Starting phenix.real_space_refine (version: dev) on Tue Mar 14 04:57:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evz_31342/03_2023/7evz_31342_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evz_31342/03_2023/7evz_31342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evz_31342/03_2023/7evz_31342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evz_31342/03_2023/7evz_31342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evz_31342/03_2023/7evz_31342_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evz_31342/03_2023/7evz_31342_updated.pdb" } resolution = 3.07 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 ------------------------------------------------------------------------------- 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= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1983 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "E PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E GLU 246": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 9078 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1838 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2296 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 6, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Unusual residues: {'JER': 1, 'PLM': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.39, per 1000 atoms: 0.59 Number of scatterers: 9078 At special positions: 0 Unit cell: (90.63, 123.975, 128.25, 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 64 16.00 O 1683 8.00 N 1521 7.00 C 5810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 282 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " 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 Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.5 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 14 sheets defined 32.4% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.828A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 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 242 through 254 Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 removed outlier: 3.939A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 350 removed outlier: 3.646A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.695A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'D' and resid 23 through 32 Processing helix chain 'D' and resid 49 through 72 Processing helix chain 'D' and resid 79 through 104 removed outlier: 3.769A pdb=" N PHE D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 84 " --> pdb=" O MET D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.546A pdb=" N TYR D 110 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 111 " --> pdb=" O THR D 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 107 through 111' Processing helix chain 'D' and resid 114 through 147 removed outlier: 3.512A pdb=" N GLU D 121 " --> pdb=" O TRP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 180 Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 200 through 235 removed outlier: 3.931A pdb=" N VAL D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 267 removed outlier: 3.545A pdb=" N LYS D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR D 257 " --> pdb=" O ALA D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.977A pdb=" N VAL D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 313 removed outlier: 3.505A pdb=" N ALA D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 316 through 324 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.861A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.087A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE B 93 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.502A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.573A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.536A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.528A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.544A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.530A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.512A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.780A pdb=" N THR E 118 " --> pdb=" O VAL E 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 115 through 117 removed outlier: 3.750A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= M, first strand: chain 'E' and resid 146 through 148 removed outlier: 7.066A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 225 through 231 removed outlier: 3.553A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1080 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: 2.69 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: 1.21 - 1.33: 2274 1.33 - 1.45: 1913 1.45 - 1.58: 4974 1.58 - 1.70: 3 1.70 - 1.82: 91 Bond restraints: 9255 Sorted by residual: bond pdb=" C31 JER D 401 " pdb=" C32 JER D 401 " ideal model delta sigma weight residual 1.543 1.361 0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" C28 JER D 401 " pdb=" C29 JER D 401 " ideal model delta sigma weight residual 1.532 1.354 0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" C28 JER D 401 " pdb=" C32 JER D 401 " ideal model delta sigma weight residual 1.537 1.651 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C10 JER D 401 " pdb=" C15 JER D 401 " ideal model delta sigma weight residual 1.460 1.374 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C22 JER D 401 " pdb=" O23 JER D 401 " ideal model delta sigma weight residual 1.332 1.410 -0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 9250 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.79: 188 106.79 - 113.59: 5102 113.59 - 120.39: 3483 120.39 - 127.19: 3634 127.19 - 133.99: 93 Bond angle restraints: 12500 Sorted by residual: angle pdb=" N PHE D 237 " pdb=" CA PHE D 237 " pdb=" C PHE D 237 " ideal model delta sigma weight residual 111.36 123.07 -11.71 1.09e+00 8.42e-01 1.15e+02 angle pdb=" N ARG D 238 " pdb=" CA ARG D 238 " pdb=" C ARG D 238 " ideal model delta sigma weight residual 113.16 123.13 -9.97 1.24e+00 6.50e-01 6.46e+01 angle pdb=" N LYS D 239 " pdb=" CA LYS D 239 " pdb=" C LYS D 239 " ideal model delta sigma weight residual 110.23 116.35 -6.12 1.45e+00 4.76e-01 1.78e+01 angle pdb=" N THR D 236 " pdb=" CA THR D 236 " pdb=" C THR D 236 " ideal model delta sigma weight residual 109.54 103.76 5.78 1.37e+00 5.33e-01 1.78e+01 angle pdb=" C26 JER D 401 " pdb=" C28 JER D 401 " pdb=" C29 JER D 401 " ideal model delta sigma weight residual 114.08 102.52 11.56 3.00e+00 1.11e-01 1.48e+01 ... (remaining 12495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5006 17.98 - 35.95: 423 35.95 - 53.93: 65 53.93 - 71.91: 11 71.91 - 89.88: 6 Dihedral angle restraints: 5511 sinusoidal: 2191 harmonic: 3320 Sorted by residual: dihedral pdb=" CB CYS D 184 " pdb=" SG CYS D 184 " pdb=" SG CYS D 191 " pdb=" CB CYS D 191 " ideal model delta sinusoidal sigma weight residual -86.00 -47.75 -38.25 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 65.20 27.80 1 1.00e+01 1.00e-02 1.11e+01 dihedral pdb=" CA ASP A 229 " pdb=" CB ASP A 229 " pdb=" CG ASP A 229 " pdb=" OD1 ASP A 229 " ideal model delta sinusoidal sigma weight residual -30.00 -87.29 57.29 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 5508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1357 0.093 - 0.186: 62 0.186 - 0.280: 4 0.280 - 0.373: 0 0.373 - 0.466: 1 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA PHE D 237 " pdb=" N PHE D 237 " pdb=" C PHE D 237 " pdb=" CB PHE D 237 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA GLU D 249 " pdb=" N GLU D 249 " pdb=" C GLU D 249 " pdb=" CB GLU D 249 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA SER D 251 " pdb=" N SER D 251 " pdb=" C SER D 251 " pdb=" CB SER D 251 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1421 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO E 236 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO C 49 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 239 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C LYS D 239 " -0.026 2.00e-02 2.50e+03 pdb=" O LYS D 239 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN D 240 " 0.009 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 289 2.71 - 3.26: 8647 3.26 - 3.80: 13775 3.80 - 4.35: 16940 4.35 - 4.90: 30045 Nonbonded interactions: 69696 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.160 2.440 nonbonded pdb=" OG SER D 192 " pdb=" O LEU D 195 " model vdw 2.180 2.440 nonbonded pdb=" OD2 ASP A 341 " pdb=" NZ LYS D 239 " model vdw 2.206 2.520 nonbonded pdb=" O THR D 236 " pdb=" OG1 THR D 236 " model vdw 2.218 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.259 2.440 ... (remaining 69691 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5810 2.51 5 N 1521 2.21 5 O 1683 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 4.620 Check model and map are aligned: 0.130 Process input model: 26.080 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.090 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: 35.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 : 0.004 0.182 9255 Z= 0.275 Angle : 0.585 11.711 12500 Z= 0.336 Chirality : 0.043 0.466 1424 Planarity : 0.003 0.053 1557 Dihedral : 13.304 89.882 3360 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 0.30 % 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: -1.99 (0.23), residues: 1126 helix: 0.22 (0.24), residues: 382 sheet: -1.46 (0.29), residues: 277 loop : -2.53 (0.23), residues: 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 1.019 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 155 average time/residue: 0.2937 time to fit residues: 59.0966 Evaluate side-chains 117 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1015 time to fit residues: 1.8669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.2980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 65 optimal weight: 0.1980 chunk 101 optimal weight: 10.0000 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 75 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS D 240 ASN E 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 9255 Z= 0.131 Angle : 0.477 7.706 12500 Z= 0.244 Chirality : 0.039 0.145 1424 Planarity : 0.003 0.055 1557 Dihedral : 5.324 67.071 1304 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 1.02 % 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: -0.83 (0.24), residues: 1126 helix: 1.60 (0.26), residues: 379 sheet: -1.02 (0.31), residues: 277 loop : -2.10 (0.25), residues: 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.850 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 130 average time/residue: 0.2296 time to fit residues: 39.0439 Evaluate side-chains 122 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0884 time to fit residues: 2.5050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.0470 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.0010 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.0980 chunk 100 optimal weight: 6.9990 overall best weight: 0.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 9255 Z= 0.159 Angle : 0.480 7.942 12500 Z= 0.245 Chirality : 0.039 0.154 1424 Planarity : 0.003 0.057 1557 Dihedral : 5.279 65.013 1304 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 1.32 % 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: -0.37 (0.25), residues: 1126 helix: 2.16 (0.27), residues: 379 sheet: -0.84 (0.31), residues: 277 loop : -1.95 (0.25), residues: 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.093 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 133 average time/residue: 0.2631 time to fit residues: 46.7267 Evaluate side-chains 127 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0847 time to fit residues: 2.6057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 102 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 32 GLN D 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 9255 Z= 0.164 Angle : 0.480 8.191 12500 Z= 0.245 Chirality : 0.039 0.162 1424 Planarity : 0.003 0.057 1557 Dihedral : 5.283 63.115 1304 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 1.73 % 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: -0.11 (0.25), residues: 1126 helix: 2.39 (0.27), residues: 380 sheet: -0.66 (0.32), residues: 274 loop : -1.84 (0.25), residues: 472 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.803 Fit side-chains outliers start: 17 outliers final: 6 residues processed: 132 average time/residue: 0.2141 time to fit residues: 37.8101 Evaluate side-chains 122 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0748 time to fit residues: 1.8788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9255 Z= 0.196 Angle : 0.512 8.843 12500 Z= 0.258 Chirality : 0.040 0.168 1424 Planarity : 0.003 0.059 1557 Dihedral : 5.362 62.942 1304 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.81 % 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: -0.02 (0.25), residues: 1126 helix: 2.50 (0.27), residues: 380 sheet: -0.69 (0.32), residues: 274 loop : -1.76 (0.25), residues: 472 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.111 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 128 average time/residue: 0.2665 time to fit residues: 45.6006 Evaluate side-chains 126 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0886 time to fit residues: 2.6558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN E 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9255 Z= 0.223 Angle : 0.518 7.293 12500 Z= 0.265 Chirality : 0.040 0.174 1424 Planarity : 0.004 0.059 1557 Dihedral : 5.469 64.099 1304 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 1.52 % 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: -0.03 (0.25), residues: 1126 helix: 2.52 (0.26), residues: 380 sheet: -0.81 (0.31), residues: 279 loop : -1.72 (0.26), residues: 467 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.021 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 134 average time/residue: 0.2541 time to fit residues: 45.5766 Evaluate side-chains 127 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0856 time to fit residues: 2.9752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 0.0270 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 9255 Z= 0.153 Angle : 0.494 9.721 12500 Z= 0.249 Chirality : 0.039 0.164 1424 Planarity : 0.003 0.059 1557 Dihedral : 5.233 57.557 1304 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.30 % 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: 0.06 (0.25), residues: 1126 helix: 2.59 (0.27), residues: 380 sheet: -0.75 (0.31), residues: 279 loop : -1.66 (0.26), residues: 467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.079 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 127 average time/residue: 0.2674 time to fit residues: 45.4674 Evaluate side-chains 121 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1064 time to fit residues: 1.7357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 0.0670 chunk 10 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 9255 Z= 0.138 Angle : 0.487 7.893 12500 Z= 0.247 Chirality : 0.039 0.160 1424 Planarity : 0.003 0.059 1557 Dihedral : 5.269 56.367 1304 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 0.51 % 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: 0.18 (0.25), residues: 1126 helix: 2.67 (0.26), residues: 383 sheet: -0.68 (0.31), residues: 279 loop : -1.61 (0.26), residues: 464 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 1.137 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 116 average time/residue: 0.2676 time to fit residues: 41.4885 Evaluate side-chains 116 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0883 time to fit residues: 2.0030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.3980 chunk 95 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.067 9255 Z= 0.142 Angle : 0.497 10.709 12500 Z= 0.250 Chirality : 0.039 0.158 1424 Planarity : 0.003 0.059 1557 Dihedral : 5.097 55.971 1304 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.00 % 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: 0.24 (0.25), residues: 1126 helix: 2.70 (0.26), residues: 383 sheet: -0.66 (0.31), residues: 279 loop : -1.55 (0.26), residues: 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.159 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2911 time to fit residues: 47.7814 Evaluate side-chains 116 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/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-4893/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-4893/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-4893/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-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.3696 > 50: distance: 4 - 9: 29.216 distance: 9 - 10: 31.696 distance: 10 - 11: 23.977 distance: 10 - 13: 31.839 distance: 11 - 12: 30.763 distance: 11 - 15: 32.163 distance: 13 - 14: 46.266 distance: 15 - 16: 34.928 distance: 16 - 17: 8.376 distance: 16 - 19: 42.686 distance: 17 - 18: 24.686 distance: 17 - 21: 28.895 distance: 19 - 20: 36.210 distance: 21 - 22: 27.802 distance: 22 - 23: 27.783 distance: 22 - 25: 29.079 distance: 23 - 24: 35.690 distance: 23 - 28: 17.390 distance: 25 - 26: 33.681 distance: 25 - 27: 13.768 distance: 28 - 29: 12.522 distance: 28 - 34: 45.360 distance: 29 - 30: 32.256 distance: 29 - 32: 23.538 distance: 30 - 31: 12.995 distance: 30 - 35: 27.106 distance: 32 - 33: 33.854 distance: 33 - 34: 52.899 distance: 35 - 36: 26.849 distance: 36 - 37: 41.325 distance: 36 - 39: 24.636 distance: 37 - 38: 42.251 distance: 37 - 42: 3.384 distance: 39 - 40: 24.444 distance: 39 - 41: 27.083 distance: 42 - 43: 6.153 distance: 43 - 44: 28.275 distance: 43 - 46: 43.123 distance: 44 - 45: 29.242 distance: 44 - 49: 22.046 distance: 46 - 47: 42.311 distance: 46 - 48: 57.370 distance: 49 - 50: 16.157 distance: 49 - 55: 36.957 distance: 50 - 51: 17.779 distance: 50 - 53: 10.715 distance: 51 - 52: 26.183 distance: 51 - 56: 27.845 distance: 53 - 54: 13.414 distance: 54 - 55: 32.062 distance: 56 - 57: 30.418 distance: 57 - 58: 4.230 distance: 58 - 59: 7.312 distance: 58 - 60: 26.227 distance: 60 - 61: 27.008 distance: 61 - 62: 10.395 distance: 61 - 64: 30.141 distance: 62 - 63: 20.584 distance: 62 - 69: 24.651 distance: 64 - 65: 47.786 distance: 65 - 66: 18.113 distance: 66 - 67: 40.948 distance: 66 - 68: 28.994 distance: 69 - 70: 13.382 distance: 70 - 71: 16.602 distance: 70 - 73: 15.224 distance: 71 - 72: 33.280 distance: 71 - 75: 12.351 distance: 73 - 74: 31.741