Starting phenix.real_space_refine on Sat Feb 24 16:44:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stb_25423/02_2024/7stb_25423_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stb_25423/02_2024/7stb_25423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stb_25423/02_2024/7stb_25423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stb_25423/02_2024/7stb_25423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stb_25423/02_2024/7stb_25423_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stb_25423/02_2024/7stb_25423_trim_updated.pdb" } resolution = 2.72 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= -0.001 sd= 0.042 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 49 5.49 5 Mg 4 5.21 5 S 119 5.16 5 C 14313 2.51 5 N 3904 2.21 5 O 4425 1.98 5 H 22555 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 93": "OD1" <-> "OD2" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 462": "OD1" <-> "OD2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C ASP 223": "OD1" <-> "OD2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 302": "OE1" <-> "OE2" Residue "F PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 229": "OD1" <-> "OD2" Residue "G PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 372": "OE1" <-> "OE2" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 460": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 45369 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 8378 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 19, 'TRANS': 495} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5027 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: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5196 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 5304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5304 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 320} Chain: "E" Number of atoms: 5525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5525 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 4539 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 3, 'TRANS': 284} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 5428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5428 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 11, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4710 Classifications: {'peptide': 293} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 6 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 804 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "I" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 303 Classifications: {'DNA': 11} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 10} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} Time building chain proxies: 18.70, per 1000 atoms: 0.41 Number of scatterers: 45369 At special positions: 0 Unit cell: (128.856, 122.248, 145.376, 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 119 16.00 P 49 15.00 Mg 4 11.99 O 4425 8.00 N 3904 7.00 C 14313 6.00 H 22555 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: 36.43 Conformation dependent library (CDL) restraints added in 4.7 seconds 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5266 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 16 sheets defined 46.2% alpha, 15.1% beta 7 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 22.54 Creating SS restraints... 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 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.610A 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 162 through 175 removed outlier: 4.348A pdb=" N PHE A 166 " --> pdb=" O MET A 163 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 167 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 171 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG A 174 " --> 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 246 through 249 No H-bonds generated for 'chain 'A' and resid 246 through 249' 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 283 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 374 through 386 removed outlier: 5.364A pdb=" N ASN A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.643A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 446 through 471 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 484 through 508 Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 566 through 589 Processing helix chain 'A' and resid 599 through 605 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 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 71 through 74 No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 86 through 98 removed outlier: 4.132A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.704A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 152 through 157 removed outlier: 4.121A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 282 through 300 Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'C' and resid 10 through 12 No H-bonds generated for 'chain 'C' and resid 10 through 12' 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 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 101 removed outlier: 3.967A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) 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 removed outlier: 4.109A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) 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 269 Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.983A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 312 removed outlier: 3.572A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 332 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 51 removed outlier: 4.499A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 91 Proline residue: D 85 - end of helix removed outlier: 4.085A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.859A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 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 153 Processing helix chain 'D' and resid 156 through 159 No H-bonds generated for 'chain 'D' and resid 156 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 Processing helix chain 'D' and resid 198 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 276 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.880A pdb=" N SER D 293 " --> pdb=" O THR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 316 through 335 removed outlier: 3.595A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 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 20 through 30 Processing helix chain 'E' and resid 49 through 61 Processing helix chain 'E' and resid 98 through 111 removed outlier: 6.890A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP E 105 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU E 111 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 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 removed outlier: 3.559A pdb=" N ARG E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 216 through 226 removed outlier: 3.697A pdb=" N ALA E 225 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER E 226 " --> pdb=" O ALA E 223 " (cutoff:3.500A) 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 291 removed outlier: 3.650A pdb=" N ALA E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 309 removed outlier: 3.664A pdb=" N ASP E 309 " --> pdb=" O PHE E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 334 Processing helix chain 'E' and resid 339 through 353 Processing helix chain 'F' and resid 18 through 31 removed outlier: 3.778A pdb=" N CYS F 27 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Proline residue: F 30 - end of helix Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 89 through 92 No H-bonds generated for 'chain 'F' and resid 89 through 92' Processing helix chain 'F' and resid 160 through 172 Processing helix chain 'F' and resid 239 through 250 removed outlier: 4.041A pdb=" N LYS F 244 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE F 245 " --> pdb=" O SER F 241 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG F 246 " --> pdb=" O PHE F 242 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LYS F 247 " --> pdb=" O ASP F 243 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 327 Processing helix chain 'G' and resid 10 through 26 Processing helix chain 'G' and resid 58 through 60 No H-bonds generated for 'chain 'G' and resid 58 through 60' Processing helix chain 'G' and resid 68 through 70 No H-bonds generated for 'chain 'G' and resid 68 through 70' Processing helix chain 'G' and resid 75 through 77 No H-bonds generated for 'chain 'G' and resid 75 through 77' Processing helix chain 'G' and resid 98 through 105 Processing helix chain 'G' and resid 128 through 130 No H-bonds generated for 'chain 'G' and resid 128 through 130' Processing helix chain 'G' and resid 162 through 173 Processing helix chain 'G' and resid 189 through 204 Processing helix chain 'G' and resid 234 through 243 removed outlier: 3.755A pdb=" N ASN G 243 " --> pdb=" O ASN G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 334 removed outlier: 4.075A pdb=" N THR G 334 " --> pdb=" O LYS G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 338 No H-bonds generated for 'chain 'G' and resid 336 through 338' Processing helix chain 'H' and resid 13 through 27 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 97 through 113 Processing helix chain 'H' and resid 214 through 219 Processing helix chain 'H' and resid 243 through 253 removed outlier: 4.670A pdb=" N VAL H 253 " --> pdb=" O PHE H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 422 Processing sheet with id= A, first strand: chain 'A' and resid 260 through 264 removed outlier: 6.351A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE A 263 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 106 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A 219 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU A 107 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE A 221 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY A 109 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 223 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR A 224 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 159 through 162 removed outlier: 6.272A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 162 through 166 removed outlier: 6.145A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 185 through 189 removed outlier: 6.389A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 186 through 190 removed outlier: 6.139A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.695A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 69 through 72 Processing sheet with id= H, first strand: chain 'F' and resid 80 through 85 removed outlier: 5.948A pdb=" N ASP F 36 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU F 51 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 305 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 232 through 238 removed outlier: 3.634A pdb=" N GLU F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 64 through 66 removed outlier: 6.804A pdb=" N GLU G 139 " --> pdb=" O LYS G 114 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE G 116 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL G 137 " --> pdb=" O PHE G 116 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE G 118 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE G 135 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL G 120 " --> pdb=" O ARG G 133 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ARG G 133 " --> pdb=" O VAL G 120 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 295 through 297 removed outlier: 6.171A pdb=" N ASN G 348 " --> pdb=" O GLN G 365 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLN G 365 " --> pdb=" O ASN G 348 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N MET G 44 " --> pdb=" O ASP G 29 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASP G 29 " --> pdb=" O MET G 44 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 93 through 95 removed outlier: 4.304A pdb=" N SER G 93 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 320 through 325 Processing sheet with id= N, first strand: chain 'H' and resid 80 through 83 Processing sheet with id= O, first strand: chain 'H' and resid 232 through 234 removed outlier: 4.047A pdb=" N GLU H 427 " --> pdb=" O SER H 443 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER H 443 " --> pdb=" O GLU H 427 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN H 96 " --> pdb=" O PRO H 208 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 406 through 411 removed outlier: 3.631A pdb=" N HIS H 406 " --> pdb=" O GLY H 266 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N HIS H 261 " --> pdb=" O ASN H 286 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ASN H 286 " --> pdb=" O HIS H 261 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 2970 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 17.59 Time building geometry restraints manager: 37.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 22500 1.06 - 1.28: 3801 1.28 - 1.50: 9706 1.50 - 1.73: 9639 1.73 - 1.95: 179 Bond restraints: 45825 Sorted by residual: bond pdb=" CB PRO E 63 " pdb=" CG PRO E 63 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 9.98e+00 bond pdb=" CG PRO E 63 " pdb=" CD PRO E 63 " ideal model delta sigma weight residual 1.503 1.403 0.100 3.40e-02 8.65e+02 8.73e+00 bond pdb=" N PRO E 63 " pdb=" CD PRO E 63 " ideal model delta sigma weight residual 1.473 1.500 -0.027 1.40e-02 5.10e+03 3.77e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N MET G 1 " pdb=" H MET G 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 45820 not shown) Histogram of bond angle deviations from ideal: 94.36 - 102.82: 90 102.82 - 111.29: 52108 111.29 - 119.75: 13937 119.75 - 128.22: 16664 128.22 - 136.68: 191 Bond angle restraints: 82990 Sorted by residual: angle pdb=" CA PRO E 63 " pdb=" N PRO E 63 " pdb=" CD PRO E 63 " ideal model delta sigma weight residual 112.00 96.94 15.06 1.40e+00 5.10e-01 1.16e+02 angle pdb=" N PRO E 63 " pdb=" CD PRO E 63 " pdb=" CG PRO E 63 " ideal model delta sigma weight residual 103.20 94.36 8.84 1.50e+00 4.44e-01 3.48e+01 angle pdb=" CA PRO E 63 " pdb=" CB PRO E 63 " pdb=" CG PRO E 63 " ideal model delta sigma weight residual 104.50 98.74 5.76 1.90e+00 2.77e-01 9.18e+00 angle pdb=" O3' DA I 0 " pdb=" P DC I 1 " pdb=" O5' DC I 1 " ideal model delta sigma weight residual 104.00 99.72 4.28 1.50e+00 4.44e-01 8.12e+00 angle pdb=" C GLY E 62 " pdb=" N PRO E 63 " pdb=" CD PRO E 63 " ideal model delta sigma weight residual 125.00 136.68 -11.68 4.10e+00 5.95e-02 8.12e+00 ... (remaining 82985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.32: 20561 31.32 - 62.63: 642 62.63 - 93.95: 29 93.95 - 125.26: 2 125.26 - 156.58: 3 Dihedral angle restraints: 21237 sinusoidal: 11945 harmonic: 9292 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 179.41 120.59 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" O1A AGS D 402 " pdb=" O3A AGS D 402 " pdb=" PA AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sinusoidal sigma weight residual -67.73 77.93 -145.66 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" O1A AGS C 402 " pdb=" O3A AGS C 402 " pdb=" PA AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sinusoidal sigma weight residual -67.73 74.68 -142.41 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 21234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2542 0.032 - 0.063: 708 0.063 - 0.095: 225 0.095 - 0.126: 151 0.126 - 0.158: 18 Chirality restraints: 3644 Sorted by residual: chirality pdb=" CA ILE F 41 " pdb=" N ILE F 41 " pdb=" C ILE F 41 " pdb=" CB ILE F 41 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA PRO E 63 " pdb=" N PRO E 63 " pdb=" C PRO E 63 " pdb=" CB PRO E 63 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE F 269 " pdb=" N ILE F 269 " pdb=" C ILE F 269 " pdb=" CB ILE F 269 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 3641 not shown) Planarity restraints: 6533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " 0.054 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO E 63 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 32 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO D 33 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 33 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 33 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 162 " -0.124 9.50e-02 1.11e+02 4.15e-02 2.06e+00 pdb=" NE ARG B 162 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 162 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 162 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 162 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 162 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG B 162 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 162 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 162 " -0.000 2.00e-02 2.50e+03 ... (remaining 6530 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 2269 2.19 - 2.80: 93700 2.80 - 3.40: 125035 3.40 - 4.00: 167475 4.00 - 4.60: 260059 Nonbonded interactions: 648538 Sorted by model distance: nonbonded pdb=" O PHE A 387 " pdb=" HD1 HIS A 438 " model vdw 1.593 1.850 nonbonded pdb=" OD1 ASP A 402 " pdb="HH12 ARG E 331 " model vdw 1.594 1.850 nonbonded pdb=" O ARG H 20 " pdb="HD21 ASN H 24 " model vdw 1.595 1.850 nonbonded pdb=" HG1 THR A 224 " pdb=" O3G AGS A 901 " model vdw 1.596 1.850 nonbonded pdb=" H LYS D 34 " pdb=" OE2 GLU D 38 " model vdw 1.598 1.850 ... (remaining 648533 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: 2.840 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: 0.600 Extract box with map and model: 14.250 Check model and map are aligned: 0.730 Set scattering table: 0.430 Process input model: 152.750 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.130 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 0.158 23270 Z= 0.161 Angle : 0.448 15.063 31605 Z= 0.246 Chirality : 0.039 0.158 3644 Planarity : 0.003 0.073 3878 Dihedral : 14.255 156.576 8866 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 2.20 (0.17), residues: 2707 helix: 2.46 (0.15), residues: 1297 sheet: 0.99 (0.22), residues: 562 loop : 0.25 (0.24), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 42 HIS 0.006 0.001 HIS D 340 PHE 0.015 0.001 PHE F 236 TYR 0.008 0.001 TYR E 287 ARG 0.007 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 410 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 3.912 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: 3 residues processed: 410 average time/residue: 3.1091 time to fit residues: 1451.5843 Evaluate side-chains 187 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 3.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 143 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 0.9980 chunk 208 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 215 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN B 146 GLN B 208 ASN C 30 GLN C 291 GLN E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23270 Z= 0.280 Angle : 0.519 5.839 31605 Z= 0.279 Chirality : 0.041 0.177 3644 Planarity : 0.004 0.044 3878 Dihedral : 12.957 154.849 3408 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 1.21 % Allowed : 9.65 % Favored : 89.14 % 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: 1.88 (0.17), residues: 2707 helix: 2.17 (0.15), residues: 1297 sheet: 0.83 (0.22), residues: 570 loop : 0.16 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 16 HIS 0.007 0.001 HIS E 341 PHE 0.019 0.001 PHE G 152 TYR 0.015 0.001 TYR B 186 ARG 0.008 0.001 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 3.369 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: B 8 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.5959 (pm20) REVERT: B 42 MET cc_start: 0.6788 (ttt) cc_final: 0.6326 (ttt) outliers start: 30 outliers final: 10 residues processed: 211 average time/residue: 3.0030 time to fit residues: 729.8452 Evaluate side-chains 175 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 170 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 270 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 146 GLN E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN G 69 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23270 Z= 0.252 Angle : 0.501 7.045 31605 Z= 0.267 Chirality : 0.040 0.169 3644 Planarity : 0.004 0.043 3878 Dihedral : 12.824 158.435 3402 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 1.01 % Allowed : 10.62 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.17), residues: 2707 helix: 2.08 (0.15), residues: 1287 sheet: 0.72 (0.21), residues: 575 loop : 0.12 (0.23), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 294 HIS 0.007 0.001 HIS D 340 PHE 0.019 0.001 PHE A 523 TYR 0.011 0.001 TYR E 42 ARG 0.008 0.000 ARG H 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 3.728 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: A 238 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.6359 (m-80) outliers start: 25 outliers final: 11 residues processed: 189 average time/residue: 2.7835 time to fit residues: 624.0063 Evaluate side-chains 169 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain H residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 251 optimal weight: 0.0270 chunk 265 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 237 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 146 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN E 336 ASN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 23270 Z= 0.153 Angle : 0.468 6.611 31605 Z= 0.247 Chirality : 0.039 0.155 3644 Planarity : 0.003 0.043 3878 Dihedral : 12.718 156.730 3402 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.59 % Favored : 97.38 % Rotamer: Outliers : 0.89 % Allowed : 11.43 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.17), residues: 2707 helix: 2.27 (0.15), residues: 1289 sheet: 0.72 (0.22), residues: 575 loop : 0.15 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 42 HIS 0.005 0.001 HIS D 340 PHE 0.012 0.001 PHE A 523 TYR 0.010 0.001 TYR A 501 ARG 0.009 0.000 ARG F 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 3.635 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: A 238 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.6246 (m-80) outliers start: 22 outliers final: 10 residues processed: 181 average time/residue: 2.6311 time to fit residues: 557.9235 Evaluate side-chains 163 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 91 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 226 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 132 GLN C 167 GLN E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23270 Z= 0.243 Angle : 0.487 5.717 31605 Z= 0.259 Chirality : 0.040 0.157 3644 Planarity : 0.003 0.047 3878 Dihedral : 12.858 157.996 3402 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.93 % Rotamer: Outliers : 1.09 % Allowed : 11.67 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.17), residues: 2707 helix: 2.13 (0.15), residues: 1290 sheet: 0.65 (0.21), residues: 576 loop : 0.02 (0.23), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 16 HIS 0.006 0.001 HIS D 340 PHE 0.017 0.001 PHE G 152 TYR 0.012 0.001 TYR B 186 ARG 0.005 0.000 ARG F 149 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 3.592 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: A 238 PHE cc_start: 0.6731 (OUTLIER) cc_final: 0.6340 (m-80) outliers start: 27 outliers final: 14 residues processed: 174 average time/residue: 2.4630 time to fit residues: 505.2749 Evaluate side-chains 165 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 198 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 266 optimal weight: 6.9990 chunk 220 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 146 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23270 Z= 0.280 Angle : 0.499 6.324 31605 Z= 0.267 Chirality : 0.040 0.177 3644 Planarity : 0.004 0.048 3878 Dihedral : 12.960 159.651 3402 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 1.41 % Allowed : 11.83 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.17), residues: 2707 helix: 2.03 (0.15), residues: 1285 sheet: 0.59 (0.21), residues: 575 loop : -0.07 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 16 HIS 0.006 0.001 HIS D 340 PHE 0.018 0.001 PHE G 152 TYR 0.012 0.001 TYR E 42 ARG 0.004 0.000 ARG F 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 150 time to evaluate : 3.908 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: A 238 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6457 (m-80) REVERT: A 584 TYR cc_start: 0.5006 (OUTLIER) cc_final: 0.4715 (t80) REVERT: F 318 GLU cc_start: 0.5569 (OUTLIER) cc_final: 0.5357 (mm-30) outliers start: 35 outliers final: 17 residues processed: 170 average time/residue: 2.6141 time to fit residues: 521.9390 Evaluate side-chains 169 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 3.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 265 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 146 GLN C 291 GLN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23270 Z= 0.311 Angle : 0.518 5.751 31605 Z= 0.278 Chirality : 0.041 0.185 3644 Planarity : 0.004 0.054 3878 Dihedral : 13.131 163.098 3402 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Rotamer: Outliers : 1.29 % Allowed : 12.24 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.17), residues: 2707 helix: 1.84 (0.15), residues: 1287 sheet: 0.46 (0.21), residues: 576 loop : -0.18 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 16 HIS 0.007 0.001 HIS D 340 PHE 0.021 0.002 PHE G 152 TYR 0.013 0.001 TYR G 229 ARG 0.009 0.001 ARG F 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 156 time to evaluate : 3.646 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: A 238 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6591 (m-80) REVERT: C 142 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7754 (tpp-160) outliers start: 32 outliers final: 18 residues processed: 175 average time/residue: 2.5762 time to fit residues: 529.5905 Evaluate side-chains 170 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 208 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 23270 Z= 0.165 Angle : 0.477 7.227 31605 Z= 0.253 Chirality : 0.039 0.153 3644 Planarity : 0.003 0.049 3878 Dihedral : 13.000 161.748 3402 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.34 % Rotamer: Outliers : 0.93 % Allowed : 12.60 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.17), residues: 2707 helix: 2.05 (0.15), residues: 1296 sheet: 0.54 (0.21), residues: 574 loop : -0.05 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 42 HIS 0.004 0.001 HIS H 263 PHE 0.010 0.001 PHE F 236 TYR 0.010 0.001 TYR E 42 ARG 0.007 0.000 ARG F 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 3.986 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: A 238 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.6505 (m-80) REVERT: C 142 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7716 (tpp-160) REVERT: C 197 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7942 (tt) outliers start: 23 outliers final: 16 residues processed: 162 average time/residue: 2.6330 time to fit residues: 507.7385 Evaluate side-chains 166 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 2.9990 chunk 253 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 411 ASN C 291 GLN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23270 Z= 0.318 Angle : 0.521 6.521 31605 Z= 0.280 Chirality : 0.041 0.192 3644 Planarity : 0.004 0.057 3878 Dihedral : 13.184 164.291 3402 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 1.09 % Allowed : 12.68 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.17), residues: 2707 helix: 1.78 (0.15), residues: 1300 sheet: 0.37 (0.21), residues: 570 loop : -0.21 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 16 HIS 0.007 0.001 HIS E 341 PHE 0.022 0.002 PHE G 152 TYR 0.014 0.001 TYR G 229 ARG 0.005 0.000 ARG F 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 3.373 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: A 238 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6601 (m-80) REVERT: C 142 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7819 (tpp-160) REVERT: C 197 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8010 (tt) outliers start: 27 outliers final: 18 residues processed: 162 average time/residue: 2.5651 time to fit residues: 488.1526 Evaluate side-chains 166 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 273 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 173 optimal weight: 0.0970 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 411 ASN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23270 Z= 0.259 Angle : 0.509 9.123 31605 Z= 0.271 Chirality : 0.040 0.160 3644 Planarity : 0.004 0.044 3878 Dihedral : 13.199 164.216 3402 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 1.13 % Allowed : 12.68 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.17), residues: 2707 helix: 1.74 (0.15), residues: 1301 sheet: 0.38 (0.21), residues: 569 loop : -0.21 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 16 HIS 0.006 0.001 HIS D 340 PHE 0.017 0.001 PHE G 152 TYR 0.015 0.001 TYR A 501 ARG 0.005 0.000 ARG B 272 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 3.896 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: A 238 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6596 (m-80) REVERT: B 13 GLU cc_start: 0.6721 (tp30) cc_final: 0.6510 (tp30) REVERT: C 197 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8021 (tt) REVERT: F 80 MET cc_start: 0.7777 (mtm) cc_final: 0.7483 (mtm) outliers start: 28 outliers final: 16 residues processed: 164 average time/residue: 2.6729 time to fit residues: 514.2150 Evaluate side-chains 167 residues out of total 2495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 3.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 191 optimal weight: 0.0970 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 411 ASN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.098959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.075995 restraints weight = 144265.448| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.92 r_work: 0.3267 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23270 Z= 0.198 Angle : 0.491 7.513 31605 Z= 0.261 Chirality : 0.040 0.153 3644 Planarity : 0.003 0.045 3878 Dihedral : 13.153 163.830 3402 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 1.01 % Allowed : 12.76 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.17), residues: 2707 helix: 1.92 (0.15), residues: 1293 sheet: 0.42 (0.21), residues: 571 loop : -0.10 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 42 HIS 0.005 0.001 HIS D 340 PHE 0.012 0.001 PHE G 152 TYR 0.010 0.001 TYR A 469 ARG 0.005 0.000 ARG B 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12343.55 seconds wall clock time: 219 minutes 7.15 seconds (13147.15 seconds total)