0.001 TYR R 391 PHE 0.032 0.001 PHE R 369 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8603) covalent geometry : angle 0.52094 (11650) SS BOND : bond 0.00350 ( 3) SS BOND : angle 0.94907 ( 6) hydrogen bonds : bond 0.03661 ( 412) hydrogen bonds : angle 4.24810 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8015 (mtmt) REVERT: A 277 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6593 (mm-30) REVERT: A 279 ILE cc_start: 0.7014 (tp) cc_final: 0.6770 (tp) REVERT: A 328 ASP cc_start: 0.7049 (m-30) cc_final: 0.6418 (m-30) REVERT: B 234 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8048 (t80) REVERT: B 262 MET cc_start: 0.8630 (ttm) cc_final: 0.8410 (ttm) REVERT: R 187 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8243 (mt) REVERT: R 377 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7892 (tp) REVERT: H 3 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7846 (mt0) REVERT: H 87 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7529 (mtt90) outliers start: 34 outliers final: 13 residues processed: 151 average time/residue: 0.5151 time to fit residues: 82.5163 Evaluate side-chains 141 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 144 SER Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 377 ILE Chi-restraints excluded: chain R residue 428 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 181 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.160921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.151038 restraints weight = 8864.940| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 0.68 r_work: 0.3436 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8606 Z= 0.142 Angle : 0.570 7.708 11656 Z= 0.302 Chirality : 0.043 0.151 1328 Planarity : 0.004 0.042 1467 Dihedral : 4.829 35.041 1172 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.83 % Allowed : 14.46 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.26), residues: 1049 helix: 2.16 (0.28), residues: 359 sheet: 0.01 (0.29), residues: 296 loop : -1.34 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 18 TYR 0.017 0.002 TYR H 59 PHE 0.032 0.002 PHE R 369 TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8603) covalent geometry : angle 0.56899 (11650) SS BOND : bond 0.00479 ( 3) SS BOND : angle 1.21304 ( 6) hydrogen bonds : bond 0.04169 ( 412) hydrogen bonds : angle 4.40032 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8020 (mtmt) REVERT: A 328 ASP cc_start: 0.6973 (m-30) cc_final: 0.6335 (m-30) REVERT: B 165 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8378 (m) REVERT: R 187 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8305 (mt) REVERT: H 3 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7851 (mt0) REVERT: H 166 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8197 (tp) outliers start: 35 outliers final: 16 residues processed: 149 average time/residue: 0.4642 time to fit residues: 73.4055 Evaluate side-chains 143 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 144 SER Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 181 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 270 ASN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN H 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.161697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.138339 restraints weight = 8770.832| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.20 r_work: 0.3134 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8606 Z= 0.124 Angle : 0.558 9.408 11656 Z= 0.291 Chirality : 0.042 0.147 1328 Planarity : 0.004 0.043 1467 Dihedral : 4.685 37.133 1172 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.94 % Allowed : 15.88 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.26), residues: 1049 helix: 2.25 (0.28), residues: 359 sheet: 0.15 (0.30), residues: 291 loop : -1.26 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 18 TYR 0.012 0.002 TYR R 391 PHE 0.032 0.001 PHE R 369 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8603) covalent geometry : angle 0.55795 (11650) SS BOND : bond 0.00443 ( 3) SS BOND : angle 1.00708 ( 6) hydrogen bonds : bond 0.03852 ( 412) hydrogen bonds : angle 4.30931 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8246 (mtmt) REVERT: A 277 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: A 328 ASP cc_start: 0.7244 (m-30) cc_final: 0.6403 (m-30) REVERT: R 187 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8291 (mt) REVERT: H 3 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7910 (mt0) REVERT: H 87 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7761 (mtt90) REVERT: H 166 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8386 (tp) outliers start: 36 outliers final: 17 residues processed: 153 average time/residue: 0.4792 time to fit residues: 77.9041 Evaluate side-chains 143 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 144 SER Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 181 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 63 optimal weight: 0.9990 chunk 96 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 7 optimal weight: 0.0030 chunk 82 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN H 82 GLN H 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.164478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.153486 restraints weight = 8940.095| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 0.56 r_work: 0.3466 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8606 Z= 0.097 Angle : 0.515 9.857 11656 Z= 0.269 Chirality : 0.041 0.137 1328 Planarity : 0.004 0.043 1467 Dihedral : 4.378 42.353 1172 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.05 % Allowed : 15.88 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.26), residues: 1049 helix: 2.49 (0.28), residues: 360 sheet: 0.48 (0.31), residues: 269 loop : -1.21 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 18 TYR 0.014 0.001 TYR H 59 PHE 0.030 0.001 PHE R 369 TRP 0.011 0.001 TRP B 297 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 8603) covalent geometry : angle 0.51475 (11650) SS BOND : bond 0.00353 ( 3) SS BOND : angle 0.71691 ( 6) hydrogen bonds : bond 0.03339 ( 412) hydrogen bonds : angle 4.13851 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8315 (tmmt) REVERT: A 24 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7946 (mtmt) REVERT: A 277 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6694 (mm-30) REVERT: A 328 ASP cc_start: 0.6962 (m-30) cc_final: 0.6267 (m-30) REVERT: R 41 ARG cc_start: 0.7522 (ttp80) cc_final: 0.7306 (ttt180) REVERT: R 187 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8204 (mt) REVERT: R 368 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5863 (ttt90) outliers start: 37 outliers final: 17 residues processed: 154 average time/residue: 0.5085 time to fit residues: 82.5361 Evaluate side-chains 149 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 144 SER Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 368 ARG Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 162 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5219 > 50: distance: 11 - 16: 20.388 distance: 16 - 17: 35.338 distance: 17 - 18: 39.238 distance: 17 - 20: 16.572 distance: 18 - 19: 40.366 distance: 18 - 24: 54.388 distance: 20 - 21: 45.273 distance: 20 - 22: 44.765 distance: 21 - 23: 54.022 distance: 24 - 25: 43.126 distance: 25 - 26: 40.771 distance: 25 - 28: 40.623 distance: 26 - 27: 57.913 distance: 26 - 32: 57.195 distance: 28 - 29: 30.091 distance: 29 - 30: 3.184 distance: 29 - 31: 40.621 distance: 32 - 33: 40.486 distance: 32 - 38: 10.999 distance: 33 - 34: 23.718 distance: 33 - 36: 11.188 distance: 34 - 35: 29.753 distance: 34 - 39: 27.661 distance: 36 - 37: 50.451 distance: 37 - 38: 52.120 distance: 39 - 40: 57.520 distance: 40 - 41: 41.025 distance: 40 - 43: 5.638 distance: 41 - 42: 51.938 distance: 41 - 46: 40.389 distance: 43 - 44: 38.983 distance: 43 - 45: 36.773 distance: 47 - 48: 55.115 distance: 48 - 50: 57.922 distance: 50 - 51: 60.163 distance: 51 - 52: 61.820 distance: 51 - 54: 19.746 distance: 52 - 53: 27.281 distance: 52 - 61: 8.717 distance: 54 - 55: 56.530 distance: 55 - 56: 37.792 distance: 56 - 57: 19.934 distance: 57 - 58: 53.214 distance: 58 - 59: 27.600 distance: 58 - 60: 6.844 distance: 61 - 62: 40.518 distance: 62 - 63: 43.357 distance: 62 - 65: 43.545 distance: 63 - 64: 27.706 distance: 63 - 69: 50.229 distance: 65 - 66: 69.522 distance: 65 - 67: 55.283 distance: 66 - 68: 51.729 distance: 69 - 70: 30.457 distance: 70 - 71: 49.732 distance: 70 - 73: 37.513 distance: 71 - 72: 58.243 distance: 71 - 78: 20.764 distance: 73 - 74: 30.949 distance: 74 - 75: 17.469 distance: 75 - 76: 41.766 distance: 75 - 77: 36.510 distance: 78 - 79: 52.565 distance: 79 - 80: 30.003 distance: 79 - 82: 12.010 distance: 80 - 81: 40.253 distance: 80 - 86: 45.736 distance: 82 - 83: 68.538 distance: 83 - 84: 33.513 distance: 84 - 85: 47.483 distance: 86 - 87: 32.243 distance: 87 - 88: 42.233 distance: 87 - 90: 51.671 distance: 88 - 89: 9.498 distance: 88 - 97: 26.941 distance: 90 - 91: 59.496 distance: 91 - 92: 32.614 distance: 92 - 93: 17.127 distance: 93 - 94: 14.691 distance: 94 - 95: 30.155 distance: 94 - 96: 15.514