Starting phenix.real_space_refine on Wed Mar 20 21:54:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/03_2024/7ste_25426_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/03_2024/7ste_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_25426/03_2024/7ste_25426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/03_2024/7ste_25426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/03_2024/7ste_25426_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/03_2024/7ste_25426_trim_updated.pdb" } resolution = 2.73 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= 0.035 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 13.07, per 1000 atoms: 0.46 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: 22.50 Conformation dependent library (CDL) restraints added in 3.0 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: 4.29 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: 10.60 Time building geometry restraints manager: 23.38 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: 13156 34.52 - 69.05: 259 69.05 - 103.57: 10 103.57 - 138.09: 5 138.09 - 172.62: 4 Dihedral angle restraints: 13434 sinusoidal: 7530 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 13431 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: 3.300 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: 0.460 Extract box with map and model: 13.140 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 90.740 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.530 ------------------------------------------------------------------------------- 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 : 14.056 172.618 5543 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 % Allowed : 0.00 % Favored : 100.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 66 HIS 0.005 0.001 HIS B 60 PHE 0.009 0.001 PHE A 96 TYR 0.027 0.001 TYR E 287 ARG 0.005 0.000 ARG E 283 *********************** 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 : 2.288 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: B 45 MET cc_start: 0.7945 (mpp) cc_final: 0.7586 (mpp) REVERT: B 119 MET cc_start: 0.4585 (tmm) cc_final: 0.3584 (mtt) REVERT: E 72 VAL cc_start: 0.8831 (t) cc_final: 0.8487 (t) REVERT: E 74 GLN cc_start: 0.7855 (mp10) cc_final: 0.7567 (mp-120) REVERT: E 161 TYR cc_start: 0.6916 (m-80) cc_final: 0.6709 (m-80) REVERT: A 287 MET cc_start: 0.5507 (ptm) cc_final: 0.5291 (ptm) REVERT: A 497 TYR cc_start: 0.7584 (t80) cc_final: 0.7331 (t80) REVERT: A 500 LYS cc_start: 0.8339 (mmtm) cc_final: 0.8100 (tmmt) outliers start: 0 outliers final: 1 residues processed: 300 average time/residue: 2.8460 time to fit residues: 933.2927 Evaluate side-chains 160 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 99 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.8379 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14488 Z= 0.362 Angle : 0.593 7.316 19588 Z= 0.290 Chirality : 0.039 0.171 2252 Planarity : 0.004 0.071 2476 Dihedral : 10.648 168.661 1993 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.07 % Allowed : 8.79 % Favored : 90.14 % 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: 2.75 (0.21), residues: 1748 helix: 2.84 (0.16), residues: 1058 sheet: -0.07 (0.40), residues: 167 loop : 0.36 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 256 HIS 0.009 0.001 HIS C 260 PHE 0.016 0.001 PHE E 305 TYR 0.018 0.001 TYR B 186 ARG 0.010 0.001 ARG D 115 *********************** 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 184 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 2.328 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: B 77 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8231 (mp0) REVERT: B 119 MET cc_start: 0.5067 (tmm) cc_final: 0.3902 (mtt) REVERT: E 32 GLN cc_start: 0.7528 (mp10) cc_final: 0.7322 (mp10) REVERT: E 72 VAL cc_start: 0.8950 (t) cc_final: 0.8681 (t) REVERT: E 74 GLN cc_start: 0.7925 (mp10) cc_final: 0.7664 (mp-120) outliers start: 17 outliers final: 6 residues processed: 175 average time/residue: 2.8003 time to fit residues: 538.4134 Evaluate side-chains 138 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain A residue 581 ILE 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: 0.8980 chunk 132 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14488 Z= 0.243 Angle : 0.531 7.713 19588 Z= 0.255 Chirality : 0.037 0.148 2252 Planarity : 0.003 0.043 2476 Dihedral : 10.532 176.746 1991 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.95 % Allowed : 10.37 % Favored : 88.69 % 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: 2.81 (0.16), residues: 1058 sheet: -0.15 (0.40), residues: 167 loop : 0.37 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 259 HIS 0.007 0.001 HIS C 260 PHE 0.013 0.001 PHE E 305 TYR 0.010 0.001 TYR D 286 ARG 0.006 0.000 ARG E 73 *********************** 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: 15 poor density : 146 time to evaluate : 2.494 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: B 45 MET cc_start: 0.7096 (mpp) cc_final: 0.6836 (mpp) REVERT: B 119 MET cc_start: 0.5444 (tmm) cc_final: 0.4305 (mtt) REVERT: B 301 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: E 72 VAL cc_start: 0.8959 (t) cc_final: 0.8673 (t) REVERT: E 74 GLN cc_start: 0.7876 (mp10) cc_final: 0.7635 (mp-120) outliers start: 15 outliers final: 5 residues processed: 152 average time/residue: 2.5445 time to fit residues: 429.5199 Evaluate side-chains 138 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 581 ILE 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: 0.0970 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 151 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8380 moved from start: 0.2915 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= 0.195 Angle : 0.517 6.821 19588 Z= 0.246 Chirality : 0.036 0.142 2252 Planarity : 0.003 0.035 2476 Dihedral : 10.313 176.424 1991 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.70 % Allowed : 11.38 % Favored : 87.93 % 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: 2.82 (0.16), residues: 1064 sheet: 0.08 (0.40), residues: 159 loop : 0.28 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 256 HIS 0.005 0.001 HIS C 260 PHE 0.010 0.001 PHE D 203 TYR 0.018 0.001 TYR B 186 ARG 0.005 0.000 ARG E 73 *********************** 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 152 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 141 time to evaluate : 2.441 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: B 119 MET cc_start: 0.5541 (tmm) cc_final: 0.4379 (mtt) REVERT: E 74 GLN cc_start: 0.7876 (mp10) cc_final: 0.7624 (mp-120) outliers start: 11 outliers final: 4 residues processed: 145 average time/residue: 2.5890 time to fit residues: 416.7872 Evaluate side-chains 133 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 20.0000 chunk 96 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8403 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14488 Z= 0.244 Angle : 0.517 7.239 19588 Z= 0.248 Chirality : 0.036 0.144 2252 Planarity : 0.003 0.035 2476 Dihedral : 10.258 178.750 1991 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.82 % Allowed : 11.82 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.21), residues: 1748 helix: 2.74 (0.16), residues: 1066 sheet: 0.08 (0.40), residues: 162 loop : 0.26 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 259 HIS 0.006 0.001 HIS C 260 PHE 0.012 0.001 PHE D 203 TYR 0.012 0.001 TYR E 161 ARG 0.005 0.000 ARG E 73 *********************** 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 150 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 2.214 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: B 119 MET cc_start: 0.5744 (tmm) cc_final: 0.4588 (mtt) REVERT: A 285 MET cc_start: 0.0982 (mmm) cc_final: 0.0355 (mmm) outliers start: 13 outliers final: 5 residues processed: 142 average time/residue: 2.4770 time to fit residues: 392.3192 Evaluate side-chains 132 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 581 ILE 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: 0.9990 chunk 99 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 78 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3202 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= 0.227 Angle : 0.520 7.039 19588 Z= 0.248 Chirality : 0.036 0.149 2252 Planarity : 0.003 0.041 2476 Dihedral : 10.016 179.104 1991 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.70 % Allowed : 12.45 % Favored : 86.85 % 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: 2.63 (0.21), residues: 1748 helix: 2.75 (0.16), residues: 1065 sheet: 0.09 (0.42), residues: 145 loop : 0.19 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 259 HIS 0.006 0.001 HIS C 260 PHE 0.014 0.001 PHE D 203 TYR 0.021 0.001 TYR B 186 ARG 0.006 0.000 ARG E 73 *********************** 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 149 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 2.380 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: B 119 MET cc_start: 0.5984 (tmm) cc_final: 0.4846 (mtt) REVERT: B 186 TYR cc_start: 0.8260 (p90) cc_final: 0.7882 (p90) REVERT: A 285 MET cc_start: 0.1148 (mmm) cc_final: 0.0914 (mmm) outliers start: 11 outliers final: 7 residues processed: 143 average time/residue: 2.6642 time to fit residues: 422.3760 Evaluate side-chains 131 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 581 ILE 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: 0.9980 chunk 123 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 142 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3269 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= 0.177 Angle : 0.514 6.960 19588 Z= 0.244 Chirality : 0.036 0.152 2252 Planarity : 0.003 0.048 2476 Dihedral : 9.664 176.517 1991 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.82 % Allowed : 12.64 % Favored : 86.54 % 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: 2.82 (0.16), residues: 1065 sheet: 0.15 (0.42), residues: 144 loop : 0.25 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 259 HIS 0.004 0.001 HIS C 260 PHE 0.010 0.001 PHE D 203 TYR 0.014 0.001 TYR B 186 ARG 0.008 0.000 ARG E 73 *********************** 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 150 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 2.254 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: B 186 TYR cc_start: 0.8251 (p90) cc_final: 0.7866 (p90) REVERT: A 285 MET cc_start: 0.1341 (mmm) cc_final: 0.1088 (mmm) outliers start: 13 outliers final: 6 residues processed: 144 average time/residue: 2.5109 time to fit residues: 401.8651 Evaluate side-chains 132 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 581 ILE 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: 0.6980 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8412 moved from start: 0.3419 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= 0.222 Angle : 0.523 7.073 19588 Z= 0.250 Chirality : 0.036 0.155 2252 Planarity : 0.003 0.051 2476 Dihedral : 9.423 172.307 1991 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.82 % Allowed : 12.58 % Favored : 86.60 % 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: 2.65 (0.21), residues: 1748 helix: 2.73 (0.16), residues: 1072 sheet: 0.19 (0.43), residues: 139 loop : 0.20 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 259 HIS 0.005 0.001 HIS E 18 PHE 0.015 0.001 PHE D 203 TYR 0.014 0.001 TYR B 186 ARG 0.007 0.000 ARG E 73 *********************** 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 143 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 2.334 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: B 119 MET cc_start: 0.6428 (ppp) cc_final: 0.4510 (mmt) REVERT: B 186 TYR cc_start: 0.8294 (p90) cc_final: 0.7903 (p90) REVERT: A 285 MET cc_start: 0.1315 (mmm) cc_final: 0.1052 (mmm) outliers start: 13 outliers final: 8 residues processed: 137 average time/residue: 2.5650 time to fit residues: 392.0274 Evaluate side-chains 130 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 142 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3458 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= 0.198 Angle : 0.520 7.002 19588 Z= 0.248 Chirality : 0.036 0.159 2252 Planarity : 0.003 0.064 2476 Dihedral : 9.169 168.657 1991 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.70 % Allowed : 13.02 % Favored : 86.28 % 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: 2.70 (0.21), residues: 1748 helix: 2.75 (0.16), residues: 1073 sheet: 0.21 (0.42), residues: 144 loop : 0.27 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 259 HIS 0.005 0.001 HIS B 60 PHE 0.012 0.001 PHE D 203 TYR 0.013 0.001 TYR B 186 ARG 0.010 0.000 ARG D 115 *********************** 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 141 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 2.378 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: B 186 TYR cc_start: 0.8309 (p90) cc_final: 0.7907 (p90) REVERT: E 74 GLN cc_start: 0.7762 (mp10) cc_final: 0.7508 (mp-120) REVERT: A 285 MET cc_start: 0.1329 (mmm) cc_final: 0.1071 (mmm) outliers start: 11 outliers final: 8 residues processed: 136 average time/residue: 2.4653 time to fit residues: 373.5197 Evaluate side-chains 134 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 581 ILE 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: 0.9980 chunk 115 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 138 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN ** E 317 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14488 Z= 0.256 Angle : 0.543 11.064 19588 Z= 0.260 Chirality : 0.036 0.164 2252 Planarity : 0.003 0.051 2476 Dihedral : 9.075 165.742 1991 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.51 % Allowed : 13.34 % Favored : 86.16 % 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: 2.61 (0.21), residues: 1748 helix: 2.66 (0.16), residues: 1073 sheet: 0.24 (0.39), residues: 163 loop : 0.25 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 259 HIS 0.006 0.001 HIS E 18 PHE 0.011 0.001 PHE D 203 TYR 0.013 0.001 TYR B 186 ARG 0.012 0.000 ARG D 115 ********************** 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 137 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 2.323 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: B 119 MET cc_start: 0.6235 (ppp) cc_final: 0.4380 (mmt) REVERT: B 186 TYR cc_start: 0.8331 (p90) cc_final: 0.7926 (p90) REVERT: A 285 MET cc_start: 0.1350 (mmm) cc_final: 0.1097 (mmm) outliers start: 8 outliers final: 8 residues processed: 134 average time/residue: 2.6180 time to fit residues: 389.6718 Evaluate side-chains 131 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 139 optimal weight: 30.0000 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 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 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** 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 = 0.3997 r_free = 0.3997 target = 0.138788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.076950 restraints weight = 69969.808| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.91 r_work: 0.2859 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14488 Z= 0.279 Angle : 0.541 7.558 19588 Z= 0.262 Chirality : 0.037 0.159 2252 Planarity : 0.003 0.055 2476 Dihedral : 9.029 164.447 1991 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.57 % Allowed : 13.53 % Favored : 85.90 % 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: 2.58 (0.21), residues: 1748 helix: 2.63 (0.16), residues: 1073 sheet: 0.17 (0.38), residues: 170 loop : 0.29 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 259 HIS 0.006 0.001 HIS E 18 PHE 0.013 0.001 PHE B 142 TYR 0.013 0.001 TYR B 186 ARG 0.011 0.000 ARG D 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9569.24 seconds wall clock time: 167 minutes 35.77 seconds (10055.77 seconds total)