Starting phenix.real_space_refine on Sat Aug 23 00:32:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vy7_43647/08_2025/8vy7_43647.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vy7_43647/08_2025/8vy7_43647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vy7_43647/08_2025/8vy7_43647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vy7_43647/08_2025/8vy7_43647.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vy7_43647/08_2025/8vy7_43647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vy7_43647/08_2025/8vy7_43647.map" } resolution = 2.68 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= 0.021 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: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 5659 2.51 5 N 1488 2.21 5 O 1601 1.98 5 F 3 1.80 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: 8811 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1753 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2564 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 401 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1743 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2299 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'A1AEI': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.38, per 1000 atoms: 0.27 Number of scatterers: 8811 At special positions: 0 Unit cell: (90.228, 120.888, 134.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 F 3 9.00 O 1601 8.00 N 1488 7.00 C 5659 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 372.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 39.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.852A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.585A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.647A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.557A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.739A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 53 through 56 removed outlier: 4.366A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.658A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 37 Processing helix chain 'R' and resid 42 through 72 Processing helix chain 'R' and resid 72 through 77 Processing helix chain 'R' and resid 78 through 112 Processing helix chain 'R' and resid 116 through 124 Processing helix chain 'R' and resid 125 through 137 Processing helix chain 'R' and resid 137 through 158 removed outlier: 3.606A pdb=" N LEU R 141 " --> pdb=" O THR R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 213 removed outlier: 4.214A pdb=" N LEU R 181 " --> pdb=" O SER R 177 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE R 189 " --> pdb=" O VAL R 185 " (cutoff:3.500A) Proline residue: R 190 - end of helix Processing helix chain 'R' and resid 228 through 257 removed outlier: 4.386A pdb=" N SER R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU R 239 " --> pdb=" O THR R 235 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER R 246 " --> pdb=" O ILE R 242 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU R 257 " --> pdb=" O THR R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 270 removed outlier: 3.751A pdb=" N LEU R 264 " --> pdb=" O ASN R 260 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET R 270 " --> pdb=" O GLN R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 282 removed outlier: 4.624A pdb=" N SER R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS R 278 " --> pdb=" O SER R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 302 removed outlier: 3.791A pdb=" N ARG R 299 " --> pdb=" O LEU R 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.545A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.705A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.695A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.778A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.621A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.744A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.666A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.628A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.722A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.722A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.911A pdb=" N ALA D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 135 through 136 removed outlier: 6.704A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1338 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: 1.32 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2778 1.34 - 1.46: 1822 1.46 - 1.57: 4307 1.57 - 1.69: 2 1.69 - 1.81: 90 Bond restraints: 8999 Sorted by residual: bond pdb=" C10 A1AEI R 501 " pdb=" N11 A1AEI R 501 " ideal model delta sigma weight residual 1.364 1.459 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C13 A1AEI R 501 " pdb=" C14 A1AEI R 501 " ideal model delta sigma weight residual 1.461 1.529 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" N16 A1AEI R 501 " pdb=" N17 A1AEI R 501 " ideal model delta sigma weight residual 1.275 1.333 -0.058 2.00e-02 2.50e+03 8.56e+00 bond pdb=" C16 CLR R 502 " pdb=" C17 CLR R 502 " ideal model delta sigma weight residual 1.554 1.607 -0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" C23 CLR R 502 " pdb=" C24 CLR R 502 " ideal model delta sigma weight residual 1.525 1.574 -0.049 2.00e-02 2.50e+03 5.94e+00 ... (remaining 8994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 11987 2.23 - 4.45: 171 4.45 - 6.68: 29 6.68 - 8.90: 11 8.90 - 11.13: 2 Bond angle restraints: 12200 Sorted by residual: angle pdb=" CA LEU A 227 " pdb=" CB LEU A 227 " pdb=" CG LEU A 227 " ideal model delta sigma weight residual 116.30 127.43 -11.13 3.50e+00 8.16e-02 1.01e+01 angle pdb=" N PRO D 224 " pdb=" CA PRO D 224 " pdb=" C PRO D 224 " ideal model delta sigma weight residual 112.10 120.32 -8.22 2.60e+00 1.48e-01 9.99e+00 angle pdb=" CA TYR D 178 " pdb=" CB TYR D 178 " pdb=" CG TYR D 178 " ideal model delta sigma weight residual 113.90 119.48 -5.58 1.80e+00 3.09e-01 9.62e+00 angle pdb=" C22 CLR R 502 " pdb=" C23 CLR R 502 " pdb=" C24 CLR R 502 " ideal model delta sigma weight residual 111.95 103.38 8.57 3.00e+00 1.11e-01 8.16e+00 angle pdb=" CA LEU R 51 " pdb=" CB LEU R 51 " pdb=" CG LEU R 51 " ideal model delta sigma weight residual 116.30 126.28 -9.98 3.50e+00 8.16e-02 8.14e+00 ... (remaining 12195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 4972 22.47 - 44.95: 332 44.95 - 67.42: 23 67.42 - 89.90: 4 89.90 - 112.37: 3 Dihedral angle restraints: 5334 sinusoidal: 2046 harmonic: 3288 Sorted by residual: dihedral pdb=" CA LYS R 217 " pdb=" C LYS R 217 " pdb=" N ILE R 218 " pdb=" CA ILE R 218 " ideal model delta harmonic sigma weight residual 180.00 -148.99 -31.01 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1109 0.055 - 0.109: 240 0.109 - 0.164: 53 0.164 - 0.218: 6 0.218 - 0.273: 2 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CB THR R 224 " pdb=" CA THR R 224 " pdb=" OG1 THR R 224 " pdb=" CG2 THR R 224 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C17 CLR R 502 " pdb=" C13 CLR R 502 " pdb=" C16 CLR R 502 " pdb=" C20 CLR R 502 " both_signs ideal model delta sigma weight residual False 2.55 2.78 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB VAL A 233 " pdb=" CA VAL A 233 " pdb=" CG1 VAL A 233 " pdb=" CG2 VAL A 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1407 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 90 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.44e+00 pdb=" C THR R 90 " 0.032 2.00e-02 2.50e+03 pdb=" O THR R 90 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL R 91 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO B 194 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 240 " 0.020 2.00e-02 2.50e+03 1.29e-02 3.34e+00 pdb=" CG TYR R 240 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR R 240 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR R 240 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR R 240 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 240 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 240 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 240 " 0.006 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1779 2.78 - 3.31: 7653 3.31 - 3.84: 15003 3.84 - 4.37: 17000 4.37 - 4.90: 30633 Nonbonded interactions: 72068 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.245 3.040 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.287 3.040 nonbonded pdb=" OE2 GLU A 14 " pdb=" OG1 THR D 57 " model vdw 2.289 3.040 nonbonded pdb=" O LEU R 133 " pdb=" OG1 THR R 137 " model vdw 2.293 3.040 nonbonded pdb=" O ASN R 21 " pdb=" OG SER R 25 " model vdw 2.294 3.040 ... (remaining 72063 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: 2.060 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: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.810 Find NCS groups from input model: 0.050 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 9000 Z= 0.240 Angle : 0.708 11.125 12202 Z= 0.357 Chirality : 0.049 0.273 1410 Planarity : 0.004 0.046 1513 Dihedral : 14.098 112.369 3205 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.25 (0.24), residues: 1120 helix: 0.36 (0.22), residues: 414 sheet: 0.59 (0.32), residues: 286 loop : -1.15 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 67 TYR 0.030 0.002 TYR R 240 PHE 0.020 0.002 PHE A 267 TRP 0.021 0.002 TRP R 297 HIS 0.005 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 8999) covalent geometry : angle 0.70833 (12200) SS BOND : bond 0.00064 ( 1) SS BOND : angle 0.28220 ( 2) hydrogen bonds : bond 0.15993 ( 467) hydrogen bonds : angle 6.11056 ( 1338) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.346 Fit side-chains REVERT: A 26 ASP cc_start: 0.7783 (m-30) cc_final: 0.7396 (m-30) REVERT: A 240 MET cc_start: 0.4803 (pmm) cc_final: 0.4514 (pmm) REVERT: B 170 ASP cc_start: 0.7977 (t70) cc_final: 0.7591 (t0) REVERT: B 191 SER cc_start: 0.8600 (t) cc_final: 0.8381 (p) REVERT: D 144 SER cc_start: 0.8624 (m) cc_final: 0.8215 (t) REVERT: R 16 GLU cc_start: 0.7587 (pt0) cc_final: 0.7328 (pt0) REVERT: R 19 ILE cc_start: 0.8249 (mm) cc_final: 0.8025 (tp) REVERT: R 87 ASN cc_start: 0.8530 (m-40) cc_final: 0.8285 (m-40) REVERT: R 95 PHE cc_start: 0.7876 (m-10) cc_final: 0.7538 (m-80) REVERT: R 301 MET cc_start: 0.4282 (tpt) cc_final: 0.3935 (tpt) outliers start: 0 outliers final: 1 residues processed: 230 average time/residue: 0.4969 time to fit residues: 123.0590 Evaluate side-chains 202 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 261 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.4832 > 50: distance: 41 - 70: 7.781 distance: 46 - 51: 3.112 distance: 47 - 81: 13.318 distance: 51 - 52: 4.733 distance: 52 - 53: 7.959 distance: 52 - 55: 3.180 distance: 53 - 54: 20.992 distance: 53 - 62: 8.194 distance: 54 - 89: 12.797 distance: 55 - 56: 5.762 distance: 56 - 57: 7.753 distance: 56 - 58: 6.856 distance: 57 - 59: 16.935 distance: 58 - 60: 8.007 distance: 59 - 61: 12.110 distance: 60 - 61: 9.468 distance: 62 - 63: 7.289 distance: 63 - 64: 12.817 distance: 63 - 66: 11.690 distance: 64 - 65: 7.658 distance: 64 - 70: 9.037 distance: 65 - 97: 33.918 distance: 66 - 67: 12.745 distance: 67 - 68: 7.438 distance: 67 - 69: 24.598 distance: 71 - 72: 3.876 distance: 71 - 74: 6.906 distance: 72 - 73: 4.734 distance: 72 - 81: 4.802 distance: 73 - 105: 23.778 distance: 75 - 76: 6.035 distance: 75 - 77: 11.391 distance: 76 - 78: 8.081 distance: 77 - 79: 7.469 distance: 78 - 80: 10.247 distance: 79 - 80: 5.025 distance: 81 - 82: 7.181 distance: 82 - 83: 9.042 distance: 82 - 85: 13.903 distance: 83 - 84: 18.757 distance: 83 - 89: 33.045 distance: 84 - 110: 29.609 distance: 85 - 86: 7.390 distance: 86 - 87: 8.549 distance: 86 - 88: 12.923 distance: 89 - 90: 30.028 distance: 90 - 91: 14.211 distance: 90 - 93: 7.696 distance: 91 - 92: 6.269 distance: 91 - 97: 11.900 distance: 92 - 118: 9.235 distance: 93 - 94: 24.781 distance: 94 - 95: 19.231 distance: 94 - 96: 3.587 distance: 97 - 98: 13.260 distance: 98 - 99: 8.973 distance: 98 - 101: 15.297 distance: 99 - 100: 9.682 distance: 99 - 105: 6.879 distance: 100 - 126: 24.580 distance: 101 - 102: 16.875 distance: 101 - 103: 16.419 distance: 102 - 104: 19.522 distance: 105 - 106: 15.441 distance: 106 - 107: 16.915 distance: 106 - 109: 5.362 distance: 107 - 108: 20.624 distance: 107 - 110: 14.006 distance: 108 - 134: 13.025 distance: 110 - 111: 16.241 distance: 111 - 112: 7.675 distance: 111 - 114: 15.806 distance: 112 - 113: 11.993 distance: 112 - 118: 4.228 distance: 113 - 142: 16.820 distance: 114 - 115: 4.879 distance: 115 - 116: 16.650 distance: 115 - 117: 13.432 distance: 119 - 120: 4.742 distance: 119 - 122: 8.964 distance: 120 - 121: 12.746 distance: 120 - 126: 4.981 distance: 121 - 152: 17.630 distance: 122 - 123: 16.156 distance: 122 - 124: 15.652 distance: 123 - 125: 9.713 distance: 126 - 127: 5.286 distance: 127 - 128: 8.453 distance: 127 - 130: 11.852 distance: 128 - 129: 10.134 distance: 129 - 160: 8.255 distance: 130 - 131: 5.013 distance: 131 - 132: 4.821 distance: 131 - 133: 3.775