Starting phenix.real_space_refine on Fri Aug 22 17:30:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8geg_29969/08_2025/8geg_29969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8geg_29969/08_2025/8geg_29969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8geg_29969/08_2025/8geg_29969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8geg_29969/08_2025/8geg_29969.map" model { file = "/net/cci-nas-00/data/ceres_data/8geg_29969/08_2025/8geg_29969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8geg_29969/08_2025/8geg_29969.cif" } resolution = 3.8 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= -0.001 sd= 0.023 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 33 5.16 5 C 4150 2.51 5 N 1141 2.21 5 O 1157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 6481 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 1925 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 645 Unresolved non-hydrogen angles: 802 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 13, 'ARG:plan': 20, 'ASN:plan1': 10, 'GLU:plan': 24, 'ASP:plan': 18, 'PHE:plan': 4, 'TYR:plan': 4, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 398 Chain: "B" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2286 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 13, 'GLN:plan1': 5, 'GLU:plan': 7, 'ASN:plan1': 8, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 200 Chain: "G" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 318 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1937 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 3, 'ASN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 119 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.63, per 1000 atoms: 0.25 Number of scatterers: 6481 At special positions: 0 Unit cell: (71.02, 96.46, 129.32, 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 33 16.00 O 1157 8.00 N 1141 7.00 C 4150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 329.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 52.3% alpha, 15.5% 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 12 through 40 removed outlier: 3.651A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.530A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 113 Processing helix chain 'A' and resid 125 through 135 Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 156 through 165 Processing helix chain 'A' and resid 172 through 181 removed outlier: 3.577A pdb=" N PHE A 178 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.913A pdb=" N ASN A 254 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.635A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.343A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.517A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'B' and resid 8 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.916A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 24 removed outlier: 4.093A 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 'R' and resid 32 through 61 removed outlier: 3.756A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.268A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.608A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.122A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 4.388A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.509A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA R 202 " --> pdb=" O ALA R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 238 Processing helix chain 'R' and resid 270 through 299 removed outlier: 4.273A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.187A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 4.010A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 5.921A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.723A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.095A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.341A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.573A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.309A 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: 3.718A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.552A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.749A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1218 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: 1.05 Time building geometry restraints manager: 0.75 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: 1317 1.33 - 1.45: 1647 1.45 - 1.57: 3605 1.57 - 1.69: 1 1.69 - 1.81: 44 Bond restraints: 6614 Sorted by residual: bond pdb=" CA ARG B 137 " pdb=" C ARG B 137 " ideal model delta sigma weight residual 1.521 1.465 0.056 1.28e-02 6.10e+03 1.88e+01 bond pdb=" CA GLU B 138 " pdb=" C GLU B 138 " ideal model delta sigma weight residual 1.522 1.487 0.036 1.20e-02 6.94e+03 8.80e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.451 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.574 -0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" CA ALA B 140 " pdb=" C ALA B 140 " ideal model delta sigma weight residual 1.525 1.492 0.033 1.32e-02 5.74e+03 6.25e+00 ... (remaining 6609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 8966 1.96 - 3.91: 98 3.91 - 5.87: 20 5.87 - 7.83: 3 7.83 - 9.78: 2 Bond angle restraints: 9089 Sorted by residual: angle pdb=" N HIS B 142 " pdb=" CA HIS B 142 " pdb=" C HIS B 142 " ideal model delta sigma weight residual 108.52 100.36 8.16 1.63e+00 3.76e-01 2.51e+01 angle pdb=" N ARG B 137 " pdb=" CA ARG B 137 " pdb=" C ARG B 137 " ideal model delta sigma weight residual 108.76 101.07 7.69 1.58e+00 4.01e-01 2.37e+01 angle pdb=" N LEU A 132 " pdb=" CA LEU A 132 " pdb=" C LEU A 132 " ideal model delta sigma weight residual 111.28 106.18 5.10 1.09e+00 8.42e-01 2.19e+01 angle pdb=" C THR B 143 " pdb=" N GLY B 144 " pdb=" CA GLY B 144 " ideal model delta sigma weight residual 122.63 116.60 6.03 1.34e+00 5.57e-01 2.03e+01 angle pdb=" N GLY B 141 " pdb=" CA GLY B 141 " pdb=" C GLY B 141 " ideal model delta sigma weight residual 113.18 122.96 -9.78 2.37e+00 1.78e-01 1.70e+01 ... (remaining 9084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 3500 16.03 - 32.06: 218 32.06 - 48.08: 39 48.08 - 64.11: 4 64.11 - 80.14: 7 Dihedral angle restraints: 3768 sinusoidal: 931 harmonic: 2837 Sorted by residual: dihedral pdb=" CA TYR B 59 " pdb=" C TYR B 59 " pdb=" N ALA B 60 " pdb=" CA ALA B 60 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ALA R 85 " pdb=" C ALA R 85 " pdb=" N VAL R 86 " pdb=" CA VAL R 86 " ideal model delta harmonic sigma weight residual 180.00 -163.24 -16.76 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 3765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 815 0.042 - 0.083: 217 0.083 - 0.125: 68 0.125 - 0.166: 2 0.166 - 0.208: 3 Chirality restraints: 1105 Sorted by residual: chirality pdb=" CA LEU B 139 " pdb=" N LEU B 139 " pdb=" C LEU B 139 " pdb=" CB LEU B 139 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 1102 not shown) Planarity restraints: 1169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 140 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.26e+00 pdb=" C ALA B 140 " 0.031 2.00e-02 2.50e+03 pdb=" O ALA B 140 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY B 141 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO R 323 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 357 " 0.012 2.00e-02 2.50e+03 1.23e-02 2.28e+00 pdb=" CG HIS A 357 " -0.027 2.00e-02 2.50e+03 pdb=" ND1 HIS A 357 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 357 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 357 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS A 357 " 0.003 2.00e-02 2.50e+03 ... (remaining 1166 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1001 2.76 - 3.29: 6506 3.29 - 3.83: 11005 3.83 - 4.36: 11133 4.36 - 4.90: 20225 Nonbonded interactions: 49870 Sorted by model distance: nonbonded pdb=" OG1 THR R 66 " pdb=" OD1 ASN R 69 " model vdw 2.221 3.040 nonbonded pdb=" O GLY B 77 " pdb=" N LEU B 95 " model vdw 2.302 3.120 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.330 3.040 nonbonded pdb=" O GLU A 327 " pdb=" N GLU A 330 " model vdw 2.377 3.120 nonbonded pdb=" OE1 GLN A 384 " pdb=" NE2 GLN R 229 " model vdw 2.385 3.120 ... (remaining 49865 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.550 Find NCS groups from input model: 0.040 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 : 0.003 0.056 6614 Z= 0.185 Angle : 0.582 9.782 9089 Z= 0.330 Chirality : 0.041 0.208 1105 Planarity : 0.003 0.040 1169 Dihedral : 12.032 80.140 1920 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 1.48 (0.28), residues: 948 helix: 2.68 (0.25), residues: 433 sheet: 0.03 (0.38), residues: 180 loop : -0.76 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 48 TYR 0.015 0.001 TYR B 59 PHE 0.015 0.001 PHE R 289 TRP 0.012 0.001 TRP A 281 HIS 0.013 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6614) covalent geometry : angle 0.58178 ( 9089) hydrogen bonds : bond 0.17454 ( 422) hydrogen bonds : angle 6.35722 ( 1218) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.247 Fit side-chains REVERT: A 281 TRP cc_start: 0.7514 (m100) cc_final: 0.7237 (m100) REVERT: B 139 LEU cc_start: 0.7897 (mt) cc_final: 0.7693 (mt) REVERT: B 333 ASP cc_start: 0.8033 (p0) cc_final: 0.7706 (p0) REVERT: R 279 MET cc_start: 0.8616 (tpp) cc_final: 0.8286 (mmm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0519 time to fit residues: 7.6697 Evaluate side-chains 70 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 75 GLN B 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.113118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096679 restraints weight = 16023.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.098818 restraints weight = 9828.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.099937 restraints weight = 6975.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.101200 restraints weight = 5599.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101828 restraints weight = 4625.088| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6614 Z= 0.169 Angle : 0.541 5.441 9089 Z= 0.298 Chirality : 0.042 0.157 1105 Planarity : 0.003 0.035 1169 Dihedral : 4.500 26.680 1027 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.69 % Allowed : 11.50 % Favored : 84.82 % 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: 1.69 (0.28), residues: 948 helix: 2.76 (0.24), residues: 446 sheet: -0.01 (0.37), residues: 184 loop : -0.58 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.026 0.001 TYR B 59 PHE 0.017 0.002 PHE B 292 TRP 0.011 0.002 TRP B 169 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6614) covalent geometry : angle 0.54059 ( 9089) hydrogen bonds : bond 0.03665 ( 422) hydrogen bonds : angle 4.66807 ( 1218) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.253 Fit side-chains REVERT: B 333 ASP cc_start: 0.8295 (p0) cc_final: 0.8027 (p0) REVERT: R 113 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7980 (t0) outliers start: 17 outliers final: 13 residues processed: 82 average time/residue: 0.0508 time to fit residues: 6.5450 Evaluate side-chains 78 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 21 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.114146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.097940 restraints weight = 15380.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.100007 restraints weight = 9593.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.101406 restraints weight = 6850.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.102143 restraints weight = 5383.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.102659 restraints weight = 4594.340| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6614 Z= 0.127 Angle : 0.485 5.391 9089 Z= 0.268 Chirality : 0.040 0.147 1105 Planarity : 0.003 0.030 1169 Dihedral : 4.260 25.559 1027 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.90 % Allowed : 17.35 % Favored : 78.74 % 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: 1.80 (0.28), residues: 948 helix: 2.91 (0.24), residues: 447 sheet: 0.05 (0.37), residues: 185 loop : -0.64 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.013 0.001 TYR B 59 PHE 0.011 0.001 PHE B 199 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6614) covalent geometry : angle 0.48536 ( 9089) hydrogen bonds : bond 0.03318 ( 422) hydrogen bonds : angle 4.26184 ( 1218) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.200 Fit side-chains REVERT: B 333 ASP cc_start: 0.8352 (p0) cc_final: 0.8050 (p0) outliers start: 18 outliers final: 14 residues processed: 82 average time/residue: 0.0405 time to fit residues: 5.1962 Evaluate side-chains 84 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.113212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.096183 restraints weight = 15757.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.098568 restraints weight = 9136.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.100184 restraints weight = 6279.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.101190 restraints weight = 4794.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.102089 restraints weight = 3991.174| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6614 Z= 0.132 Angle : 0.480 5.394 9089 Z= 0.265 Chirality : 0.040 0.153 1105 Planarity : 0.003 0.029 1169 Dihedral : 4.109 22.345 1027 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.42 % Allowed : 17.79 % Favored : 76.79 % 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: 1.80 (0.28), residues: 948 helix: 2.94 (0.24), residues: 453 sheet: -0.09 (0.36), residues: 185 loop : -0.67 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 27 TYR 0.016 0.001 TYR R 141 PHE 0.021 0.001 PHE B 292 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6614) covalent geometry : angle 0.47970 ( 9089) hydrogen bonds : bond 0.03175 ( 422) hydrogen bonds : angle 4.08627 ( 1218) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.247 Fit side-chains REVERT: B 333 ASP cc_start: 0.8358 (p0) cc_final: 0.7849 (p0) REVERT: B 339 TRP cc_start: 0.7487 (OUTLIER) cc_final: 0.7267 (m-10) REVERT: G 48 ASP cc_start: 0.8054 (m-30) cc_final: 0.7505 (t70) outliers start: 25 outliers final: 17 residues processed: 92 average time/residue: 0.0515 time to fit residues: 7.0617 Evaluate side-chains 84 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS R 296 HIS R 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.114208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.097832 restraints weight = 15559.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.099942 restraints weight = 9738.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.101353 restraints weight = 6940.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.102065 restraints weight = 5430.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.102865 restraints weight = 4662.770| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6614 Z= 0.118 Angle : 0.485 5.658 9089 Z= 0.263 Chirality : 0.040 0.150 1105 Planarity : 0.003 0.029 1169 Dihedral : 4.032 27.931 1027 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 5.42 % Allowed : 18.22 % Favored : 76.36 % 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: 1.80 (0.28), residues: 948 helix: 3.03 (0.24), residues: 452 sheet: -0.25 (0.36), residues: 187 loop : -0.70 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 265 TYR 0.015 0.001 TYR R 141 PHE 0.022 0.001 PHE B 292 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6614) covalent geometry : angle 0.48522 ( 9089) hydrogen bonds : bond 0.03051 ( 422) hydrogen bonds : angle 3.94373 ( 1218) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.296 Fit side-chains REVERT: B 333 ASP cc_start: 0.8391 (p0) cc_final: 0.7883 (p0) REVERT: R 174 TYR cc_start: 0.7073 (p90) cc_final: 0.6703 (p90) REVERT: R 318 ASN cc_start: 0.8606 (t0) cc_final: 0.8403 (t0) outliers start: 25 outliers final: 17 residues processed: 88 average time/residue: 0.0534 time to fit residues: 7.1127 Evaluate side-chains 87 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 94 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.114287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.097913 restraints weight = 15611.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.099983 restraints weight = 9653.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.101005 restraints weight = 6920.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.102323 restraints weight = 5645.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.102975 restraints weight = 4650.741| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6614 Z= 0.108 Angle : 0.468 5.384 9089 Z= 0.255 Chirality : 0.040 0.149 1105 Planarity : 0.003 0.029 1169 Dihedral : 3.985 27.006 1027 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.21 % Allowed : 19.31 % Favored : 75.49 % 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: 1.84 (0.28), residues: 948 helix: 3.07 (0.24), residues: 452 sheet: -0.30 (0.36), residues: 189 loop : -0.65 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 27 TYR 0.016 0.001 TYR R 141 PHE 0.027 0.001 PHE B 292 TRP 0.015 0.001 TRP A 277 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6614) covalent geometry : angle 0.46789 ( 9089) hydrogen bonds : bond 0.02977 ( 422) hydrogen bonds : angle 3.87939 ( 1218) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.164 Fit side-chains REVERT: B 333 ASP cc_start: 0.8399 (p0) cc_final: 0.7815 (p0) REVERT: R 174 TYR cc_start: 0.7007 (p90) cc_final: 0.6695 (p90) outliers start: 24 outliers final: 18 residues processed: 91 average time/residue: 0.0455 time to fit residues: 6.4701 Evaluate side-chains 88 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 321 PHE 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: 61.6068 > 50: distance: 49 - 54: 4.108 distance: 54 - 55: 14.510 distance: 55 - 56: 11.230 distance: 55 - 58: 17.348 distance: 56 - 57: 17.458 distance: 56 - 61: 6.862 distance: 58 - 59: 9.952 distance: 58 - 60: 5.905 distance: 61 - 62: 11.054 distance: 62 - 63: 9.742 distance: 62 - 65: 10.382 distance: 63 - 64: 18.724 distance: 63 - 66: 3.993 distance: 66 - 67: 20.859 distance: 67 - 68: 17.092 distance: 67 - 70: 13.258 distance: 68 - 69: 17.559 distance: 68 - 71: 12.213 distance: 71 - 72: 23.154 distance: 71 - 77: 18.720 distance: 72 - 73: 6.562 distance: 72 - 75: 20.735 distance: 73 - 74: 29.552 distance: 73 - 78: 15.638 distance: 75 - 76: 12.064 distance: 76 - 77: 21.465 distance: 78 - 79: 8.579 distance: 79 - 80: 17.480 distance: 79 - 82: 8.647 distance: 80 - 81: 15.066 distance: 80 - 83: 16.594 distance: 83 - 84: 8.554 distance: 84 - 85: 24.085 distance: 84 - 87: 28.575 distance: 85 - 86: 20.298 distance: 85 - 88: 7.584 distance: 88 - 89: 18.432 distance: 89 - 90: 9.252 distance: 89 - 92: 10.936 distance: 90 - 91: 7.649 distance: 90 - 93: 10.569 distance: 93 - 94: 11.499 distance: 94 - 95: 19.346 distance: 94 - 97: 8.962 distance: 95 - 96: 12.969 distance: 95 - 101: 4.447 distance: 97 - 98: 13.997 distance: 98 - 99: 12.830 distance: 98 - 100: 15.972 distance: 101 - 102: 9.310 distance: 101 - 107: 7.093 distance: 102 - 103: 6.576 distance: 102 - 105: 9.403 distance: 103 - 104: 5.357 distance: 103 - 108: 3.673 distance: 105 - 106: 6.630 distance: 106 - 107: 18.004 distance: 108 - 109: 10.712 distance: 109 - 110: 10.976 distance: 109 - 112: 4.478 distance: 110 - 111: 9.218 distance: 110 - 119: 5.865 distance: 112 - 113: 4.393 distance: 113 - 115: 8.157 distance: 114 - 116: 5.398 distance: 115 - 117: 5.202 distance: 116 - 118: 7.618 distance: 117 - 118: 3.280