Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 03:01:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/04_2023/7p1h_13159_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/04_2023/7p1h_13159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/04_2023/7p1h_13159.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/04_2023/7p1h_13159.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/04_2023/7p1h_13159_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/04_2023/7p1h_13159_trim_updated.pdb" } resolution = 3.9 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= 0.000 sd= 0.000 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 3 5.49 5 S 34 5.16 5 C 4454 2.51 5 N 1171 2.21 5 O 1377 1.98 5 H 6917 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 20": "OD1" <-> "OD2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 355": "OD1" <-> "OD2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 13957 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6173 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 376} Chain: "B" Number of atoms: 5670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5670 Classifications: {'peptide': 365} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2082 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.27, per 1000 atoms: 0.45 Number of scatterers: 13957 At special positions: 0 Unit cell: (119, 108.8, 82.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 34 16.00 P 3 15.00 O 1377 8.00 N 1171 7.00 C 4454 6.00 H 6917 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 11.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 8 sheets defined 40.5% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 20 through 35 Proline residue: A 25 - end of helix Proline residue: A 29 - end of helix removed outlier: 3.854A pdb=" N ILE A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 106 through 122 Processing helix chain 'A' and resid 134 through 142 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 228 through 231 No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.643A pdb=" N ASP A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 324 through 327 removed outlier: 3.674A pdb=" N PHE A 327 " --> pdb=" O LYS A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 327' Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.701A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 removed outlier: 4.164A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 261 removed outlier: 4.353A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.554A pdb=" N ARG B 290 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.856A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 removed outlier: 3.517A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.810A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 10 removed outlier: 3.507A pdb=" N ASP P 8 " --> pdb=" O ALA P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 41 No H-bonds generated for 'chain 'P' and resid 39 through 41' Processing helix chain 'P' and resid 44 through 50 Processing helix chain 'P' and resid 57 through 61 Processing helix chain 'P' and resid 120 through 136 Processing sheet with id= A, first strand: chain 'A' and resid 219 through 221 Processing sheet with id= B, first strand: chain 'A' and resid 126 through 129 Processing sheet with id= C, first strand: chain 'A' and resid 151 through 153 removed outlier: 8.425A pdb=" N THR A 171 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE A 190 " --> pdb=" O THR A 171 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.816A pdb=" N VAL B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= F, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.767A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N MET B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 176 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= H, first strand: chain 'P' and resid 63 through 65 removed outlier: 3.632A pdb=" N LEU P 63 " --> pdb=" O CYS P 70 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP P 86 " --> pdb=" O ILE P 73 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP P 75 " --> pdb=" O SER P 84 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER P 84 " --> pdb=" O ASP P 75 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN P 99 " --> pdb=" O GLY P 114 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY P 23 " --> pdb=" O VAL P 30 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL P 30 " --> pdb=" O GLY P 23 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 687 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: 4.96 Time building geometry restraints manager: 12.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6909 1.03 - 1.22: 11 1.22 - 1.42: 2972 1.42 - 1.61: 4151 1.61 - 1.81: 60 Bond restraints: 14103 Sorted by residual: bond pdb=" C4 ATP B 402 " pdb=" C5 ATP B 402 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.80e+01 bond pdb=" C5 ATP B 402 " pdb=" C6 ATP B 402 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.61e+01 bond pdb=" C8 ATP B 402 " pdb=" N7 ATP B 402 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.30e+01 bond pdb=" C4 ATP B 402 " pdb=" N9 ATP B 402 " ideal model delta sigma weight residual 1.374 1.328 0.046 1.00e-02 1.00e+04 2.09e+01 bond pdb=" C5 ATP B 402 " pdb=" N7 ATP B 402 " ideal model delta sigma weight residual 1.387 1.342 0.045 1.00e-02 1.00e+04 2.05e+01 ... (remaining 14098 not shown) Histogram of bond angle deviations from ideal: 97.27 - 105.13: 161 105.13 - 112.99: 16713 112.99 - 120.84: 5280 120.84 - 128.70: 3312 128.70 - 136.56: 43 Bond angle restraints: 25509 Sorted by residual: angle pdb=" PB ATP B 402 " pdb=" O3B ATP B 402 " pdb=" PG ATP B 402 " ideal model delta sigma weight residual 139.87 120.02 19.85 1.00e+00 1.00e+00 3.94e+02 angle pdb=" PA ATP B 402 " pdb=" O3A ATP B 402 " pdb=" PB ATP B 402 " ideal model delta sigma weight residual 136.83 122.53 14.30 1.00e+00 1.00e+00 2.05e+02 angle pdb=" C5 ATP B 402 " pdb=" C4 ATP B 402 " pdb=" N3 ATP B 402 " ideal model delta sigma weight residual 126.80 119.27 7.53 1.00e+00 1.00e+00 5.67e+01 angle pdb=" N3 ATP B 402 " pdb=" C4 ATP B 402 " pdb=" N9 ATP B 402 " ideal model delta sigma weight residual 127.04 134.55 -7.51 1.15e+00 7.59e-01 4.28e+01 angle pdb=" N LEU A 217 " pdb=" CA LEU A 217 " pdb=" C LEU A 217 " ideal model delta sigma weight residual 110.80 97.76 13.04 2.13e+00 2.20e-01 3.75e+01 ... (remaining 25504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 4958 17.47 - 34.93: 440 34.93 - 52.40: 119 52.40 - 69.86: 96 69.86 - 87.33: 16 Dihedral angle restraints: 5629 sinusoidal: 2608 harmonic: 3021 Sorted by residual: dihedral pdb=" CA LEU A 217 " pdb=" C LEU A 217 " pdb=" N THR A 218 " pdb=" CA THR A 218 " ideal model delta harmonic sigma weight residual 180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA SER A 127 " pdb=" C SER A 127 " pdb=" N ALA A 128 " pdb=" CA ALA A 128 " ideal model delta harmonic sigma weight residual 180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ASP A 129 " pdb=" C ASP A 129 " pdb=" N LEU A 130 " pdb=" CA LEU A 130 " ideal model delta harmonic sigma weight residual -180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 5626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 642 0.037 - 0.075: 282 0.075 - 0.112: 115 0.112 - 0.149: 37 0.149 - 0.186: 6 Chirality restraints: 1082 Sorted by residual: chirality pdb=" CA LYS A 402 " pdb=" N LYS A 402 " pdb=" C LYS A 402 " pdb=" CB LYS A 402 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CG LEU A 399 " pdb=" CB LEU A 399 " pdb=" CD1 LEU A 399 " pdb=" CD2 LEU A 399 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CA VAL A 179 " pdb=" N VAL A 179 " pdb=" C VAL A 179 " pdb=" CB VAL A 179 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 1079 not shown) Planarity restraints: 2105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 265 " -0.024 2.00e-02 2.50e+03 4.85e-02 2.36e+01 pdb=" C ASN A 265 " 0.084 2.00e-02 2.50e+03 pdb=" O ASN A 265 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS A 266 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 106 " 0.090 9.50e-02 1.11e+02 3.90e-02 1.47e+01 pdb=" NE ARG A 106 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 106 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 106 " -0.043 2.00e-02 2.50e+03 pdb=" NH2 ARG A 106 " -0.026 2.00e-02 2.50e+03 pdb="HH11 ARG A 106 " 0.014 2.00e-02 2.50e+03 pdb="HH12 ARG A 106 " 0.006 2.00e-02 2.50e+03 pdb="HH21 ARG A 106 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 106 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " 0.069 9.50e-02 1.11e+02 3.37e-02 1.41e+01 pdb=" NE ARG A 278 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " -0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " -0.026 2.00e-02 2.50e+03 pdb="HH11 ARG A 278 " 0.009 2.00e-02 2.50e+03 pdb="HH12 ARG A 278 " 0.007 2.00e-02 2.50e+03 pdb="HH21 ARG A 278 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 278 " 0.013 2.00e-02 2.50e+03 ... (remaining 2102 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 491 2.09 - 2.71: 24558 2.71 - 3.34: 41383 3.34 - 3.97: 51868 3.97 - 4.60: 81348 Nonbonded interactions: 199648 Sorted by model distance: nonbonded pdb=" H THR B 201 " pdb=" OE1 GLU B 205 " model vdw 1.457 1.850 nonbonded pdb=" HZ1 LYS A 176 " pdb=" OD2 ASP A 183 " model vdw 1.524 1.850 nonbonded pdb=" O SER B 344 " pdb=" HG SER B 348 " model vdw 1.526 1.850 nonbonded pdb=" O ALA A 103 " pdb=" HG SER A 104 " model vdw 1.537 1.850 nonbonded pdb=" OD2 ASP B 288 " pdb=" HZ1 LYS P 69 " model vdw 1.537 1.850 ... (remaining 199643 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.200 Extract box with map and model: 7.660 Check model and map are aligned: 0.190 Set scattering table: 0.100 Process input model: 45.940 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 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 0.076 7186 Z= 0.334 Angle : 1.010 19.849 9739 Z= 0.630 Chirality : 0.051 0.186 1082 Planarity : 0.007 0.051 1253 Dihedral : 14.138 87.170 2650 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.60 (0.25), residues: 887 helix: -1.09 (0.24), residues: 327 sheet: -0.25 (0.39), residues: 154 loop : -1.25 (0.30), residues: 406 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.4242 time to fit residues: 117.2535 Evaluate side-chains 132 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 79 optimal weight: 0.0670 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A 368 ASN B 12 ASN B 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 7186 Z= 0.193 Angle : 0.651 6.768 9739 Z= 0.350 Chirality : 0.043 0.157 1082 Planarity : 0.005 0.046 1253 Dihedral : 6.977 47.131 969 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.53 (0.27), residues: 887 helix: 0.33 (0.28), residues: 328 sheet: -0.36 (0.39), residues: 161 loop : -0.83 (0.30), residues: 398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 143 average time/residue: 0.3750 time to fit residues: 74.0904 Evaluate side-chains 129 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1658 time to fit residues: 4.0835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 7186 Z= 0.268 Angle : 0.652 6.543 9739 Z= 0.351 Chirality : 0.042 0.164 1082 Planarity : 0.005 0.059 1253 Dihedral : 6.651 52.267 969 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.46 (0.28), residues: 887 helix: 0.53 (0.29), residues: 323 sheet: -0.22 (0.41), residues: 146 loop : -0.94 (0.30), residues: 418 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 121 average time/residue: 0.3789 time to fit residues: 63.6018 Evaluate side-chains 112 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2473 time to fit residues: 4.1289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 7186 Z= 0.268 Angle : 0.638 7.690 9739 Z= 0.346 Chirality : 0.042 0.147 1082 Planarity : 0.006 0.074 1253 Dihedral : 6.532 68.405 969 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.64 (0.28), residues: 887 helix: 0.31 (0.29), residues: 333 sheet: -0.43 (0.40), residues: 155 loop : -0.96 (0.31), residues: 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 115 average time/residue: 0.3464 time to fit residues: 56.8595 Evaluate side-chains 105 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1699 time to fit residues: 3.5565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.6398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 7186 Z= 0.191 Angle : 0.569 6.012 9739 Z= 0.303 Chirality : 0.041 0.152 1082 Planarity : 0.005 0.070 1253 Dihedral : 6.351 78.841 969 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.45 (0.28), residues: 887 helix: 0.39 (0.29), residues: 326 sheet: -0.24 (0.41), residues: 152 loop : -0.80 (0.32), residues: 409 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 104 average time/residue: 0.3693 time to fit residues: 53.5800 Evaluate side-chains 101 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1685 time to fit residues: 2.8033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 0.0060 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 7186 Z= 0.228 Angle : 0.582 6.398 9739 Z= 0.311 Chirality : 0.041 0.148 1082 Planarity : 0.005 0.074 1253 Dihedral : 6.305 85.447 969 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.56 (0.28), residues: 887 helix: 0.33 (0.29), residues: 326 sheet: -0.34 (0.40), residues: 156 loop : -0.88 (0.32), residues: 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 108 average time/residue: 0.3675 time to fit residues: 56.6229 Evaluate side-chains 105 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1986 time to fit residues: 4.2627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 7.9990 chunk 48 optimal weight: 0.0370 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.7193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 7186 Z= 0.141 Angle : 0.538 7.021 9739 Z= 0.282 Chirality : 0.041 0.145 1082 Planarity : 0.005 0.060 1253 Dihedral : 5.925 79.198 969 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.17 (0.29), residues: 887 helix: 0.76 (0.30), residues: 327 sheet: -0.28 (0.40), residues: 156 loop : -0.68 (0.33), residues: 404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 110 average time/residue: 0.4064 time to fit residues: 61.1610 Evaluate side-chains 106 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3014 time to fit residues: 3.1906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 7186 Z= 0.153 Angle : 0.531 6.876 9739 Z= 0.279 Chirality : 0.040 0.145 1082 Planarity : 0.005 0.062 1253 Dihedral : 5.747 74.462 969 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.12 (0.29), residues: 887 helix: 0.90 (0.30), residues: 320 sheet: -0.23 (0.41), residues: 150 loop : -0.74 (0.32), residues: 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.3881 time to fit residues: 56.4376 Evaluate side-chains 100 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 1.169 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2210 time to fit residues: 1.8044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.7566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 7186 Z= 0.151 Angle : 0.534 6.653 9739 Z= 0.279 Chirality : 0.040 0.144 1082 Planarity : 0.005 0.062 1253 Dihedral : 5.593 69.597 969 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.10 (0.29), residues: 887 helix: 0.91 (0.30), residues: 321 sheet: -0.25 (0.41), residues: 150 loop : -0.71 (0.32), residues: 416 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 105 average time/residue: 0.3930 time to fit residues: 56.7590 Evaluate side-chains 103 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1710 time to fit residues: 2.0538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.7684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 7186 Z= 0.137 Angle : 0.527 7.209 9739 Z= 0.273 Chirality : 0.040 0.143 1082 Planarity : 0.005 0.059 1253 Dihedral : 5.423 67.713 969 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.08 (0.29), residues: 887 helix: 1.03 (0.31), residues: 322 sheet: 0.04 (0.41), residues: 149 loop : -0.66 (0.32), residues: 416 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 110 average time/residue: 0.4320 time to fit residues: 64.1921 Evaluate side-chains 104 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1550 time to fit residues: 1.9296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.088875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.071633 restraints weight = 84775.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.074846 restraints weight = 42922.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.076951 restraints weight = 26860.153| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.8017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 7186 Z= 0.189 Angle : 0.554 7.254 9739 Z= 0.291 Chirality : 0.040 0.145 1082 Planarity : 0.005 0.066 1253 Dihedral : 5.504 64.162 969 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.16 (0.29), residues: 887 helix: 0.84 (0.30), residues: 321 sheet: -0.32 (0.40), residues: 150 loop : -0.71 (0.32), residues: 416 =============================================================================== Job complete usr+sys time: 3362.90 seconds wall clock time: 60 minutes 25.93 seconds (3625.93 seconds total)