Starting phenix.real_space_refine on Tue Mar 11 17:47:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ge1_29952/03_2025/8ge1_29952.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ge1_29952/03_2025/8ge1_29952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ge1_29952/03_2025/8ge1_29952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ge1_29952/03_2025/8ge1_29952.map" model { file = "/net/cci-nas-00/data/ceres_data/8ge1_29952/03_2025/8ge1_29952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ge1_29952/03_2025/8ge1_29952.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.035 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 39 5.16 5 C 4169 2.51 5 N 1133 2.21 5 O 1123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6464 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1670 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 177 Chain: "B" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2349 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 5, 'TRANS': 327} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 6, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 149 Chain: "G" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 356 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2074 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 126 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: 5.65, per 1000 atoms: 0.87 Number of scatterers: 6464 At special positions: 0 Unit cell: (72.08, 97.52, 126.14, 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 39 16.00 O 1123 8.00 N 1133 7.00 C 4169 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 1.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 48.3% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.806A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.544A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (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: 3.612A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.538A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 9 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.566A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 30 through 61 removed outlier: 3.584A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.602A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.621A 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 Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.069A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.938A 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 178 through 187 Processing helix chain 'R' and resid 196 through 237 removed outlier: 5.185A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix Processing helix chain 'R' and resid 269 through 299 removed outlier: 4.531A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.871A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.321A 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 207 through 214 removed outlier: 4.483A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.188A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.630A 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: 4.147A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.611A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.651A 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: 6.252A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.997A 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: 3.547A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.115A 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: 6.374A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.912A 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: 3.648A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1167 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: 1.96 Time building geometry restraints manager: 1.85 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: 2084 1.34 - 1.45: 966 1.45 - 1.57: 3501 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 6605 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 7.04e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.439 -0.045 2.00e-02 2.50e+03 5.11e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.567 -0.044 2.00e-02 2.50e+03 4.79e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.563 -0.043 2.00e-02 2.50e+03 4.68e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.322 0.031 2.00e-02 2.50e+03 2.37e+00 ... (remaining 6600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 8882 1.51 - 3.01: 118 3.01 - 4.52: 21 4.52 - 6.02: 12 6.02 - 7.53: 2 Bond angle restraints: 9035 Sorted by residual: angle pdb=" N GLN R 299 " pdb=" CA GLN R 299 " pdb=" C GLN R 299 " ideal model delta sigma weight residual 113.56 108.25 5.31 1.39e+00 5.18e-01 1.46e+01 angle pdb=" CA GLN R 299 " pdb=" CB GLN R 299 " pdb=" CG GLN R 299 " ideal model delta sigma weight residual 114.10 120.93 -6.83 2.00e+00 2.50e-01 1.17e+01 angle pdb=" C GLY A 49 " pdb=" N GLU A 50 " pdb=" CA GLU A 50 " ideal model delta sigma weight residual 122.61 127.54 -4.93 1.56e+00 4.11e-01 9.97e+00 angle pdb=" N GLN R 231 " pdb=" CA GLN R 231 " pdb=" CB GLN R 231 " ideal model delta sigma weight residual 110.28 115.07 -4.79 1.55e+00 4.16e-01 9.57e+00 angle pdb=" C ARG A 283 " pdb=" N THR A 284 " pdb=" CA THR A 284 " ideal model delta sigma weight residual 123.47 127.84 -4.37 1.53e+00 4.27e-01 8.17e+00 ... (remaining 9030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3525 17.91 - 35.82: 248 35.82 - 53.73: 33 53.73 - 71.64: 4 71.64 - 89.55: 2 Dihedral angle restraints: 3812 sinusoidal: 1164 harmonic: 2648 Sorted by residual: 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 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA LEU R 144 " pdb=" C LEU R 144 " pdb=" N LEU R 145 " pdb=" CA LEU R 145 " ideal model delta harmonic sigma weight residual 180.00 164.08 15.92 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CG LYS B 209 " pdb=" CD LYS B 209 " pdb=" CE LYS B 209 " pdb=" NZ LYS B 209 " ideal model delta sinusoidal sigma weight residual 180.00 129.03 50.97 3 1.50e+01 4.44e-03 8.96e+00 ... (remaining 3809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 710 0.033 - 0.065: 246 0.065 - 0.098: 80 0.098 - 0.130: 42 0.130 - 0.163: 2 Chirality restraints: 1080 Sorted by residual: 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 2.56 -0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CA GLN R 231 " pdb=" N GLN R 231 " pdb=" C GLN R 231 " pdb=" CB GLN R 231 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1077 not shown) Planarity restraints: 1142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.43e+00 pdb=" C ILE R 205 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE R 205 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL R 206 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 343 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" CG ASP A 343 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASP A 343 " -0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP A 343 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.010 2.00e-02 2.50e+03 7.96e-03 1.27e+00 pdb=" CG TYR B 59 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.000 2.00e-02 2.50e+03 ... (remaining 1139 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 585 2.74 - 3.28: 6463 3.28 - 3.82: 10904 3.82 - 4.36: 11865 4.36 - 4.90: 21836 Nonbonded interactions: 51653 Sorted by model distance: nonbonded pdb=" OG SER B 279 " pdb=" OD2 ASP G 48 " model vdw 2.203 3.040 nonbonded pdb=" O ARG A 283 " pdb=" OG1 THR A 284 " model vdw 2.217 3.040 nonbonded pdb=" OG SER B 281 " pdb=" O HIS G 44 " model vdw 2.240 3.040 nonbonded pdb=" NH2 ARG R 221 " pdb=" OE2 GLU R 225 " model vdw 2.327 3.120 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.334 3.040 ... (remaining 51648 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 0.053 6605 Z= 0.194 Angle : 0.506 7.531 9035 Z= 0.278 Chirality : 0.041 0.163 1080 Planarity : 0.003 0.027 1142 Dihedral : 12.486 89.546 2089 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.28), residues: 892 helix: 2.56 (0.25), residues: 392 sheet: 0.47 (0.38), residues: 168 loop : -0.32 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 93 PHE 0.016 0.001 PHE B 234 TYR 0.019 0.001 TYR B 59 ARG 0.004 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.786 Fit side-chains REVERT: A 60 MET cc_start: 0.8388 (mpp) cc_final: 0.8080 (mpp) REVERT: A 343 ASP cc_start: 0.8477 (m-30) cc_final: 0.8208 (m-30) REVERT: B 61 MET cc_start: 0.8325 (ppp) cc_final: 0.8110 (ttp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1703 time to fit residues: 22.8877 Evaluate side-chains 81 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN R 93 HIS ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.108573 restraints weight = 10180.717| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.80 r_work: 0.3264 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6605 Z= 0.171 Angle : 0.484 7.507 9035 Z= 0.261 Chirality : 0.042 0.141 1080 Planarity : 0.003 0.022 1142 Dihedral : 3.944 24.089 980 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.91 % Allowed : 7.99 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.28), residues: 892 helix: 2.78 (0.25), residues: 402 sheet: 0.59 (0.38), residues: 162 loop : -0.27 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.005 0.001 HIS R 93 PHE 0.011 0.001 PHE B 234 TYR 0.016 0.001 TYR B 59 ARG 0.003 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.711 Fit side-chains REVERT: G 48 ASP cc_start: 0.8270 (t0) cc_final: 0.8064 (t0) REVERT: R 93 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.8498 (t-90) outliers start: 5 outliers final: 3 residues processed: 96 average time/residue: 0.1714 time to fit residues: 22.6149 Evaluate side-chains 86 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 228 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.5734 > 50: distance: 70 - 145: 29.281 distance: 73 - 142: 25.457 distance: 81 - 131: 30.418 distance: 84 - 128: 37.073 distance: 91 - 93: 33.654 distance: 93 - 94: 4.627 distance: 94 - 95: 41.543 distance: 94 - 97: 40.303 distance: 95 - 96: 51.306 distance: 95 - 101: 47.799 distance: 97 - 98: 13.707 distance: 98 - 99: 11.676 distance: 98 - 100: 40.635 distance: 101 - 102: 29.036 distance: 102 - 103: 27.080 distance: 103 - 104: 12.937 distance: 103 - 106: 6.527 distance: 106 - 107: 31.980 distance: 107 - 108: 29.884 distance: 107 - 110: 26.022 distance: 108 - 109: 46.753 distance: 108 - 114: 47.172 distance: 110 - 111: 37.515 distance: 111 - 112: 56.715 distance: 114 - 115: 53.253 distance: 115 - 118: 6.653 distance: 116 - 117: 5.652 distance: 116 - 122: 41.427 distance: 118 - 119: 62.436 distance: 119 - 121: 41.203 distance: 122 - 123: 12.556 distance: 123 - 124: 29.749 distance: 123 - 126: 42.744 distance: 124 - 125: 36.875 distance: 124 - 128: 31.553 distance: 126 - 127: 34.949 distance: 128 - 129: 31.270 distance: 129 - 130: 20.876 distance: 129 - 132: 32.112 distance: 130 - 131: 20.972 distance: 130 - 134: 38.877 distance: 132 - 133: 40.926 distance: 134 - 135: 36.024 distance: 135 - 136: 19.814 distance: 135 - 138: 24.145 distance: 136 - 137: 46.709 distance: 136 - 142: 30.652 distance: 137 - 198: 32.473 distance: 138 - 139: 27.603 distance: 138 - 140: 22.589 distance: 139 - 141: 59.068 distance: 142 - 143: 17.462 distance: 143 - 146: 11.895 distance: 144 - 145: 9.957 distance: 144 - 154: 13.097 distance: 146 - 147: 11.984 distance: 147 - 148: 23.501 distance: 147 - 149: 12.639 distance: 148 - 150: 31.162 distance: 149 - 151: 27.625 distance: 150 - 152: 7.289 distance: 151 - 152: 12.421 distance: 152 - 153: 12.351 distance: 154 - 155: 11.880 distance: 155 - 156: 46.185 distance: 155 - 158: 11.980 distance: 156 - 157: 5.810 distance: 156 - 162: 61.723 distance: 158 - 159: 36.052 distance: 159 - 160: 23.390 distance: 159 - 161: 19.936 distance: 162 - 163: 25.385 distance: 163 - 164: 10.558 distance: 163 - 166: 24.495 distance: 164 - 165: 17.969 distance: 164 - 170: 27.095 distance: 166 - 167: 41.394 distance: 167 - 168: 25.909 distance: 167 - 169: 17.103