Starting phenix.real_space_refine on Fri Aug 22 22:43:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wq4_32699/08_2025/7wq4_32699.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wq4_32699/08_2025/7wq4_32699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wq4_32699/08_2025/7wq4_32699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wq4_32699/08_2025/7wq4_32699.map" model { file = "/net/cci-nas-00/data/ceres_data/7wq4_32699/08_2025/7wq4_32699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wq4_32699/08_2025/7wq4_32699.cif" } resolution = 2.6 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= -0.000 sd= 0.006 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 53 5.16 5 C 5277 2.51 5 N 1451 2.21 5 O 1509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 8290 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2225 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 12, 'TRANS': 269} Chain breaks: 1 Chain: "L" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 95 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "A" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1927 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "G" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.30, per 1000 atoms: 0.28 Number of scatterers: 8290 At special positions: 0 Unit cell: (88.218, 97.344, 123.708, 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 53 16.00 O 1509 8.00 N 1451 7.00 C 5277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 175 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 0.67 Conformation dependent library (CDL) restraints added in 427.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 42.5% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'R' and resid 26 through 52 removed outlier: 3.907A pdb=" N LEU R 30 " --> pdb=" O VAL R 26 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 88 Proline residue: R 80 - end of helix Processing helix chain 'R' and resid 95 through 100 removed outlier: 4.096A pdb=" N LYS R 99 " --> pdb=" O SER R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 129 removed outlier: 3.720A pdb=" N PHE R 106 " --> pdb=" O HIS R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 158 Processing helix chain 'R' and resid 159 through 164 removed outlier: 4.166A pdb=" N TYR R 164 " --> pdb=" O TYR R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 196 Processing helix chain 'R' and resid 196 through 215 Processing helix chain 'R' and resid 224 through 249 removed outlier: 3.794A pdb=" N ARG R 228 " --> pdb=" O GLY R 224 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TRP R 249 " --> pdb=" O PHE R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 262 removed outlier: 3.515A pdb=" N HIS R 253 " --> pdb=" O TRP R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 293 removed outlier: 3.696A pdb=" N ASN R 284 " --> pdb=" O VAL R 280 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 296 through 301 removed outlier: 3.642A pdb=" N ARG R 300 " --> pdb=" O SER R 296 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS R 301 " --> pdb=" O LYS R 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 296 through 301' Processing helix chain 'R' and resid 302 through 307 removed outlier: 3.528A pdb=" N ILE R 306 " --> pdb=" O GLY R 302 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS R 307 " --> pdb=" O PHE R 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 302 through 307' Processing helix chain 'L' and resid 3 through 12 removed outlier: 3.554A pdb=" N GLY L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.583A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.077A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.588A pdb=" N LEU A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.549A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 removed outlier: 3.840A pdb=" N PHE A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.602A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.641A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.022A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.845A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.518A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'R' and resid 165 through 169 Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 76 removed outlier: 4.181A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY A 40 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.508A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.688A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.541A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.683A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.110A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.068A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.608A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.316A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1212 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: 1.25 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2702 1.34 - 1.46: 1972 1.46 - 1.58: 3709 1.58 - 1.70: 10 1.70 - 1.81: 74 Bond restraints: 8467 Sorted by residual: bond pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " ideal model delta sigma weight residual 1.332 1.651 -0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 1.332 1.650 -0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" C15 CLR R 402 " pdb=" C16 CLR R 402 " ideal model delta sigma weight residual 1.541 1.708 -0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" C15 CLR R 401 " pdb=" C16 CLR R 401 " ideal model delta sigma weight residual 1.541 1.705 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" C8 CLR R 402 " pdb=" C9 CLR R 402 " ideal model delta sigma weight residual 1.535 1.671 -0.136 2.00e-02 2.50e+03 4.62e+01 ... (remaining 8462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 11412 2.71 - 5.41: 58 5.41 - 8.12: 12 8.12 - 10.83: 3 10.83 - 13.53: 4 Bond angle restraints: 11489 Sorted by residual: angle pdb=" N VAL R 295 " pdb=" CA VAL R 295 " pdb=" C VAL R 295 " ideal model delta sigma weight residual 113.71 106.66 7.05 9.50e-01 1.11e+00 5.51e+01 angle pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " pdb=" C7 CLR R 401 " ideal model delta sigma weight residual 125.11 111.58 13.53 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " pdb=" C7 CLR R 402 " ideal model delta sigma weight residual 125.11 111.81 13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" CA ALA R 170 " pdb=" C ALA R 170 " pdb=" O ALA R 170 " ideal model delta sigma weight residual 122.03 117.50 4.53 1.17e+00 7.31e-01 1.50e+01 angle pdb=" C10 CLR R 401 " pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 122.94 111.81 11.13 3.00e+00 1.11e-01 1.38e+01 ... (remaining 11484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.16: 4849 12.16 - 24.32: 191 24.32 - 36.47: 60 36.47 - 48.63: 26 48.63 - 60.79: 9 Dihedral angle restraints: 5135 sinusoidal: 2094 harmonic: 3041 Sorted by residual: dihedral pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" CB PHE B 234 " pdb=" CG PHE B 234 " ideal model delta sinusoidal sigma weight residual -180.00 -120.16 -59.84 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG R 184 " pdb=" CA ARG R 184 " pdb=" CB ARG R 184 " pdb=" CG ARG R 184 " ideal model delta sinusoidal sigma weight residual -60.00 -117.77 57.77 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CG ARG R 184 " pdb=" CD ARG R 184 " pdb=" NE ARG R 184 " pdb=" CZ ARG R 184 " ideal model delta sinusoidal sigma weight residual 180.00 139.10 40.90 2 1.50e+01 4.44e-03 9.14e+00 ... (remaining 5132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1271 0.110 - 0.221: 27 0.221 - 0.331: 4 0.331 - 0.442: 2 0.442 - 0.552: 2 Chirality restraints: 1306 Sorted by residual: chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.38 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" C13 CLR R 401 " pdb=" C12 CLR R 401 " pdb=" C14 CLR R 401 " pdb=" C17 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.39 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" C9 CLR R 402 " pdb=" C10 CLR R 402 " pdb=" C11 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.45 -2.86 0.42 2.00e-01 2.50e+01 4.35e+00 ... (remaining 1303 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 101 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C VAL R 101 " 0.021 2.00e-02 2.50e+03 pdb=" O VAL R 101 " -0.008 2.00e-02 2.50e+03 pdb=" N HIS R 102 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO B 236 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 158 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO R 159 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 159 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 159 " -0.015 5.00e-02 4.00e+02 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 2 2.10 - 2.80: 2089 2.80 - 3.50: 11004 3.50 - 4.20: 19240 4.20 - 4.90: 34386 Nonbonded interactions: 66721 Sorted by model distance: nonbonded pdb=" OD1 ASN N 35 " pdb=" CB ASP N 50 " model vdw 1.399 3.440 nonbonded pdb=" CG2 VAL R 174 " pdb=" NE2 HIS R 176 " model vdw 2.067 3.540 nonbonded pdb=" O TYR R 129 " pdb=" OG SER R 133 " model vdw 2.247 3.040 nonbonded pdb=" O THR R 191 " pdb=" OG SER R 195 " model vdw 2.250 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.289 3.040 ... (remaining 66716 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.300 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 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 : 0.007 0.319 8470 Z= 0.384 Angle : 0.615 13.533 11495 Z= 0.339 Chirality : 0.052 0.552 1306 Planarity : 0.003 0.027 1450 Dihedral : 8.519 60.788 3162 Min Nonbonded Distance : 1.399 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.45 % Allowed : 3.38 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.24), residues: 1032 helix: 0.15 (0.26), residues: 373 sheet: -0.58 (0.31), residues: 237 loop : -1.48 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 72 TYR 0.005 0.001 TYR N 60 PHE 0.010 0.001 PHE R 103 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00736 ( 8467) covalent geometry : angle 0.61460 (11489) SS BOND : bond 0.00085 ( 3) SS BOND : angle 0.48101 ( 6) hydrogen bonds : bond 0.12329 ( 430) hydrogen bonds : angle 5.57269 ( 1212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 251 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: R 184 ARG cc_start: 0.5524 (OUTLIER) cc_final: 0.4897 (mtp-110) REVERT: A 15 ARG cc_start: 0.6050 (ttt90) cc_final: 0.5842 (ttm-80) REVERT: A 17 LYS cc_start: 0.6310 (mttt) cc_final: 0.5857 (pttp) REVERT: A 69 ILE cc_start: 0.8297 (mt) cc_final: 0.8074 (mm) REVERT: A 75 GLN cc_start: 0.7309 (tt0) cc_final: 0.6941 (tm130) REVERT: A 191 TYR cc_start: 0.7616 (m-10) cc_final: 0.7346 (m-10) REVERT: A 208 ARG cc_start: 0.6356 (mtm-85) cc_final: 0.5994 (tpt90) REVERT: B 44 GLN cc_start: 0.7850 (mt0) cc_final: 0.7582 (mt0) REVERT: B 188 MET cc_start: 0.8239 (mmm) cc_final: 0.8029 (mmm) REVERT: B 197 ARG cc_start: 0.6792 (mtm180) cc_final: 0.6497 (mtp85) REVERT: B 234 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: B 254 ASP cc_start: 0.7784 (p0) cc_final: 0.7549 (p0) REVERT: N 65 LYS cc_start: 0.7321 (mttt) cc_final: 0.6892 (tmtt) REVERT: N 80 TYR cc_start: 0.6848 (m-80) cc_final: 0.6631 (m-80) outliers start: 4 outliers final: 0 residues processed: 255 average time/residue: 0.6187 time to fit residues: 166.5776 Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 55 GLN R 82 GLN R 253 HIS A 52 GLN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 GLN A 244 ASN B 35 ASN B 91 HIS B 176 GLN B 220 GLN B 259 GLN N 77 ASN G 11 GLN G 24 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.159875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125607 restraints weight = 8896.579| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.85 r_work: 0.3344 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 8470 Z= 0.178 Angle : 0.580 7.388 11495 Z= 0.307 Chirality : 0.044 0.144 1306 Planarity : 0.004 0.029 1450 Dihedral : 5.340 54.739 1286 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.49 % Allowed : 14.30 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.26), residues: 1032 helix: 1.11 (0.26), residues: 398 sheet: -0.25 (0.31), residues: 236 loop : -0.92 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 137 TYR 0.012 0.002 TYR A 243 PHE 0.016 0.002 PHE A 215 TRP 0.017 0.002 TRP B 339 HIS 0.011 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8467) covalent geometry : angle 0.57996 (11489) SS BOND : bond 0.00201 ( 3) SS BOND : angle 0.91440 ( 6) hydrogen bonds : bond 0.04529 ( 430) hydrogen bonds : angle 4.41320 ( 1212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7084 (mt) REVERT: R 88 LEU cc_start: 0.6872 (mt) cc_final: 0.6488 (mt) REVERT: R 96 LEU cc_start: 0.6298 (pt) cc_final: 0.5708 (tp) REVERT: R 166 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: R 298 HIS cc_start: 0.7006 (t70) cc_final: 0.6305 (m-70) REVERT: A 15 ARG cc_start: 0.7316 (ttt90) cc_final: 0.7018 (ttm-80) REVERT: A 20 GLU cc_start: 0.7509 (tp30) cc_final: 0.7262 (tp30) REVERT: A 73 LYS cc_start: 0.9013 (mttp) cc_final: 0.8652 (mttt) REVERT: A 208 ARG cc_start: 0.7439 (mtm-85) cc_final: 0.6663 (tpt90) REVERT: A 222 GLU cc_start: 0.7763 (pm20) cc_final: 0.7319 (pt0) REVERT: B 57 LYS cc_start: 0.9031 (pttm) cc_final: 0.8762 (pttt) REVERT: B 186 ASP cc_start: 0.8473 (m-30) cc_final: 0.8158 (m-30) REVERT: B 188 MET cc_start: 0.8960 (mmm) cc_final: 0.8547 (mmm) REVERT: B 197 ARG cc_start: 0.8037 (mtm180) cc_final: 0.7548 (mtp85) REVERT: B 212 ASP cc_start: 0.8043 (t0) cc_final: 0.7839 (t0) REVERT: B 260 GLU cc_start: 0.7530 (tt0) cc_final: 0.7330 (tt0) REVERT: B 263 THR cc_start: 0.8624 (t) cc_final: 0.8095 (m) outliers start: 31 outliers final: 15 residues processed: 188 average time/residue: 0.6139 time to fit residues: 122.1016 Evaluate side-chains 155 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 82 GLN A 75 GLN B 35 ASN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.156882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122178 restraints weight = 8917.989| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.92 r_work: 0.3316 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8470 Z= 0.140 Angle : 0.542 8.546 11495 Z= 0.285 Chirality : 0.043 0.178 1306 Planarity : 0.004 0.028 1450 Dihedral : 4.715 57.678 1280 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.62 % Allowed : 15.20 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.26), residues: 1032 helix: 1.58 (0.27), residues: 393 sheet: 0.18 (0.33), residues: 223 loop : -0.62 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.013 0.001 TYR A 243 PHE 0.013 0.002 PHE B 151 TRP 0.014 0.002 TRP B 169 HIS 0.008 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8467) covalent geometry : angle 0.53559 (11489) SS BOND : bond 0.00325 ( 3) SS BOND : angle 3.73323 ( 6) hydrogen bonds : bond 0.04114 ( 430) hydrogen bonds : angle 4.30038 ( 1212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7287 (mt) REVERT: R 96 LEU cc_start: 0.6340 (pt) cc_final: 0.5761 (tp) REVERT: R 166 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: R 298 HIS cc_start: 0.6900 (t70) cc_final: 0.6482 (m-70) REVERT: A 15 ARG cc_start: 0.7412 (ttt90) cc_final: 0.7110 (ttm-80) REVERT: A 20 GLU cc_start: 0.7635 (tp30) cc_final: 0.7403 (tp30) REVERT: A 157 LYS cc_start: 0.8137 (mptt) cc_final: 0.7932 (mtmm) REVERT: A 208 ARG cc_start: 0.7470 (mtm-85) cc_final: 0.6829 (mmm-85) REVERT: A 238 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8190 (mtt) REVERT: B 29 THR cc_start: 0.7159 (OUTLIER) cc_final: 0.6403 (p) REVERT: B 57 LYS cc_start: 0.8953 (pttm) cc_final: 0.8723 (pttt) REVERT: B 186 ASP cc_start: 0.8456 (m-30) cc_final: 0.8183 (m-30) REVERT: B 188 MET cc_start: 0.8940 (mmm) cc_final: 0.8592 (mmm) REVERT: B 197 ARG cc_start: 0.8097 (mtm180) cc_final: 0.7469 (mtp85) REVERT: B 212 ASP cc_start: 0.8206 (t0) cc_final: 0.7926 (t0) REVERT: B 220 GLN cc_start: 0.8121 (tt0) cc_final: 0.7831 (tt0) REVERT: B 234 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8293 (m-80) REVERT: B 263 THR cc_start: 0.8671 (t) cc_final: 0.8162 (m) REVERT: G 37 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8198 (mp) REVERT: G 42 GLU cc_start: 0.7840 (pp20) cc_final: 0.7248 (mm-30) outliers start: 41 outliers final: 16 residues processed: 163 average time/residue: 0.6437 time to fit residues: 110.9249 Evaluate side-chains 150 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 82 GLN A 75 GLN ** A 82 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 = 0.3845 r_free = 0.3845 target = 0.156615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121382 restraints weight = 9108.632| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.96 r_work: 0.3301 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8470 Z= 0.127 Angle : 0.520 7.350 11495 Z= 0.274 Chirality : 0.042 0.174 1306 Planarity : 0.003 0.028 1450 Dihedral : 4.618 56.621 1280 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.83 % Allowed : 17.57 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.26), residues: 1032 helix: 1.88 (0.27), residues: 392 sheet: 0.33 (0.32), residues: 231 loop : -0.60 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.011 0.001 TYR A 243 PHE 0.013 0.002 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8467) covalent geometry : angle 0.51500 (11489) SS BOND : bond 0.00259 ( 3) SS BOND : angle 3.20036 ( 6) hydrogen bonds : bond 0.03941 ( 430) hydrogen bonds : angle 4.20749 ( 1212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7276 (mt) REVERT: R 136 LEU cc_start: 0.7901 (tt) cc_final: 0.7638 (tp) REVERT: R 166 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: R 298 HIS cc_start: 0.7295 (t70) cc_final: 0.6508 (m-70) REVERT: A 20 GLU cc_start: 0.7650 (tp30) cc_final: 0.7404 (tp30) REVERT: A 51 LYS cc_start: 0.7491 (pptt) cc_final: 0.7280 (mmmt) REVERT: A 196 GLU cc_start: 0.8339 (tp30) cc_final: 0.8137 (mm-30) REVERT: A 208 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.6864 (mmm-85) REVERT: A 222 GLU cc_start: 0.7813 (pm20) cc_final: 0.7447 (pt0) REVERT: A 238 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8218 (mtt) REVERT: A 242 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7286 (tt0) REVERT: B 57 LYS cc_start: 0.8940 (pttm) cc_final: 0.8689 (pttt) REVERT: B 186 ASP cc_start: 0.8470 (m-30) cc_final: 0.8224 (m-30) REVERT: B 188 MET cc_start: 0.8916 (mmm) cc_final: 0.8603 (mmm) REVERT: B 197 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7610 (mtp85) REVERT: B 212 ASP cc_start: 0.8237 (t0) cc_final: 0.8007 (t70) REVERT: B 220 GLN cc_start: 0.8083 (tt0) cc_final: 0.7769 (tt0) REVERT: B 234 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8219 (m-80) REVERT: B 263 THR cc_start: 0.8771 (t) cc_final: 0.8222 (m) REVERT: G 37 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8101 (mp) REVERT: G 42 GLU cc_start: 0.7817 (pp20) cc_final: 0.7335 (mm-30) outliers start: 34 outliers final: 17 residues processed: 163 average time/residue: 0.6529 time to fit residues: 112.0658 Evaluate side-chains 159 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 82 GLN R 102 HIS A 75 GLN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.116611 restraints weight = 9007.661| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.95 r_work: 0.3243 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8470 Z= 0.212 Angle : 0.624 8.131 11495 Z= 0.330 Chirality : 0.046 0.188 1306 Planarity : 0.004 0.036 1450 Dihedral : 5.252 58.220 1280 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.28 % Allowed : 18.58 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.26), residues: 1032 helix: 1.64 (0.26), residues: 390 sheet: 0.45 (0.32), residues: 226 loop : -0.73 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 15 TYR 0.016 0.002 TYR A 243 PHE 0.016 0.002 PHE B 151 TRP 0.017 0.002 TRP A 96 HIS 0.011 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 8467) covalent geometry : angle 0.61954 (11489) SS BOND : bond 0.00376 ( 3) SS BOND : angle 3.37826 ( 6) hydrogen bonds : bond 0.05086 ( 430) hydrogen bonds : angle 4.52818 ( 1212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 136 LEU cc_start: 0.7866 (tt) cc_final: 0.7427 (mp) REVERT: R 140 ARG cc_start: 0.7391 (ttt180) cc_final: 0.7001 (ttm-80) REVERT: R 166 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: R 298 HIS cc_start: 0.7475 (t70) cc_final: 0.6599 (m-70) REVERT: A 10 LYS cc_start: 0.7413 (mttt) cc_final: 0.7167 (mmtp) REVERT: A 194 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8198 (ttt-90) REVERT: A 208 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.6888 (mmm-85) REVERT: A 242 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7420 (tt0) REVERT: B 57 LYS cc_start: 0.8957 (pttm) cc_final: 0.8669 (pttt) REVERT: B 59 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8601 (t80) REVERT: B 134 ARG cc_start: 0.7450 (ptm-80) cc_final: 0.6625 (tpp-160) REVERT: B 155 ASN cc_start: 0.7760 (p0) cc_final: 0.7477 (t0) REVERT: B 188 MET cc_start: 0.8949 (mmm) cc_final: 0.8611 (mmm) REVERT: B 197 ARG cc_start: 0.8289 (mtm180) cc_final: 0.7747 (mtp85) REVERT: B 234 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: B 263 THR cc_start: 0.8894 (t) cc_final: 0.8304 (m) REVERT: B 304 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7933 (mtp85) REVERT: G 37 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8130 (mp) REVERT: G 42 GLU cc_start: 0.7827 (pp20) cc_final: 0.7353 (mm-30) outliers start: 38 outliers final: 18 residues processed: 156 average time/residue: 0.7202 time to fit residues: 117.8274 Evaluate side-chains 145 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 236 ARG Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN A 75 GLN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.154805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119921 restraints weight = 8991.168| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.94 r_work: 0.3294 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8470 Z= 0.119 Angle : 0.513 6.262 11495 Z= 0.272 Chirality : 0.042 0.150 1306 Planarity : 0.003 0.036 1450 Dihedral : 4.832 55.580 1280 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.49 % Allowed : 18.69 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.26), residues: 1032 helix: 2.00 (0.26), residues: 390 sheet: 0.54 (0.32), residues: 224 loop : -0.68 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 15 TYR 0.014 0.001 TYR R 129 PHE 0.013 0.001 PHE A 74 TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8467) covalent geometry : angle 0.51002 (11489) SS BOND : bond 0.00296 ( 3) SS BOND : angle 2.35954 ( 6) hydrogen bonds : bond 0.03896 ( 430) hydrogen bonds : angle 4.20140 ( 1212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 136 LEU cc_start: 0.7808 (tt) cc_final: 0.7553 (tp) REVERT: R 166 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: R 200 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7864 (p) REVERT: R 298 HIS cc_start: 0.7480 (t70) cc_final: 0.6506 (m-70) REVERT: A 10 LYS cc_start: 0.7342 (mttt) cc_final: 0.7109 (mmtp) REVERT: A 73 LYS cc_start: 0.8971 (mttp) cc_final: 0.8688 (mttt) REVERT: A 208 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.6843 (mmm-85) REVERT: A 222 GLU cc_start: 0.7870 (pm20) cc_final: 0.7495 (pt0) REVERT: A 242 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7425 (tt0) REVERT: B 57 LYS cc_start: 0.8934 (pttm) cc_final: 0.8540 (ptpt) REVERT: B 134 ARG cc_start: 0.7387 (ptm-80) cc_final: 0.6574 (tpp-160) REVERT: B 155 ASN cc_start: 0.7731 (p0) cc_final: 0.7484 (t0) REVERT: B 188 MET cc_start: 0.8912 (mmm) cc_final: 0.8605 (mmm) REVERT: B 197 ARG cc_start: 0.8210 (mtm180) cc_final: 0.7753 (mtp85) REVERT: B 214 ARG cc_start: 0.7968 (mmt180) cc_final: 0.7693 (mpp-170) REVERT: B 220 GLN cc_start: 0.8061 (tt0) cc_final: 0.7795 (tt0) REVERT: B 234 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: B 263 THR cc_start: 0.8825 (t) cc_final: 0.8228 (m) REVERT: G 37 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8091 (mp) REVERT: G 42 GLU cc_start: 0.7782 (pp20) cc_final: 0.7333 (mm-30) outliers start: 31 outliers final: 17 residues processed: 164 average time/residue: 0.5828 time to fit residues: 101.0063 Evaluate side-chains 156 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 166 GLN Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 297 LYS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.6057 > 50: distance: 51 - 76: 6.504 distance: 59 - 65: 5.710 distance: 60 - 90: 20.217 distance: 65 - 66: 4.459 distance: 66 - 67: 3.028 distance: 66 - 69: 6.372 distance: 67 - 68: 5.417 distance: 67 - 76: 3.518 distance: 69 - 70: 8.848 distance: 70 - 71: 7.496 distance: 70 - 72: 4.798 distance: 72 - 74: 5.282 distance: 74 - 75: 3.604 distance: 76 - 77: 9.147 distance: 77 - 80: 4.934 distance: 78 - 82: 5.370 distance: 80 - 81: 9.882 distance: 82 - 83: 6.280 distance: 83 - 84: 6.179 distance: 83 - 86: 5.937 distance: 84 - 85: 7.108 distance: 84 - 90: 21.299 distance: 86 - 87: 3.294 distance: 87 - 88: 4.011 distance: 87 - 89: 7.396 distance: 90 - 91: 22.179 distance: 91 - 92: 17.424 distance: 91 - 94: 22.679 distance: 92 - 93: 19.168 distance: 92 - 96: 9.577 distance: 94 - 95: 15.518 distance: 96 - 97: 16.922 distance: 97 - 98: 5.713 distance: 97 - 100: 6.378 distance: 98 - 99: 12.275 distance: 98 - 110: 11.627 distance: 100 - 101: 4.466 distance: 101 - 102: 4.177 distance: 101 - 103: 7.031 distance: 102 - 104: 5.076 distance: 103 - 105: 3.957 distance: 104 - 105: 3.877 distance: 105 - 107: 3.043 distance: 106 - 108: 7.933 distance: 108 - 109: 7.864 distance: 110 - 111: 14.724 distance: 111 - 112: 5.414 distance: 111 - 114: 6.134 distance: 112 - 113: 7.574 distance: 112 - 118: 9.582 distance: 113 - 145: 5.801 distance: 114 - 115: 4.045 distance: 116 - 117: 3.251 distance: 118 - 119: 9.835 distance: 118 - 124: 12.999 distance: 119 - 120: 3.087 distance: 119 - 122: 9.596 distance: 120 - 121: 6.878 distance: 120 - 125: 3.546 distance: 121 - 150: 8.685 distance: 122 - 123: 12.569 distance: 123 - 124: 6.560 distance: 125 - 126: 6.530 distance: 126 - 127: 4.321 distance: 126 - 129: 5.696 distance: 127 - 128: 7.943 distance: 127 - 135: 4.801 distance: 128 - 158: 7.418 distance: 129 - 130: 9.122 distance: 130 - 131: 3.563 distance: 131 - 133: 4.998 distance: 132 - 134: 7.941 distance: 133 - 134: 5.753 distance: 135 - 136: 3.039 distance: 138 - 166: 5.361 distance: 139 - 140: 6.417 distance: 140 - 141: 3.111 distance: 140 - 142: 4.734 distance: 141 - 143: 6.786 distance: 142 - 144: 8.220 distance: 143 - 144: 11.348 distance: 146 - 147: 3.498 distance: 147 - 148: 5.011