Starting phenix.real_space_refine on Thu Mar 14 08:12:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/03_2024/7dfl_30665_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/03_2024/7dfl_30665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/03_2024/7dfl_30665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/03_2024/7dfl_30665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/03_2024/7dfl_30665_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/03_2024/7dfl_30665_neut_updated.pdb" } resolution = 3.3 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= 0.078 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 66 5.16 5 C 5729 2.51 5 N 1535 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 153": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8987 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2273 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "A" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1847 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain breaks: 2 Chain: "C" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1808 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.22, per 1000 atoms: 0.58 Number of scatterers: 8987 At special positions: 0 Unit cell: (90.72, 119.88, 126.36, 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 66 16.00 O 1657 8.00 N 1535 7.00 C 5729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 180 " distance=2.04 Simple disulfide: pdb=" SG CYS R 441 " - pdb=" SG CYS R 444 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 229 " distance=1.95 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 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.7 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 13 sheets defined 33.5% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'R' and resid 29 through 52 Processing helix chain 'R' and resid 61 through 79 removed outlier: 4.084A pdb=" N TYR R 65 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 89 Processing helix chain 'R' and resid 97 through 130 Processing helix chain 'R' and resid 141 through 163 removed outlier: 4.816A pdb=" N TRP R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL R 159 " --> pdb=" O SER R 155 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE R 160 " --> pdb=" O PHE R 156 " (cutoff:3.500A) Proline residue: R 161 - end of helix Processing helix chain 'R' and resid 169 through 171 No H-bonds generated for 'chain 'R' and resid 169 through 171' Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 200 through 217 Processing helix chain 'R' and resid 409 through 438 Proline residue: R 430 - end of helix removed outlier: 3.735A pdb=" N PHE R 434 " --> pdb=" O PRO R 430 " (cutoff:3.500A) Processing helix chain 'R' and resid 446 through 466 removed outlier: 3.586A pdb=" N ASN R 460 " --> pdb=" O LEU R 456 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER R 461 " --> pdb=" O GLY R 457 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR R 462 " --> pdb=" O TYR R 458 " (cutoff:3.500A) Proline residue: R 465 - end of helix Processing helix chain 'R' and resid 469 through 471 No H-bonds generated for 'chain 'R' and resid 469 through 471' Processing helix chain 'R' and resid 476 through 481 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'A' and resid 7 through 36 removed outlier: 4.128A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 247 through 259 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 277 through 283 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 336 through 355 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 53 through 55 No H-bonds generated for 'chain 'C' and resid 53 through 55' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.970A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.047A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.861A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.847A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 240 through 245 removed outlier: 4.086A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 276 through 278 Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.936A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 268 through 274 removed outlier: 4.112A pdb=" N SER A 225 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A 200 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LEU A 42 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG A 202 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU A 44 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 204 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'C' and resid 115 through 117 removed outlier: 5.827A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU C 45 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'C' and resid 146 through 149 removed outlier: 7.459A pdb=" N LYS C 244 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL C 149 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU C 246 " --> pdb=" O VAL C 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 226 through 231 removed outlier: 6.055A pdb=" N LEU C 178 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU C 187 " --> pdb=" O LEU C 178 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1098 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: 2.80 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2897 1.35 - 1.47: 2300 1.47 - 1.59: 3884 1.59 - 1.71: 0 1.71 - 1.84: 100 Bond restraints: 9181 Sorted by residual: bond pdb=" C VAL R 80 " pdb=" O VAL R 80 " ideal model delta sigma weight residual 1.233 1.285 -0.052 1.02e-02 9.61e+03 2.60e+01 bond pdb=" N THR C 118 " pdb=" CA THR C 118 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.23e-02 6.61e+03 1.76e+01 bond pdb=" N PRO C 236 " pdb=" CD PRO C 236 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" N LEU C 187 " pdb=" CA LEU C 187 " ideal model delta sigma weight residual 1.456 1.503 -0.046 1.22e-02 6.72e+03 1.44e+01 bond pdb=" N VAL R 80 " pdb=" CA VAL R 80 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.19e-02 7.06e+03 1.30e+01 ... (remaining 9176 not shown) Histogram of bond angle deviations from ideal: 96.80 - 104.25: 118 104.25 - 111.70: 4235 111.70 - 119.14: 3207 119.14 - 126.59: 4731 126.59 - 134.04: 136 Bond angle restraints: 12427 Sorted by residual: angle pdb=" N ARG R 218 " pdb=" CA ARG R 218 " pdb=" C ARG R 218 " ideal model delta sigma weight residual 110.80 121.85 -11.05 2.13e+00 2.20e-01 2.69e+01 angle pdb=" N SER C 136 " pdb=" CA SER C 136 " pdb=" C SER C 136 " ideal model delta sigma weight residual 110.80 100.47 10.33 2.13e+00 2.20e-01 2.35e+01 angle pdb=" N ARG R 134 " pdb=" CA ARG R 134 " pdb=" C ARG R 134 " ideal model delta sigma weight residual 108.58 99.99 8.59 1.82e+00 3.02e-01 2.23e+01 angle pdb=" N HIS R 406 " pdb=" CA HIS R 406 " pdb=" C HIS R 406 " ideal model delta sigma weight residual 108.02 116.30 -8.28 1.78e+00 3.16e-01 2.16e+01 angle pdb=" N CYS R 445 " pdb=" CA CYS R 445 " pdb=" C CYS R 445 " ideal model delta sigma weight residual 110.80 101.30 9.50 2.13e+00 2.20e-01 1.99e+01 ... (remaining 12422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 5048 16.82 - 33.65: 340 33.65 - 50.47: 54 50.47 - 67.29: 9 67.29 - 84.12: 6 Dihedral angle restraints: 5457 sinusoidal: 2162 harmonic: 3295 Sorted by residual: dihedral pdb=" C SER C 136 " pdb=" N SER C 136 " pdb=" CA SER C 136 " pdb=" CB SER C 136 " ideal model delta harmonic sigma weight residual -122.60 -110.84 -11.76 0 2.50e+00 1.60e-01 2.21e+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 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ARG R 134 " pdb=" C ARG R 134 " pdb=" N TYR R 135 " pdb=" CA TYR R 135 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1233 0.085 - 0.169: 142 0.169 - 0.254: 14 0.254 - 0.339: 2 0.339 - 0.423: 2 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA SER C 136 " pdb=" N SER C 136 " pdb=" C SER C 136 " pdb=" CB SER C 136 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA SER B 67 " pdb=" N SER B 67 " pdb=" C SER B 67 " pdb=" CB SER B 67 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA ARG R 218 " pdb=" N ARG R 218 " pdb=" C ARG R 218 " pdb=" CB ARG R 218 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1390 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 235 " 0.061 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO C 236 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 435 " -0.029 2.00e-02 2.50e+03 2.46e-02 1.06e+01 pdb=" CG PHE R 435 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE R 435 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 435 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE R 435 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 435 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE R 435 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " -0.025 2.00e-02 2.50e+03 2.02e-02 7.15e+00 pdb=" CG PHE B 234 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " -0.004 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 34 2.51 - 3.11: 7019 3.11 - 3.70: 13399 3.70 - 4.30: 19462 4.30 - 4.90: 32443 Nonbonded interactions: 72357 Sorted by model distance: nonbonded pdb=" SD MET A 203 " pdb=" CE MET A 227 " model vdw 1.910 3.820 nonbonded pdb=" O ILE B 43 " pdb=" NH2 ARG B 304 " model vdw 2.129 2.520 nonbonded pdb=" O ILE R 37 " pdb=" OG1 THR R 41 " model vdw 2.165 2.440 nonbonded pdb=" OG SER B 227 " pdb=" OD1 ASP B 247 " model vdw 2.186 2.440 nonbonded pdb=" OD2 ASP B 212 " pdb=" N GLU B 215 " model vdw 2.297 2.520 ... (remaining 72352 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: 0.010 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: 3.810 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.480 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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: