Starting phenix.real_space_refine on Thu Feb 15 03:20:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/02_2024/7tj9_25920_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/02_2024/7tj9_25920.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/02_2024/7tj9_25920_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/02_2024/7tj9_25920_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/02_2024/7tj9_25920_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/02_2024/7tj9_25920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/02_2024/7tj9_25920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/02_2024/7tj9_25920_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/02_2024/7tj9_25920_updated.pdb" } resolution = 2.9 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= 0.036 sd= 0.047 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 P 4 5.49 5 S 92 5.16 5 C 7379 2.51 5 N 1642 2.21 5 O 1858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 982": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10975 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 9054 Classifications: {'peptide': 1111} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 1072} Chain breaks: 3 Chain: "B" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1322 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 515 Unusual residues: {'CLR': 2, 'NAG': 1, 'PEV': 3, 'PLM': 8, 'POV': 3, 'Q7G': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.26, per 1000 atoms: 0.48 Number of scatterers: 10975 At special positions: 0 Unit cell: (126.963, 114.15, 114.15, 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 92 16.00 P 4 15.00 O 1858 8.00 N 1642 7.00 C 7379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 267 " - pdb=" SG CYS A 307 " distance=2.05 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 664 " distance=2.03 Simple disulfide: pdb=" SG CYS A 696 " - pdb=" SG CYS A 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A1087 " - pdb=" SG CYS A1107 " distance=2.03 Simple disulfide: pdb=" SG CYS A1451 " - pdb=" SG CYS A1466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 48 " distance=2.03 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 120 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A2412 " - " ASN A1103 " " NAG B 301 " - " ASN B 121 " " NAG B 302 " - " ASN B 95 " " NAG B 303 " - " ASN B 113 " " NAG B 304 " - " ASN B 109 " " NAG C 1 " - " ASN A 309 " Time building additional restraints: 13.46 Conformation dependent library (CDL) restraints added in 3.4 seconds 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 5 sheets defined 62.9% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'A' and resid 144 through 166 Processing helix chain 'A' and resid 179 through 195 removed outlier: 3.506A pdb=" N LEU A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 218 removed outlier: 3.518A pdb=" N THR A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 221 through 259 removed outlier: 3.787A pdb=" N ILE A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL A 240 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 355 through 365 Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.988A pdb=" N ILE A 372 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 403 Processing helix chain 'A' and resid 508 through 524 Processing helix chain 'A' and resid 532 through 558 removed outlier: 3.749A pdb=" N LEU A 537 " --> pdb=" O THR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 removed outlier: 3.706A pdb=" N PHE A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 584 Processing helix chain 'A' and resid 596 through 609 removed outlier: 4.282A pdb=" N MET A 600 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR A 609 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 655 removed outlier: 4.732A pdb=" N VAL A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ALA A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASN A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 691 through 699 removed outlier: 3.597A pdb=" N ASP A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 732 Proline residue: A 707 - end of helix Processing helix chain 'A' and resid 922 through 932 Processing helix chain 'A' and resid 934 through 953 removed outlier: 3.906A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 952 " --> pdb=" O THR A 948 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A 953 " --> pdb=" O GLY A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 990 removed outlier: 3.646A pdb=" N ILE A 966 " --> pdb=" O LYS A 962 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 996 Processing helix chain 'A' and resid 999 through 1018 removed outlier: 3.920A pdb=" N LYS A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1040 removed outlier: 3.602A pdb=" N SER A1028 " --> pdb=" O PRO A1025 " (cutoff:3.500A) Proline residue: A1034 - end of helix removed outlier: 3.628A pdb=" N GLN A1040 " --> pdb=" O VAL A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1055 Processing helix chain 'A' and resid 1059 through 1080 Processing helix chain 'A' and resid 1104 through 1108 Processing helix chain 'A' and resid 1128 through 1139 Processing helix chain 'A' and resid 1144 through 1153 Processing helix chain 'A' and resid 1167 through 1179 removed outlier: 3.748A pdb=" N ILE A1174 " --> pdb=" O CYS A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1203 Processing helix chain 'A' and resid 1212 through 1226 removed outlier: 4.313A pdb=" N LYS A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A1217 " --> pdb=" O LYS A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1249 removed outlier: 3.588A pdb=" N THR A1249 " --> pdb=" O PHE A1245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1245 through 1249' Processing helix chain 'A' and resid 1251 through 1270 removed outlier: 3.530A pdb=" N MET A1268 " --> pdb=" O GLN A1264 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET A1269 " --> pdb=" O ALA A1265 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE A1270 " --> pdb=" O ILE A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1304 removed outlier: 3.524A pdb=" N ILE A1281 " --> pdb=" O LEU A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1334 Proline residue: A1332 - end of helix Processing helix chain 'A' and resid 1344 through 1357 removed outlier: 3.574A pdb=" N SER A1351 " --> pdb=" O LEU A1347 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG A1352 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE A1353 " --> pdb=" O LEU A1349 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A1354 " --> pdb=" O LEU A1350 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N HIS A1355 " --> pdb=" O SER A1351 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N MET A1356 " --> pdb=" O ARG A1352 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU A1357 " --> pdb=" O ILE A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1402 Proline residue: A1372 - end of helix Proline residue: A1378 - end of helix Processing helix chain 'A' and resid 1420 through 1431 Processing helix chain 'A' and resid 1436 through 1446 removed outlier: 4.015A pdb=" N ASN A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N SER A1446 " --> pdb=" O ALA A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1502 Processing helix chain 'B' and resid 153 through 185 Processing sheet with id= A, first strand: chain 'A' and resid 265 through 269 Processing sheet with id= B, first strand: chain 'A' and resid 1086 through 1088 Processing sheet with id= C, first strand: chain 'B' and resid 34 through 36 removed outlier: 6.666A pdb=" N ARG B 144 " --> pdb=" O ALA B 35 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 41 through 43 Processing sheet with id= E, first strand: chain 'B' and resid 134 through 143 removed outlier: 3.592A pdb=" N VAL B 122 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR B 75 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR B 64 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU B 73 " --> pdb=" O TYR B 64 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1659 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: 2.77 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3070 1.34 - 1.46: 2878 1.46 - 1.59: 4970 1.59 - 1.71: 177 1.71 - 1.84: 157 Bond restraints: 11252 Sorted by residual: bond pdb=" C29 POV A2403 " pdb="C210 POV A2403 " ideal model delta sigma weight residual 1.333 1.638 -0.305 2.00e-02 2.50e+03 2.33e+02 bond pdb=" C13 Q7G A2418 " pdb=" C14 Q7G A2418 " ideal model delta sigma weight residual 1.599 1.318 0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C07 Q7G A2418 " pdb=" C15 Q7G A2418 " ideal model delta sigma weight residual 1.779 1.515 0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" O14 POV A2408 " pdb=" P POV A2408 " ideal model delta sigma weight residual 1.496 1.748 -0.252 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C73 Q7G A2418 " pdb=" O72 Q7G A2418 " ideal model delta sigma weight residual 1.338 1.577 -0.239 2.00e-02 2.50e+03 1.42e+02 ... (remaining 11247 not shown) Histogram of bond angle deviations from ideal: 90.40 - 99.16: 5 99.16 - 107.92: 450 107.92 - 116.68: 7278 116.68 - 125.43: 7257 125.43 - 134.19: 185 Bond angle restraints: 15175 Sorted by residual: angle pdb=" C74 Q7G A2418 " pdb=" C73 Q7G A2418 " pdb=" C76 Q7G A2418 " ideal model delta sigma weight residual 109.92 131.39 -21.47 3.00e+00 1.11e-01 5.12e+01 angle pdb=" C51 Q7G A2418 " pdb=" C61 Q7G A2418 " pdb=" O61 Q7G A2418 " ideal model delta sigma weight residual 109.51 130.90 -21.39 3.00e+00 1.11e-01 5.08e+01 angle pdb=" C74 Q7G A2418 " pdb=" C73 Q7G A2418 " pdb=" O80 Q7G A2418 " ideal model delta sigma weight residual 109.75 90.40 19.35 3.00e+00 1.11e-01 4.16e+01 angle pdb=" O3P PEV A2411 " pdb=" P PEV A2411 " pdb=" O4P PEV A2411 " ideal model delta sigma weight residual 93.57 110.99 -17.42 3.00e+00 1.11e-01 3.37e+01 angle pdb=" O3P PEV A2401 " pdb=" P PEV A2401 " pdb=" O4P PEV A2401 " ideal model delta sigma weight residual 93.57 110.49 -16.92 3.00e+00 1.11e-01 3.18e+01 ... (remaining 15170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.44: 6515 29.44 - 58.87: 292 58.87 - 88.31: 37 88.31 - 117.74: 27 117.74 - 147.18: 5 Dihedral angle restraints: 6876 sinusoidal: 3148 harmonic: 3728 Sorted by residual: dihedral pdb=" CB CYS A 267 " pdb=" SG CYS A 267 " pdb=" SG CYS A 307 " pdb=" CB CYS A 307 " ideal model delta sinusoidal sigma weight residual -86.00 -155.57 69.57 1 1.00e+01 1.00e-02 6.25e+01 dihedral pdb=" CA HIS A 560 " pdb=" C HIS A 560 " pdb=" N PRO A 561 " pdb=" CA PRO A 561 " ideal model delta harmonic sigma weight residual 180.00 -151.62 -28.38 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" C4B Q7G A2418 " pdb=" C5B Q7G A2418 " pdb=" C6B Q7G A2418 " pdb=" O6B Q7G A2418 " ideal model delta sinusoidal sigma weight residual 143.94 -68.88 -147.18 1 3.00e+01 1.11e-03 1.96e+01 ... (remaining 6873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 1712 0.180 - 0.360: 10 0.360 - 0.540: 3 0.540 - 0.720: 1 0.720 - 0.900: 1 Chirality restraints: 1727 Sorted by residual: chirality pdb=" C1 NAG B 301 " pdb=" ND2 ASN B 121 " pdb=" C2 NAG B 301 " pdb=" O5 NAG B 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" C02 Q7G A2418 " pdb=" C03 Q7G A2418 " pdb=" C06 Q7G A2418 " pdb=" C10 Q7G A2418 " both_signs ideal model delta sigma weight residual False 2.14 2.84 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C2 POV A2402 " pdb=" C1 POV A2402 " pdb=" C3 POV A2402 " pdb=" O21 POV A2402 " both_signs ideal model delta sigma weight residual False 2.43 2.92 -0.49 2.00e-01 2.50e+01 5.99e+00 ... (remaining 1724 not shown) Planarity restraints: 1797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 303 " -0.331 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG B 303 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B 303 " -0.140 2.00e-02 2.50e+03 pdb=" N2 NAG B 303 " 0.511 2.00e-02 2.50e+03 pdb=" O7 NAG B 303 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 301 " 0.289 2.00e-02 2.50e+03 2.42e-01 7.32e+02 pdb=" C7 NAG B 301 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG B 301 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG B 301 " -0.412 2.00e-02 2.50e+03 pdb=" O7 NAG B 301 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2412 " 0.239 2.00e-02 2.50e+03 2.00e-01 5.00e+02 pdb=" C7 NAG A2412 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG A2412 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG A2412 " -0.336 2.00e-02 2.50e+03 pdb=" O7 NAG A2412 " -0.006 2.00e-02 2.50e+03 ... (remaining 1794 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 433 2.71 - 3.26: 11177 3.26 - 3.81: 17225 3.81 - 4.35: 21641 4.35 - 4.90: 36754 Nonbonded interactions: 87230 Sorted by model distance: nonbonded pdb=" O THR A 207 " pdb=" OG1 THR A 210 " model vdw 2.167 2.440 nonbonded pdb=" OD1 ASN A 149 " pdb=" OH TYR A 196 " model vdw 2.210 2.440 nonbonded pdb=" O ALA A 642 " pdb=" OG SER A 677 " model vdw 2.238 2.440 nonbonded pdb=" O THR B 111 " pdb=" OD1 ASP B 114 " model vdw 2.253 3.040 nonbonded pdb=" O PHE A1072 " pdb=" OH TYR A1172 " model vdw 2.297 2.440 ... (remaining 87225 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 4.040 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 27.010 Find NCS groups from input model: 0.210 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:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -oh -his -flip -keep -allalt -limit120 -pen9999 -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: