Starting phenix.real_space_refine on Sat Mar 16 07:02:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/03_2024/7p1h_13159_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/03_2024/7p1h_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_13159/03_2024/7p1h_13159.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/03_2024/7p1h_13159.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/03_2024/7p1h_13159_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/03_2024/7p1h_13159_trim_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.73, per 1000 atoms: 0.48 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: 12.20 Conformation dependent library (CDL) restraints added in 1.8 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: 2.65 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: 12.60 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: 5824 17.47 - 34.93: 528 34.93 - 52.40: 180 52.40 - 69.86: 123 69.86 - 87.33: 16 Dihedral angle restraints: 6671 sinusoidal: 3650 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 6668 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.200 Extract box with map and model: 7.390 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 50.860 Find NCS groups from input model: 0.280 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.630 ------------------------------------------------------------------------------- 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 : 14.378 87.170 2681 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 % Allowed : 7.05 % Favored : 92.95 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.006 TRP B 86 HIS 0.008 0.002 HIS B 40 PHE 0.029 0.003 PHE A 321 TYR 0.037 0.005 TYR A 144 ARG 0.058 0.008 ARG A 278 *********************** 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 : 1.217 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 REVERT: A 321 PHE cc_start: 0.8119 (m-80) cc_final: 0.7415 (m-80) REVERT: B 153 MET cc_start: 0.8489 (tmm) cc_final: 0.8277 (tmm) REVERT: B 208 ILE cc_start: 0.9124 (mt) cc_final: 0.8733 (tp) REVERT: B 292 ASP cc_start: 0.8639 (m-30) cc_final: 0.8230 (t0) REVERT: P 99 ASN cc_start: 0.7840 (m110) cc_final: 0.7575 (m-40) REVERT: P 125 LYS cc_start: 0.8703 (tttt) cc_final: 0.8353 (tmtt) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.4215 time to fit residues: 116.8925 Evaluate side-chains 135 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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: 3.9990 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.0040 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 79 optimal weight: 0.0970 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.3234 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= 0.189 Angle : 0.646 6.960 9739 Z= 0.350 Chirality : 0.043 0.157 1082 Planarity : 0.005 0.048 1253 Dihedral : 7.082 35.006 1000 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.91 % Allowed : 13.19 % Favored : 85.90 % 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: -0.48 (0.27), residues: 887 helix: 0.32 (0.28), residues: 328 sheet: -0.20 (0.40), residues: 156 loop : -0.81 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 87 HIS 0.012 0.002 HIS A 301 PHE 0.013 0.001 PHE B 255 TYR 0.027 0.002 TYR A 214 ARG 0.006 0.001 ARG A 106 *********************** 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 151 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 1.082 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: B 153 MET cc_start: 0.8481 (tmm) cc_final: 0.8278 (tmm) REVERT: B 208 ILE cc_start: 0.9025 (mt) cc_final: 0.8590 (tp) REVERT: B 263 GLN cc_start: 0.8394 (mt0) cc_final: 0.8189 (mp10) REVERT: B 292 ASP cc_start: 0.8535 (m-30) cc_final: 0.8097 (t0) REVERT: P 18 ASP cc_start: -0.0498 (t0) cc_final: -0.0734 (t0) REVERT: P 39 PHE cc_start: 0.5006 (m-10) cc_final: 0.4409 (m-10) REVERT: P 125 LYS cc_start: 0.8679 (tttt) cc_final: 0.8412 (tmtt) outliers start: 7 outliers final: 7 residues processed: 148 average time/residue: 0.3674 time to fit residues: 74.7344 Evaluate side-chains 122 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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** ** A 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6728 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 7186 Z= 0.327 Angle : 0.699 6.614 9739 Z= 0.380 Chirality : 0.044 0.221 1082 Planarity : 0.006 0.060 1253 Dihedral : 6.795 32.677 1000 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.48 % Allowed : 13.45 % Favored : 84.07 % 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: -0.66 (0.28), residues: 887 helix: 0.29 (0.28), residues: 337 sheet: -0.39 (0.40), residues: 154 loop : -1.02 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 87 HIS 0.007 0.002 HIS A 301 PHE 0.020 0.002 PHE B 266 TYR 0.053 0.002 TYR A 214 ARG 0.003 0.001 ARG A 58 *********************** 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 137 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.979 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: B 208 ILE cc_start: 0.9148 (mt) cc_final: 0.8834 (tp) REVERT: B 263 GLN cc_start: 0.8365 (mt0) cc_final: 0.8114 (mp10) REVERT: B 292 ASP cc_start: 0.8780 (m-30) cc_final: 0.8448 (t0) REVERT: B 369 ILE cc_start: 0.8676 (tt) cc_final: 0.8375 (tp) outliers start: 19 outliers final: 18 residues processed: 128 average time/residue: 0.3628 time to fit residues: 64.4014 Evaluate side-chains 124 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 301 HIS Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain P residue 16 CYS Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 113 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 70 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.6616 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7186 Z= 0.147 Angle : 0.549 5.896 9739 Z= 0.293 Chirality : 0.041 0.142 1082 Planarity : 0.005 0.049 1253 Dihedral : 6.080 52.334 1000 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.83 % Allowed : 15.40 % Favored : 82.77 % 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: -0.05 (0.29), residues: 887 helix: 0.78 (0.30), residues: 333 sheet: -0.15 (0.41), residues: 151 loop : -0.59 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 340 HIS 0.004 0.001 HIS A 396 PHE 0.009 0.001 PHE P 39 TYR 0.014 0.001 TYR P 128 ARG 0.003 0.000 ARG A 106 *********************** 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 132 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.246 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: B 208 ILE cc_start: 0.9106 (mt) cc_final: 0.8769 (tp) REVERT: B 263 GLN cc_start: 0.8344 (mt0) cc_final: 0.8057 (mp10) REVERT: B 369 ILE cc_start: 0.8684 (tt) cc_final: 0.8398 (tp) outliers start: 14 outliers final: 14 residues processed: 125 average time/residue: 0.3456 time to fit residues: 60.6567 Evaluate side-chains 123 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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: 0.6841 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7186 Z= 0.276 Angle : 0.620 6.582 9739 Z= 0.335 Chirality : 0.042 0.149 1082 Planarity : 0.005 0.071 1253 Dihedral : 6.238 45.428 1000 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.87 % Allowed : 15.27 % Favored : 81.85 % 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: -0.60 (0.28), residues: 887 helix: 0.35 (0.29), residues: 327 sheet: -0.33 (0.39), residues: 151 loop : -0.97 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 340 HIS 0.007 0.002 HIS B 88 PHE 0.013 0.002 PHE A 321 TYR 0.022 0.002 TYR A 223 ARG 0.003 0.001 ARG B 37 *********************** 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 131 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.215 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: B 263 GLN cc_start: 0.8509 (mt0) cc_final: 0.8158 (mp10) REVERT: P 39 PHE cc_start: 0.5528 (m-10) cc_final: 0.5108 (m-10) outliers start: 22 outliers final: 17 residues processed: 122 average time/residue: 0.3501 time to fit residues: 60.1467 Evaluate side-chains 114 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 214 TYR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain P residue 16 CYS Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 113 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.6916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 7186 Z= 0.302 Angle : 0.628 6.614 9739 Z= 0.343 Chirality : 0.042 0.148 1082 Planarity : 0.006 0.078 1253 Dihedral : 6.433 56.170 1000 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.92 % Allowed : 16.19 % Favored : 79.90 % 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: -1.07 (0.28), residues: 887 helix: -0.11 (0.27), residues: 340 sheet: -0.57 (0.40), residues: 150 loop : -1.20 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 185 HIS 0.014 0.002 HIS B 101 PHE 0.018 0.002 PHE A 343 TYR 0.029 0.002 TYR A 223 ARG 0.004 0.001 ARG B 39 *********************** 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 128 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 1.168 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: A 146 SER cc_start: 0.7666 (OUTLIER) cc_final: 0.7199 (t) REVERT: B 119 MET cc_start: 0.8481 (mmm) cc_final: 0.8221 (mtm) REVERT: B 208 ILE cc_start: 0.9184 (mm) cc_final: 0.8495 (tp) REVERT: B 263 GLN cc_start: 0.8562 (mt0) cc_final: 0.8176 (mp10) outliers start: 30 outliers final: 25 residues processed: 117 average time/residue: 0.3473 time to fit residues: 57.3081 Evaluate side-chains 121 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain P residue 16 CYS Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 99 ASN Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 113 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS B 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7186 Z= 0.173 Angle : 0.554 6.628 9739 Z= 0.294 Chirality : 0.041 0.145 1082 Planarity : 0.005 0.067 1253 Dihedral : 6.068 56.498 1000 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.00 % Allowed : 17.62 % Favored : 79.37 % 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: -0.73 (0.28), residues: 887 helix: 0.21 (0.28), residues: 341 sheet: -0.47 (0.40), residues: 150 loop : -1.01 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 185 HIS 0.004 0.001 HIS A 396 PHE 0.010 0.001 PHE A 321 TYR 0.014 0.001 TYR A 223 ARG 0.003 0.000 ARG B 39 *********************** 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 121 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 1.057 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: A 172 PHE cc_start: 0.6327 (OUTLIER) cc_final: 0.6048 (m-80) REVERT: B 119 MET cc_start: 0.8445 (mmm) cc_final: 0.8164 (mtm) REVERT: B 196 ARG cc_start: 0.7754 (ttm-80) cc_final: 0.7485 (tpt-90) REVERT: B 263 GLN cc_start: 0.8473 (mt0) cc_final: 0.8118 (mp10) outliers start: 23 outliers final: 21 residues processed: 108 average time/residue: 0.3497 time to fit residues: 52.3998 Evaluate side-chains 117 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain P residue 16 CYS Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 99 ASN Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 113 MET 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: 3.9990 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 77 optimal weight: 0.3980 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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: 0.6903 moved from start: 0.7548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7186 Z= 0.203 Angle : 0.563 6.842 9739 Z= 0.300 Chirality : 0.041 0.149 1082 Planarity : 0.005 0.073 1253 Dihedral : 5.947 51.943 1000 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.87 % Allowed : 18.54 % Favored : 78.59 % 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: -0.74 (0.28), residues: 887 helix: 0.31 (0.28), residues: 332 sheet: -0.49 (0.40), residues: 150 loop : -1.10 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.007 0.002 HIS A 300 PHE 0.014 0.002 PHE A 321 TYR 0.022 0.001 TYR A 223 ARG 0.003 0.000 ARG B 62 *********************** 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 121 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 1.208 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: A 113 ASN cc_start: 0.6324 (OUTLIER) cc_final: 0.5920 (t0) REVERT: B 119 MET cc_start: 0.8344 (mmm) cc_final: 0.8138 (mtm) REVERT: B 263 GLN cc_start: 0.8490 (mt0) cc_final: 0.8103 (mp10) REVERT: P 39 PHE cc_start: 0.5771 (m-10) cc_final: 0.5493 (m-10) outliers start: 22 outliers final: 21 residues processed: 110 average time/residue: 0.3927 time to fit residues: 58.8004 Evaluate side-chains 115 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain P residue 16 CYS Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 99 ASN Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.6846 moved from start: 0.7733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7186 Z= 0.147 Angle : 0.535 7.664 9739 Z= 0.281 Chirality : 0.040 0.138 1082 Planarity : 0.005 0.064 1253 Dihedral : 5.753 54.103 1000 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.48 % Allowed : 18.54 % Favored : 78.98 % 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: -0.44 (0.29), residues: 887 helix: 0.62 (0.29), residues: 334 sheet: -0.38 (0.40), residues: 150 loop : -0.97 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 86 HIS 0.007 0.001 HIS A 300 PHE 0.012 0.001 PHE B 200 TYR 0.016 0.001 TYR P 128 ARG 0.002 0.000 ARG B 39 *********************** 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 122 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.181 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: A 113 ASN cc_start: 0.6265 (OUTLIER) cc_final: 0.5851 (t0) REVERT: A 172 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5941 (m-80) REVERT: B 263 GLN cc_start: 0.8410 (mt0) cc_final: 0.8060 (mp10) REVERT: P 74 ARG cc_start: 0.5152 (mtm180) cc_final: 0.4283 (ttp-110) outliers start: 19 outliers final: 15 residues processed: 112 average time/residue: 0.4095 time to fit residues: 61.8785 Evaluate side-chains 121 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 99 ASN Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 111 LEU 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: 5.9990 chunk 87 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 69 optimal weight: 0.0870 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 2.3564 ------------------------------------------------------------------------------- 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: 0.6934 moved from start: 0.8057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7186 Z= 0.228 Angle : 0.578 7.170 9739 Z= 0.308 Chirality : 0.041 0.144 1082 Planarity : 0.005 0.071 1253 Dihedral : 5.963 51.256 1000 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.61 % Allowed : 18.80 % Favored : 78.59 % 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: -0.70 (0.28), residues: 887 helix: 0.36 (0.29), residues: 332 sheet: -0.51 (0.40), residues: 150 loop : -1.07 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 87 HIS 0.006 0.002 HIS A 300 PHE 0.015 0.002 PHE A 321 TYR 0.021 0.001 TYR A 223 ARG 0.003 0.001 ARG B 147 ********************** 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 120 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.175 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: A 113 ASN cc_start: 0.6387 (OUTLIER) cc_final: 0.5987 (t0) REVERT: A 172 PHE cc_start: 0.6308 (OUTLIER) cc_final: 0.5949 (m-80) REVERT: B 119 MET cc_start: 0.8366 (mmm) cc_final: 0.8016 (mtm) REVERT: B 263 GLN cc_start: 0.8486 (mt0) cc_final: 0.8117 (mp10) REVERT: P 39 PHE cc_start: 0.5878 (m-10) cc_final: 0.5570 (m-10) REVERT: P 74 ARG cc_start: 0.5272 (mtm180) cc_final: 0.4427 (ttp-110) outliers start: 20 outliers final: 18 residues processed: 111 average time/residue: 0.4105 time to fit residues: 61.7094 Evaluate side-chains 117 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 99 ASN Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.088311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.071871 restraints weight = 84613.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.075028 restraints weight = 41959.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.077098 restraints weight = 25778.665| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.8162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7186 Z= 0.142 Angle : 0.533 6.921 9739 Z= 0.278 Chirality : 0.040 0.136 1082 Planarity : 0.005 0.063 1253 Dihedral : 5.643 52.450 1000 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.09 % Allowed : 19.71 % Favored : 78.20 % 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: -0.40 (0.29), residues: 887 helix: 0.61 (0.29), residues: 338 sheet: -0.37 (0.41), residues: 150 loop : -0.90 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 86 HIS 0.006 0.001 HIS A 300 PHE 0.009 0.001 PHE A 321 TYR 0.016 0.001 TYR P 128 ARG 0.002 0.000 ARG B 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3432.19 seconds wall clock time: 61 minutes 18.31 seconds (3678.31 seconds total)