Starting phenix.real_space_refine on Fri Dec 8 11:33:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/12_2023/7wcm_32424_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/12_2023/7wcm_32424.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/12_2023/7wcm_32424_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/12_2023/7wcm_32424_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/12_2023/7wcm_32424_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/12_2023/7wcm_32424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/12_2023/7wcm_32424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/12_2023/7wcm_32424_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/12_2023/7wcm_32424_updated.pdb" } resolution = 2.33 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= 0.000 sd= 0.007 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 57 5.16 5 C 5222 2.51 5 N 1435 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 223": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "B ASP 49": "OD1" <-> "OD2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "R PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8232 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1947 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2272 Unusual residues: {'8VP': 1} Classifications: {'peptide': 289, 'undetermined': 1} Link IDs: {'PTRANS': 9, 'TRANS': 279, None: 1} Not linked: pdbres="VAL R 300 " pdbres="8VP R 401 " Chain breaks: 1 Time building chain proxies: 4.71, per 1000 atoms: 0.57 Number of scatterers: 8232 At special positions: 0 Unit cell: (81.696, 102.12, 131.054, 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 57 16.00 O 1518 8.00 N 1435 7.00 C 5222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 155 " 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: 3.12 Conformation dependent library (CDL) restraints added in 1.4 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 10 sheets defined 40.4% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.551A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.572A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 Processing helix chain 'B' and resid 14 through 36 Processing helix chain 'B' and resid 41 through 47 removed outlier: 5.253A pdb=" N ASN B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 22 removed outlier: 3.831A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 6 through 35 removed outlier: 3.699A pdb=" N VAL R 25 " --> pdb=" O THR R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 61 removed outlier: 4.000A pdb=" N LEU R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 67 Processing helix chain 'R' and resid 75 through 108 removed outlier: 3.966A pdb=" N VAL R 85 " --> pdb=" O ARG R 81 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR R 86 " --> pdb=" O MET R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 116 Processing helix chain 'R' and resid 119 through 142 Proline residue: R 140 - end of helix Processing helix chain 'R' and resid 163 through 172 Processing helix chain 'R' and resid 174 through 209 Processing helix chain 'R' and resid 222 through 250 removed outlier: 4.402A pdb=" N CYS R 237 " --> pdb=" O SER R 233 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TRP R 238 " --> pdb=" O PHE R 234 " (cutoff:3.500A) Proline residue: R 240 - end of helix Processing helix chain 'R' and resid 254 through 262 removed outlier: 3.903A pdb=" N LEU R 258 " --> pdb=" O HIS R 255 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU R 260 " --> pdb=" O TYR R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 279 removed outlier: 4.321A pdb=" N SER R 272 " --> pdb=" O GLY R 268 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU R 273 " --> pdb=" O VAL R 269 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 284 through 299 removed outlier: 3.687A pdb=" N LEU R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY R 296 " --> pdb=" O HIS R 292 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL R 297 " --> pdb=" O MET R 293 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 359 through 364 removed outlier: 7.103A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR A 364 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU A 291 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 69 through 74 removed outlier: 6.869A pdb=" N ALA B 84 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET B 72 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 82 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP B 74 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU B 80 " --> pdb=" O TRP B 74 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ASP B 94 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LYS B 100 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 116 removed outlier: 6.967A pdb=" N GLY B 126 " --> pdb=" O MET B 112 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS B 114 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 124 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR B 116 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR B 122 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY B 127 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 148 " --> pdb=" O ILE B 134 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN B 136 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL B 146 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 157 through 162 removed outlier: 6.732A pdb=" N SER B 171 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS B 160 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 169 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE B 162 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLN B 167 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B 168 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 181 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN B 187 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 203 removed outlier: 6.982A pdb=" N GLY B 213 " --> pdb=" O MET B 199 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU B 201 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 211 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU B 203 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU B 209 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B 231 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP B 223 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N CYS B 229 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 240 through 245 removed outlier: 6.769A pdb=" N GLY B 255 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE B 243 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA B 253 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE B 245 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA B 251 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 273 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP B 265 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLU B 271 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 284 through 289 removed outlier: 6.466A pdb=" N GLY B 299 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL B 287 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 297 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE B 289 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU B 295 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASP B 309 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B 315 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 57 through 62 removed outlier: 6.798A pdb=" N ILE B 349 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 61 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 347 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.949A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1137 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: 2.37 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2690 1.34 - 1.46: 1962 1.46 - 1.58: 3666 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 8400 Sorted by residual: bond pdb=" C12 8VP R 401 " pdb=" S11 8VP R 401 " ideal model delta sigma weight residual 1.544 1.764 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C10 8VP R 401 " pdb=" S11 8VP R 401 " ideal model delta sigma weight residual 1.517 1.710 -0.193 2.00e-02 2.50e+03 9.36e+01 bond pdb=" C9 8VP R 401 " pdb=" N13 8VP R 401 " ideal model delta sigma weight residual 1.564 1.448 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C10 8VP R 401 " pdb=" C9 8VP R 401 " ideal model delta sigma weight residual 1.440 1.360 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C12 8VP R 401 " pdb=" N13 8VP R 401 " ideal model delta sigma weight residual 1.421 1.343 0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 8395 not shown) Histogram of bond angle deviations from ideal: 90.05 - 98.85: 1 98.85 - 107.64: 260 107.64 - 116.44: 5385 116.44 - 125.24: 5590 125.24 - 134.04: 133 Bond angle restraints: 11369 Sorted by residual: angle pdb=" C14 8VP R 401 " pdb=" C12 8VP R 401 " pdb=" S11 8VP R 401 " ideal model delta sigma weight residual 136.23 116.57 19.66 3.00e+00 1.11e-01 4.29e+01 angle pdb=" C10 8VP R 401 " pdb=" S11 8VP R 401 " pdb=" C12 8VP R 401 " ideal model delta sigma weight residual 107.45 90.05 17.40 3.00e+00 1.11e-01 3.36e+01 angle pdb=" C14 8VP R 401 " pdb=" C12 8VP R 401 " pdb=" N13 8VP R 401 " ideal model delta sigma weight residual 115.50 131.32 -15.82 3.00e+00 1.11e-01 2.78e+01 angle pdb=" C18 8VP R 401 " pdb=" N17 8VP R 401 " pdb=" C20 8VP R 401 " ideal model delta sigma weight residual 109.47 121.79 -12.32 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C16 8VP R 401 " pdb=" N17 8VP R 401 " pdb=" C20 8VP R 401 " ideal model delta sigma weight residual 109.48 121.44 -11.96 3.00e+00 1.11e-01 1.59e+01 ... (remaining 11364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.74: 4709 22.74 - 45.47: 254 45.47 - 68.21: 12 68.21 - 90.95: 18 90.95 - 113.68: 1 Dihedral angle restraints: 4994 sinusoidal: 1962 harmonic: 3032 Sorted by residual: dihedral pdb=" CA ASP A 310 " pdb=" C ASP A 310 " pdb=" N TYR A 311 " pdb=" CA TYR A 311 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" C16 8VP R 401 " pdb=" C18 8VP R 401 " pdb=" N17 8VP R 401 " pdb=" C19 8VP R 401 " ideal model delta sinusoidal sigma weight residual 53.00 -60.68 113.68 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 4991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.071: 1279 1.071 - 2.143: 0 2.143 - 3.214: 0 3.214 - 4.286: 0 4.286 - 5.357: 1 Chirality restraints: 1280 Sorted by residual: chirality pdb=" C14 8VP R 401 " pdb=" C12 8VP R 401 " pdb=" C15 8VP R 401 " pdb=" C19 8VP R 401 " both_signs ideal model delta sigma weight residual False 2.68 -2.67 5.36 2.00e-01 2.50e+01 7.17e+02 chirality pdb=" CA VAL N 37 " pdb=" N VAL N 37 " pdb=" C VAL N 37 " pdb=" CB VAL N 37 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CA TYR B 70 " pdb=" N TYR B 70 " pdb=" C TYR B 70 " pdb=" CB TYR B 70 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 1277 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 70 " -0.027 2.00e-02 2.50e+03 2.03e-02 8.28e+00 pdb=" CG TYR B 70 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 70 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 70 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 70 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 70 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 70 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 70 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 246 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO B 247 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 183 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C PHE R 183 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE R 183 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE R 184 " 0.011 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2054 2.80 - 3.33: 7606 3.33 - 3.85: 13333 3.85 - 4.38: 15891 4.38 - 4.90: 27144 Nonbonded interactions: 66028 Sorted by model distance: nonbonded pdb=" NE2 GLN A 29 " pdb=" OD1 ASP A 33 " model vdw 2.281 2.520 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 197 " model vdw 2.301 2.520 nonbonded pdb=" O GLN R 148 " pdb=" NZ LYS R 152 " model vdw 2.306 2.520 nonbonded pdb=" O TYR B 96 " pdb=" OG1 THR B 97 " model vdw 2.337 2.440 nonbonded pdb=" OD1 ASN A 292 " pdb=" N LYS A 293 " model vdw 2.356 2.520 ... (remaining 66023 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: 0.790 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: 5.280 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.670 Find NCS groups from input model: 0.240 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:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.220 8400 Z= 0.296 Angle : 0.702 19.655 11369 Z= 0.350 Chirality : 0.156 5.357 1280 Planarity : 0.004 0.052 1448 Dihedral : 14.138 113.684 3030 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 1.05 (0.26), residues: 1031 helix: 1.81 (0.27), residues: 411 sheet: 1.03 (0.35), residues: 208 loop : -0.61 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 93 HIS 0.015 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.049 0.002 TYR B 70 ARG 0.002 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.990 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 1.5911 time to fit residues: 218.5683 Evaluate side-chains 120 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.899 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 59 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 279 ASN R 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8400 Z= 0.166 Angle : 0.551 9.304 11369 Z= 0.300 Chirality : 0.043 0.195 1280 Planarity : 0.004 0.051 1448 Dihedral : 5.781 69.737 1146 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.47 % Allowed : 6.43 % Favored : 92.10 % 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: 1.43 (0.26), residues: 1031 helix: 2.35 (0.26), residues: 415 sheet: 1.15 (0.35), residues: 206 loop : -0.66 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 93 HIS 0.010 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR A 339 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.956 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 120 average time/residue: 1.5949 time to fit residues: 200.9336 Evaluate side-chains 122 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 4 average time/residue: 0.7740 time to fit residues: 4.7013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 5 GLN R 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8400 Z= 0.138 Angle : 0.508 9.228 11369 Z= 0.274 Chirality : 0.042 0.279 1280 Planarity : 0.003 0.050 1448 Dihedral : 4.878 38.534 1146 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.90 % Allowed : 8.80 % Favored : 90.29 % 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: 1.58 (0.26), residues: 1031 helix: 2.62 (0.26), residues: 414 sheet: 0.97 (0.35), residues: 214 loop : -0.62 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 93 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.013 0.001 TYR A 339 ARG 0.006 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.980 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 123 average time/residue: 1.5987 time to fit residues: 206.4816 Evaluate side-chains 118 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5743 time to fit residues: 3.3154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 26 optimal weight: 0.0470 chunk 82 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 186 GLN N 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8400 Z= 0.242 Angle : 0.627 9.855 11369 Z= 0.342 Chirality : 0.046 0.263 1280 Planarity : 0.004 0.051 1448 Dihedral : 5.370 43.299 1146 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.35 % Allowed : 9.82 % Favored : 88.83 % 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: 1.32 (0.26), residues: 1031 helix: 2.23 (0.26), residues: 417 sheet: 1.07 (0.34), residues: 217 loop : -0.74 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.002 PHE A 212 TYR 0.016 0.002 TYR A 339 ARG 0.006 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.003 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 121 average time/residue: 1.6484 time to fit residues: 209.1953 Evaluate side-chains 121 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.7471 time to fit residues: 5.4671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 0.0040 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.0000 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8400 Z= 0.125 Angle : 0.486 7.842 11369 Z= 0.263 Chirality : 0.041 0.251 1280 Planarity : 0.003 0.050 1448 Dihedral : 4.719 39.980 1146 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.47 % Allowed : 10.50 % Favored : 88.04 % 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: 1.58 (0.26), residues: 1031 helix: 2.63 (0.26), residues: 414 sheet: 1.00 (0.34), residues: 214 loop : -0.64 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 93 HIS 0.002 0.001 HIS A 41 PHE 0.013 0.001 PHE A 212 TYR 0.012 0.001 TYR A 339 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.711 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 125 average time/residue: 1.5951 time to fit residues: 209.9546 Evaluate side-chains 121 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.8001 time to fit residues: 3.0618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 5 GLN R 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8400 Z= 0.203 Angle : 0.585 9.804 11369 Z= 0.318 Chirality : 0.044 0.264 1280 Planarity : 0.004 0.050 1448 Dihedral : 5.170 42.627 1146 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.14 % Allowed : 10.50 % Favored : 87.36 % 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: 1.40 (0.26), residues: 1031 helix: 2.37 (0.26), residues: 417 sheet: 1.20 (0.35), residues: 206 loop : -0.79 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.004 0.001 HIS B 65 PHE 0.015 0.002 PHE A 212 TYR 0.014 0.002 TYR A 339 ARG 0.006 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.056 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 124 average time/residue: 1.6273 time to fit residues: 211.6860 Evaluate side-chains 122 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.4927 time to fit residues: 3.5390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 45 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN R 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8400 Z= 0.196 Angle : 0.581 9.377 11369 Z= 0.315 Chirality : 0.044 0.259 1280 Planarity : 0.004 0.051 1448 Dihedral : 5.177 41.854 1146 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.47 % Allowed : 11.17 % Favored : 87.36 % 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: 1.37 (0.26), residues: 1031 helix: 2.33 (0.26), residues: 416 sheet: 1.22 (0.35), residues: 206 loop : -0.80 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.003 0.001 HIS A 41 PHE 0.015 0.002 PHE A 212 TYR 0.014 0.002 TYR A 339 ARG 0.007 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.109 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 122 average time/residue: 1.5977 time to fit residues: 204.6523 Evaluate side-chains 123 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.6606 time to fit residues: 3.5162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 50.0347 > 50: distance: 7 - 9: 7.021 distance: 9 - 10: 12.010 distance: 10 - 11: 3.537 distance: 11 - 12: 7.114 distance: 11 - 13: 8.752 distance: 13 - 14: 6.952 distance: 14 - 15: 11.574 distance: 14 - 17: 6.419 distance: 15 - 16: 21.680 distance: 15 - 21: 6.226 distance: 17 - 18: 4.167 distance: 18 - 19: 3.711 distance: 18 - 20: 14.464 distance: 21 - 22: 6.999 distance: 22 - 23: 7.005 distance: 22 - 25: 15.912 distance: 23 - 24: 4.609 distance: 23 - 28: 11.922 distance: 25 - 26: 15.850 distance: 25 - 27: 24.741 distance: 28 - 29: 7.220 distance: 29 - 30: 13.550 distance: 29 - 32: 6.047 distance: 30 - 31: 9.986 distance: 30 - 37: 5.517 distance: 32 - 33: 8.237 distance: 33 - 34: 8.028 distance: 34 - 35: 11.664 distance: 34 - 36: 15.560 distance: 37 - 38: 9.157 distance: 37 - 43: 17.611 distance: 38 - 39: 13.812 distance: 38 - 41: 20.832 distance: 39 - 40: 20.004 distance: 39 - 44: 31.324 distance: 41 - 42: 11.515 distance: 42 - 43: 15.269 distance: 44 - 45: 16.959 distance: 45 - 46: 19.209 distance: 46 - 47: 17.074 distance: 46 - 48: 11.243 distance: 48 - 49: 17.981 distance: 49 - 50: 5.299 distance: 50 - 51: 10.618 distance: 50 - 52: 16.068 distance: 52 - 53: 8.888 distance: 53 - 54: 6.895 distance: 53 - 56: 10.545 distance: 54 - 55: 14.097 distance: 54 - 58: 7.385 distance: 56 - 57: 14.774 distance: 58 - 59: 6.967 distance: 59 - 60: 5.331 distance: 59 - 62: 3.886 distance: 60 - 61: 12.688 distance: 60 - 66: 5.593 distance: 61 - 103: 14.143 distance: 62 - 63: 6.441 distance: 63 - 64: 7.047 distance: 63 - 65: 5.024 distance: 66 - 67: 8.558 distance: 67 - 68: 7.956 distance: 67 - 70: 16.751 distance: 68 - 69: 23.870 distance: 68 - 77: 6.093 distance: 70 - 71: 4.589 distance: 71 - 72: 17.357 distance: 72 - 73: 10.836 distance: 73 - 74: 8.537 distance: 74 - 75: 8.280 distance: 74 - 76: 11.371