Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 19:43:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/04_2023/7ste_25426_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/04_2023/7ste_25426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/04_2023/7ste_25426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/04_2023/7ste_25426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/04_2023/7ste_25426_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/04_2023/7ste_25426_trim_updated.pdb" } resolution = 2.73 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= 0.035 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 P 11 5.49 5 Mg 1 5.21 5 S 67 5.16 5 C 8982 2.51 5 N 2487 2.21 5 O 2701 1.98 5 H 14379 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B ASP 255": "OD1" <-> "OD2" Residue "C ASP 225": "OD1" <-> "OD2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "E ASP 6": "OD1" <-> "OD2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 28628 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 5028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5028 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5146 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 12, 'TRANS': 311} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5218 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "E" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5470 Classifications: {'peptide': 340} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 7626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7626 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 17, 'TRANS': 450} Chain breaks: 6 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.75, per 1000 atoms: 0.41 Number of scatterers: 28628 At special positions: 0 Unit cell: (113.988, 122.248, 123.9, 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) S 67 16.00 P 11 15.00 Mg 1 11.99 O 2701 8.00 N 2487 7.00 C 8982 6.00 H 14379 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: 24.74 Conformation dependent library (CDL) restraints added in 2.4 seconds 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 6 sheets defined 58.1% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 55 through 66 Processing helix chain 'B' and resid 86 through 98 Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 221 through 228 removed outlier: 3.674A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 282 through 300 Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 31 through 43 removed outlier: 4.171A pdb=" N LYS C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 75 through 78 No H-bonds generated for 'chain 'C' and resid 75 through 78' Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 124 through 136 Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 171 through 184 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 256 through 270 Processing helix chain 'C' and resid 274 through 287 removed outlier: 4.054A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 removed outlier: 3.561A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 334 removed outlier: 3.854A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 36 through 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 43 through 55 Processing helix chain 'D' and resid 71 through 80 Processing helix chain 'D' and resid 88 through 91 No H-bonds generated for 'chain 'D' and resid 88 through 91' Processing helix chain 'D' and resid 104 through 115 Processing helix chain 'D' and resid 123 through 128 removed outlier: 3.521A pdb=" N ASN D 128 " --> pdb=" O HIS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 178 through 183 removed outlier: 3.805A pdb=" N ARG D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 228 through 245 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 265 through 277 Processing helix chain 'D' and resid 280 through 292 removed outlier: 3.703A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 309 Processing helix chain 'D' and resid 316 through 335 removed outlier: 3.588A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 20 through 35 removed outlier: 4.005A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 49 through 61 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 106 through 118 Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 148 through 160 Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 195 through 209 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 292 removed outlier: 3.703A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 315 through 334 Processing helix chain 'E' and resid 338 through 353 Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.509A pdb=" N ILE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 165 through 175 removed outlier: 3.803A pdb=" N TYR A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 195 through 210 Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 270 through 291 removed outlier: 5.762A pdb=" N LYS A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N MET A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 removed outlier: 3.927A pdb=" N ASP A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 335 through 347 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 374 through 390 removed outlier: 4.424A pdb=" N TYR A 384 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASN A 385 " --> pdb=" O GLU A 382 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASN A 388 " --> pdb=" O ASN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 Processing helix chain 'A' and resid 414 through 429 removed outlier: 3.672A pdb=" N GLU A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 487 through 502 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 565 through 583 Processing sheet with id= A, first strand: chain 'B' and resid 159 through 162 removed outlier: 6.653A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 162 through 166 removed outlier: 5.927A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 185 through 189 removed outlier: 3.568A pdb=" N GLY D 65 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 186 through 190 removed outlier: 6.372A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.747A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 219 through 224 removed outlier: 6.532A pdb=" N LYS A 261 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N SER A 108 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE A 263 " --> pdb=" O SER A 108 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 2052 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: 10.31 Time building geometry restraints manager: 25.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14348 1.03 - 1.23: 33 1.23 - 1.42: 5817 1.42 - 1.62: 8566 1.62 - 1.81: 103 Bond restraints: 28867 Sorted by residual: bond pdb=" N ASP B 229 " pdb=" CA ASP B 229 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.83e-02 2.99e+03 1.96e+00 bond pdb=" C4 ADP D 801 " pdb=" C5 ADP D 801 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 ... (remaining 28862 not shown) Histogram of bond angle deviations from ideal: 98.82 - 107.03: 448 107.03 - 115.23: 37358 115.23 - 123.43: 12225 123.43 - 131.64: 2266 131.64 - 139.84: 27 Bond angle restraints: 52324 Sorted by residual: angle pdb=" C VAL B 228 " pdb=" N ASP B 229 " pdb=" CA ASP B 229 " ideal model delta sigma weight residual 126.32 134.35 -8.03 1.74e+00 3.30e-01 2.13e+01 angle pdb=" C ASP B 229 " pdb=" CA ASP B 229 " pdb=" CB ASP B 229 " ideal model delta sigma weight residual 110.04 105.42 4.62 1.51e+00 4.39e-01 9.36e+00 angle pdb=" C2' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" O3' ATP A 801 " ideal model delta sigma weight residual 111.83 105.64 6.19 2.67e+00 1.40e-01 5.37e+00 angle pdb=" C1' ATP A 801 " pdb=" C2' ATP A 801 " pdb=" O2' ATP A 801 " ideal model delta sigma weight residual 110.58 104.34 6.24 2.79e+00 1.28e-01 4.99e+00 angle pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" O3' ATP A 801 " ideal model delta sigma weight residual 111.06 105.50 5.56 2.50e+00 1.60e-01 4.95e+00 ... (remaining 52319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.52: 11391 34.52 - 69.05: 120 69.05 - 103.57: 10 103.57 - 138.09: 5 138.09 - 172.62: 4 Dihedral angle restraints: 11530 sinusoidal: 5626 harmonic: 5904 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 127.39 172.62 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.08 -149.08 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 82.53 -142.53 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 11527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1994 0.059 - 0.117: 235 0.117 - 0.176: 20 0.176 - 0.235: 1 0.235 - 0.293: 2 Chirality restraints: 2252 Sorted by residual: chirality pdb=" C3' ATP A 801 " pdb=" C2' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" O3' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C2' ATP A 801 " pdb=" C1' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" O2' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O4' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2249 not shown) Planarity restraints: 4172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " -0.037 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO E 63 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 287 " 0.011 2.00e-02 2.50e+03 9.19e-03 2.53e+00 pdb=" CG TYR E 287 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR E 287 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR E 287 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 287 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 287 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 287 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 287 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR E 287 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR E 287 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR E 287 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR E 287 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 228 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C VAL B 228 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL B 228 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP B 229 " 0.009 2.00e-02 2.50e+03 ... (remaining 4169 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1556 2.20 - 2.80: 59852 2.80 - 3.40: 79595 3.40 - 4.00: 102318 4.00 - 4.60: 161076 Nonbonded interactions: 404397 Sorted by model distance: nonbonded pdb=" OE1 GLU B 301 " pdb=" HH TYR C 308 " model vdw 1.600 1.850 nonbonded pdb="HH22 ARG D 91 " pdb=" O SER D 119 " model vdw 1.626 1.850 nonbonded pdb=" O ASN A 383 " pdb=" HG1 THR A 386 " model vdw 1.627 1.850 nonbonded pdb=" H LYS D 71 " pdb=" O3B ADP D 801 " model vdw 1.651 1.850 nonbonded pdb=" OD1 ASP D 37 " pdb=" HZ1 LYS D 50 " model vdw 1.663 1.850 ... (remaining 404392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 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: 0.420 Extract box with map and model: 14.350 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 88.120 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 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:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.002 0.026 14488 Z= 0.115 Angle : 0.483 8.034 19588 Z= 0.238 Chirality : 0.037 0.293 2252 Planarity : 0.003 0.057 2476 Dihedral : 13.773 172.618 5512 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.21), residues: 1748 helix: 3.26 (0.16), residues: 1048 sheet: -0.05 (0.41), residues: 166 loop : 0.53 (0.28), residues: 534 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 2.519 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 outliers start: 0 outliers final: 1 residues processed: 300 average time/residue: 2.9014 time to fit residues: 951.2119 Evaluate side-chains 157 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 2.435 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 3.2114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN E 336 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 14488 Z= 0.388 Angle : 0.602 7.466 19588 Z= 0.294 Chirality : 0.039 0.162 2252 Planarity : 0.004 0.082 2476 Dihedral : 10.228 169.617 1960 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.21), residues: 1748 helix: 2.75 (0.16), residues: 1064 sheet: 0.02 (0.42), residues: 149 loop : 0.29 (0.27), residues: 535 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 2.361 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 outliers start: 20 outliers final: 8 residues processed: 177 average time/residue: 2.8865 time to fit residues: 564.1196 Evaluate side-chains 140 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 2.567 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 1.5838 time to fit residues: 12.8319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 141 optimal weight: 30.0000 chunk 157 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 14488 Z= 0.207 Angle : 0.532 8.165 19588 Z= 0.254 Chirality : 0.037 0.142 2252 Planarity : 0.003 0.040 2476 Dihedral : 10.138 176.297 1960 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.21), residues: 1748 helix: 2.84 (0.16), residues: 1057 sheet: -0.02 (0.43), residues: 148 loop : 0.30 (0.27), residues: 543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 2.476 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 outliers start: 20 outliers final: 9 residues processed: 150 average time/residue: 2.5743 time to fit residues: 429.6822 Evaluate side-chains 137 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 2.329 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 1.0802 time to fit residues: 9.6103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.6980 chunk 119 optimal weight: 0.0980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 151 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 14488 Z= 0.220 Angle : 0.527 7.013 19588 Z= 0.250 Chirality : 0.036 0.135 2252 Planarity : 0.003 0.032 2476 Dihedral : 10.035 177.497 1960 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.21), residues: 1748 helix: 2.80 (0.16), residues: 1064 sheet: 0.10 (0.43), residues: 141 loop : 0.25 (0.27), residues: 543 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 2.524 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 outliers start: 13 outliers final: 4 residues processed: 143 average time/residue: 2.5951 time to fit residues: 412.5768 Evaluate side-chains 133 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 2.486 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 2.8500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 30.0000 chunk 96 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 116 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 14488 Z= 0.209 Angle : 0.516 6.967 19588 Z= 0.246 Chirality : 0.036 0.139 2252 Planarity : 0.003 0.041 2476 Dihedral : 9.915 179.604 1960 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.21), residues: 1748 helix: 2.78 (0.16), residues: 1065 sheet: 0.07 (0.42), residues: 141 loop : 0.25 (0.27), residues: 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 2.607 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 outliers start: 14 outliers final: 4 residues processed: 144 average time/residue: 2.5197 time to fit residues: 406.7103 Evaluate side-chains 134 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 2.670 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 2.2371 time to fit residues: 5.8246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 78 optimal weight: 0.0270 chunk 14 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 14488 Z= 0.226 Angle : 0.521 7.062 19588 Z= 0.248 Chirality : 0.036 0.138 2252 Planarity : 0.003 0.035 2476 Dihedral : 9.693 179.595 1960 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.21), residues: 1748 helix: 2.78 (0.16), residues: 1064 sheet: 0.08 (0.42), residues: 142 loop : 0.24 (0.27), residues: 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 2.480 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 outliers start: 12 outliers final: 6 residues processed: 142 average time/residue: 2.5979 time to fit residues: 411.4159 Evaluate side-chains 128 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 2.608 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 2.4184 time to fit residues: 6.1823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 105 optimal weight: 0.2980 chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 14488 Z= 0.162 Angle : 0.510 6.804 19588 Z= 0.240 Chirality : 0.036 0.144 2252 Planarity : 0.002 0.033 2476 Dihedral : 9.337 176.211 1960 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.21), residues: 1748 helix: 2.88 (0.16), residues: 1063 sheet: 0.08 (0.42), residues: 142 loop : 0.31 (0.28), residues: 543 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 2.346 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 outliers start: 11 outliers final: 10 residues processed: 136 average time/residue: 2.5511 time to fit residues: 389.6026 Evaluate side-chains 135 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 2.393 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 3 average time/residue: 1.4345 time to fit residues: 8.2504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 0.0970 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN C 128 ASN A 341 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 14488 Z= 0.161 Angle : 0.508 6.734 19588 Z= 0.238 Chirality : 0.036 0.142 2252 Planarity : 0.002 0.031 2476 Dihedral : 9.044 171.881 1960 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.21), residues: 1748 helix: 2.92 (0.16), residues: 1062 sheet: 0.13 (0.42), residues: 144 loop : 0.33 (0.28), residues: 542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 2.249 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 outliers start: 12 outliers final: 8 residues processed: 138 average time/residue: 2.5354 time to fit residues: 391.5599 Evaluate side-chains 131 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 2.462 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 1 average time/residue: 0.5427 time to fit residues: 4.2799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 14488 Z= 0.236 Angle : 0.524 8.900 19588 Z= 0.250 Chirality : 0.036 0.156 2252 Planarity : 0.003 0.032 2476 Dihedral : 8.891 168.641 1960 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.21), residues: 1748 helix: 2.80 (0.16), residues: 1066 sheet: 0.09 (0.41), residues: 150 loop : 0.31 (0.28), residues: 532 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 2.382 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 outliers start: 13 outliers final: 10 residues processed: 141 average time/residue: 2.6417 time to fit residues: 414.9051 Evaluate side-chains 134 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 2.400 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 3 average time/residue: 1.4024 time to fit residues: 8.1015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 138 optimal weight: 30.0000 chunk 14 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN A 341 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 14488 Z= 0.211 Angle : 0.528 7.788 19588 Z= 0.250 Chirality : 0.036 0.149 2252 Planarity : 0.003 0.070 2476 Dihedral : 8.703 165.101 1960 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.21), residues: 1748 helix: 2.80 (0.16), residues: 1067 sheet: 0.13 (0.41), residues: 148 loop : 0.33 (0.28), residues: 533 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 2.593 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 outliers start: 13 outliers final: 8 residues processed: 141 average time/residue: 2.5212 time to fit residues: 398.0751 Evaluate side-chains 136 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 2.459 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 1 average time/residue: 0.4403 time to fit residues: 3.7705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 30.0000 chunk 58 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.138981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.077366 restraints weight = 69763.698| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.96 r_work: 0.2864 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 14488 Z= 0.282 Angle : 0.545 8.567 19588 Z= 0.261 Chirality : 0.037 0.159 2252 Planarity : 0.003 0.054 2476 Dihedral : 8.664 162.996 1960 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.21), residues: 1748 helix: 2.70 (0.16), residues: 1073 sheet: 0.18 (0.38), residues: 168 loop : 0.31 (0.29), residues: 507 =============================================================================== Job complete usr+sys time: 9725.64 seconds wall clock time: 171 minutes 26.10 seconds (10286.10 seconds total)