Starting phenix.real_space_refine on Wed Feb 14 16:36:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arh_11882/02_2024/7arh_11882_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arh_11882/02_2024/7arh_11882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arh_11882/02_2024/7arh_11882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arh_11882/02_2024/7arh_11882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arh_11882/02_2024/7arh_11882_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arh_11882/02_2024/7arh_11882_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 56 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 6159 2.51 5 N 1692 2.21 5 O 1748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E GLU 67": "OE1" <-> "OE2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E ARG 125": "NH1" <-> "NH2" Residue "E ASP 136": "OD1" <-> "OD2" Residue "E ARG 139": "NH1" <-> "NH2" Residue "E ASP 156": "OD1" <-> "OD2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 312": "OD1" <-> "OD2" Residue "E PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E ASP 369": "OD1" <-> "OD2" Residue "E PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 379": "OD1" <-> "OD2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F ARG 151": "NH1" <-> "NH2" Residue "F ASP 170": "OD1" <-> "OD2" Residue "F ASP 205": "OD1" <-> "OD2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ASP 23": "OD1" <-> "OD2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "V ASP 8": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9649 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2969 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Chain: "E" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3159 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 14, 'TRANS': 394} Chain: "F" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1671 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 8, 'TRANS': 216} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1721 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 216} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "V" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 73 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'Z41': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Chain: "V" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.55, per 1000 atoms: 0.58 Number of scatterers: 9649 At special positions: 0 Unit cell: (85.176, 90.246, 154.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1748 8.00 N 1692 7.00 C 6159 6.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 2.0 seconds 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 10 sheets defined 33.5% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'C' and resid 9 through 11 No H-bonds generated for 'chain 'C' and resid 9 through 11' Processing helix chain 'C' and resid 23 through 27 removed outlier: 4.013A pdb=" N SER C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 23 through 27' Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.762A pdb=" N ILE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 58 removed outlier: 3.703A pdb=" N VAL C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 148 through 154 removed outlier: 3.919A pdb=" N GLN C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 257 through 303 removed outlier: 3.819A pdb=" N ARG C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET C 266 " --> pdb=" O MET C 262 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 284 " --> pdb=" O PHE C 280 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA C 298 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE C 299 " --> pdb=" O GLY C 295 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 removed outlier: 3.506A pdb=" N MET C 311 " --> pdb=" O PRO C 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 307 through 311' Processing helix chain 'C' and resid 313 through 338 removed outlier: 4.129A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 378 removed outlier: 3.971A pdb=" N ILE C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU C 377 " --> pdb=" O MET C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 389 removed outlier: 3.695A pdb=" N ALA C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 32 removed outlier: 3.994A pdb=" N SER E 27 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE E 29 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER E 30 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 58 removed outlier: 3.697A pdb=" N VAL E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA E 47 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN E 56 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 86 removed outlier: 4.122A pdb=" N ASP E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 155 through 158 No H-bonds generated for 'chain 'E' and resid 155 through 158' Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 255 through 258 No H-bonds generated for 'chain 'E' and resid 255 through 258' Processing helix chain 'E' and resid 261 through 269 removed outlier: 3.663A pdb=" N ILE E 268 " --> pdb=" O ASP E 264 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG E 269 " --> pdb=" O ILE E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 283 removed outlier: 3.676A pdb=" N VAL E 277 " --> pdb=" O TYR E 273 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 291 Processing helix chain 'E' and resid 293 through 296 No H-bonds generated for 'chain 'E' and resid 293 through 296' Processing helix chain 'E' and resid 299 through 307 removed outlier: 3.573A pdb=" N ALA E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 340 removed outlier: 3.523A pdb=" N ILE E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHE E 319 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL E 320 " --> pdb=" O ARG E 316 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY E 327 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS E 333 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY E 334 " --> pdb=" O GLY E 330 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE E 337 " --> pdb=" O CYS E 333 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 356 removed outlier: 3.763A pdb=" N GLU E 350 " --> pdb=" O THR E 346 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP E 351 " --> pdb=" O PRO E 347 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS E 354 " --> pdb=" O GLU E 350 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E 355 " --> pdb=" O TRP E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 404 removed outlier: 3.610A pdb=" N PHE E 381 " --> pdb=" O TRP E 377 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Proline residue: E 398 - end of helix removed outlier: 3.928A pdb=" N ASN E 404 " --> pdb=" O ARG E 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 56 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.617A pdb=" N ASN F 86 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN F 87 " --> pdb=" O LEU F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 83 through 87' Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.940A pdb=" N VAL F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 104 through 108' Processing helix chain 'F' and resid 110 through 114 Processing helix chain 'F' and resid 122 through 124 No H-bonds generated for 'chain 'F' and resid 122 through 124' Processing helix chain 'F' and resid 127 through 133 Processing helix chain 'F' and resid 143 through 145 No H-bonds generated for 'chain 'F' and resid 143 through 145' Processing helix chain 'F' and resid 148 through 151 No H-bonds generated for 'chain 'F' and resid 148 through 151' Processing helix chain 'F' and resid 183 through 194 removed outlier: 3.609A pdb=" N LEU F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY F 189 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU F 190 " --> pdb=" O GLN F 186 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN F 192 " --> pdb=" O LEU F 188 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 211 removed outlier: 3.769A pdb=" N ARG F 211 " --> pdb=" O LEU F 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.813A pdb=" N GLY D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 52 through 56' Processing helix chain 'D' and resid 78 through 87 removed outlier: 3.621A pdb=" N ALA D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 107 No H-bonds generated for 'chain 'D' and resid 104 through 107' Processing helix chain 'D' and resid 111 through 114 No H-bonds generated for 'chain 'D' and resid 111 through 114' Processing helix chain 'D' and resid 122 through 125 No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 127 through 133 Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 151 through 153 No H-bonds generated for 'chain 'D' and resid 151 through 153' Processing helix chain 'D' and resid 183 through 194 removed outlier: 3.918A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ARG D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 67 through 69 Processing sheet with id= B, first strand: chain 'C' and resid 93 through 96 Processing sheet with id= C, first strand: chain 'C' and resid 143 through 146 removed outlier: 8.128A pdb=" N VAL C 144 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASN C 185 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU C 146 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE C 187 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG C 182 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL C 164 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY C 112 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N MET C 201 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 115 " --> pdb=" O MET C 201 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 251 through 253 removed outlier: 3.559A pdb=" N LYS E 252 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY E 66 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 226 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA E 93 " --> pdb=" O LYS E 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.635A pdb=" N VAL E 115 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA E 204 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 165 through 170 removed outlier: 4.095A pdb=" N ILE E 168 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL E 185 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 6 through 9 removed outlier: 3.572A pdb=" N LEU F 6 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 14 through 16 Processing sheet with id= I, first strand: chain 'F' and resid 37 through 41 removed outlier: 6.606A pdb=" N PHE F 199 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE F 40 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL F 201 " --> pdb=" O ILE F 40 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 37 through 41 removed outlier: 6.546A pdb=" N PHE D 199 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE D 40 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL D 201 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 200 " --> pdb=" O VAL D 167 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3165 1.34 - 1.46: 1139 1.46 - 1.57: 5407 1.57 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 9804 Sorted by residual: bond pdb=" C19 Z41 C 401 " pdb=" O3 Z41 C 401 " ideal model delta sigma weight residual 1.333 1.456 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" C16 Z41 C 401 " pdb=" O2 Z41 C 401 " ideal model delta sigma weight residual 1.332 1.453 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C1 PLM V 201 " pdb=" C2 PLM V 201 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C1 PLM V 201 " pdb=" O2 PLM V 201 " ideal model delta sigma weight residual 1.249 1.220 0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" N THR D 62 " pdb=" CA THR D 62 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.78e+00 ... (remaining 9799 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.19: 305 107.19 - 113.89: 5593 113.89 - 120.60: 3739 120.60 - 127.30: 3529 127.30 - 134.00: 96 Bond angle restraints: 13262 Sorted by residual: angle pdb=" C PRO D 61 " pdb=" N THR D 62 " pdb=" CA THR D 62 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.24e+01 angle pdb=" C VAL C 130 " pdb=" N ASN C 131 " pdb=" CA ASN C 131 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C20 Z41 C 401 " pdb=" C19 Z41 C 401 " pdb=" O3 Z41 C 401 " ideal model delta sigma weight residual 110.49 120.47 -9.98 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CA LEU E 129 " pdb=" C LEU E 129 " pdb=" N PRO E 130 " ideal model delta sigma weight residual 118.44 123.05 -4.61 1.59e+00 3.96e-01 8.42e+00 angle pdb=" CA LEU D 206 " pdb=" CB LEU D 206 " pdb=" CG LEU D 206 " ideal model delta sigma weight residual 116.30 126.40 -10.10 3.50e+00 8.16e-02 8.33e+00 ... (remaining 13257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5494 17.79 - 35.57: 386 35.57 - 53.35: 60 53.35 - 71.14: 7 71.14 - 88.92: 8 Dihedral angle restraints: 5955 sinusoidal: 2370 harmonic: 3585 Sorted by residual: dihedral pdb=" CA GLN D 16 " pdb=" C GLN D 16 " pdb=" N GLU D 17 " pdb=" CA GLU D 17 " ideal model delta harmonic sigma weight residual 180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CB GLU D 171 " pdb=" CG GLU D 171 " pdb=" CD GLU D 171 " pdb=" OE1 GLU D 171 " ideal model delta sinusoidal sigma weight residual 0.00 -88.92 88.92 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA SER D 19 " pdb=" C SER D 19 " pdb=" N VAL D 20 " pdb=" CA VAL D 20 " ideal model delta harmonic sigma weight residual 180.00 164.02 15.98 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 5952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 986 0.036 - 0.072: 393 0.072 - 0.109: 123 0.109 - 0.145: 45 0.145 - 0.181: 6 Chirality restraints: 1553 Sorted by residual: chirality pdb=" CA THR D 62 " pdb=" N THR D 62 " pdb=" C THR D 62 " pdb=" CB THR D 62 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CA THR E 346 " pdb=" N THR E 346 " pdb=" C THR E 346 " pdb=" CB THR E 346 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA THR C 126 " pdb=" N THR C 126 " pdb=" C THR C 126 " pdb=" CB THR C 126 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 1550 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 346 " 0.038 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO E 347 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 347 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 347 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 126 " -0.035 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO C 127 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 127 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 127 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 61 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.55e+00 pdb=" C PRO D 61 " 0.033 2.00e-02 2.50e+03 pdb=" O PRO D 61 " -0.012 2.00e-02 2.50e+03 pdb=" N THR D 62 " -0.011 2.00e-02 2.50e+03 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3083 2.84 - 3.35: 7611 3.35 - 3.87: 14845 3.87 - 4.38: 16738 4.38 - 4.90: 28932 Nonbonded interactions: 71209 Sorted by model distance: nonbonded pdb=" O CYS F 12 " pdb=" OG SER F 63 " model vdw 2.324 2.440 nonbonded pdb=" O ASP C 123 " pdb=" OG1 THR C 126 " model vdw 2.340 2.440 nonbonded pdb=" O CYS D 12 " pdb=" OG SER D 63 " model vdw 2.368 2.440 nonbonded pdb=" O ALA F 120 " pdb=" OG SER F 124 " model vdw 2.376 2.440 nonbonded pdb=" O TYR E 382 " pdb=" OG1 THR E 386 " model vdw 2.382 2.440 ... (remaining 71204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 3 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 or (resid 16 and (name N or name CA or name \ C or name O or name CB )) or resid 17 through 18 or (resid 19 through 21 and (n \ ame N or name CA or name C or name O or name CB )) or resid 22 or (resid 23 and \ (name N or name CA or name C or name O or name CB )) or resid 24 through 30 or ( \ resid 31 and (name N or name CA or name C or name O or name CB )) or resid 32 th \ rough 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) o \ r resid 37 through 54 or (resid 55 and (name N or name CA or name C or name O or \ name CB )) or resid 56 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 170 or (resid 171 and (name N or na \ me CA or name C or name O or name CB )) or resid 172 through 176 or (resid 177 t \ hrough 181 and (name N or name CA or name C or name O or name CB )) or resid 182 \ through 193 or (resid 194 and (name N or name CA or name C or name O or name CB \ )) or resid 195 through 227)) selection = chain 'F' } 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 3.550 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.460 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.003 0.123 9804 Z= 0.210 Angle : 0.724 10.104 13262 Z= 0.357 Chirality : 0.046 0.181 1553 Planarity : 0.005 0.057 1698 Dihedral : 12.333 88.925 3647 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.20 % Allowed : 6.95 % Favored : 92.86 % 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: -5.69 (0.16), residues: 1249 helix: -5.09 (0.05), residues: 447 sheet: -1.64 (0.42), residues: 132 loop : -3.33 (0.17), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 138 HIS 0.003 0.000 HIS D 137 PHE 0.010 0.001 PHE F 199 TYR 0.007 0.001 TYR C 199 ARG 0.006 0.000 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 360 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 TYR cc_start: 0.8222 (m-10) cc_final: 0.8012 (m-80) REVERT: C 157 ASN cc_start: 0.8380 (t0) cc_final: 0.8044 (t0) REVERT: C 175 MET cc_start: 0.4499 (ppp) cc_final: 0.4133 (ppp) REVERT: C 195 GLU cc_start: 0.8358 (pp20) cc_final: 0.7944 (pp20) REVERT: C 292 GLU cc_start: 0.7886 (pp20) cc_final: 0.7471 (pp20) REVERT: C 293 LYS cc_start: 0.7197 (mttm) cc_final: 0.6946 (mttm) REVERT: C 312 MET cc_start: 0.7471 (ttt) cc_final: 0.7073 (ttp) REVERT: E 11 LEU cc_start: 0.6280 (mp) cc_final: 0.5698 (tt) REVERT: F 142 ARG cc_start: 0.7755 (tpp80) cc_final: 0.7515 (tpp80) REVERT: D 30 PHE cc_start: 0.7834 (t80) cc_final: 0.7491 (t80) REVERT: D 94 GLN cc_start: 0.7184 (pt0) cc_final: 0.6909 (pt0) REVERT: D 137 HIS cc_start: 0.8051 (p90) cc_final: 0.7721 (p-80) outliers start: 2 outliers final: 0 residues processed: 361 average time/residue: 0.2482 time to fit residues: 118.2167 Evaluate side-chains 239 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 0.0770 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN C 131 ASN C 204 ASN C 301 GLN C 317 GLN C 339 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN E 174 ASN E 213 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN D 10 ASN D 137 HIS D 141 HIS D 152 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9804 Z= 0.359 Angle : 0.695 8.504 13262 Z= 0.352 Chirality : 0.045 0.155 1553 Planarity : 0.005 0.050 1698 Dihedral : 6.101 65.281 1394 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.72 % Allowed : 18.20 % Favored : 78.08 % 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: -4.13 (0.19), residues: 1249 helix: -3.42 (0.15), residues: 430 sheet: -1.62 (0.38), residues: 189 loop : -2.55 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 246 HIS 0.006 0.001 HIS D 141 PHE 0.020 0.002 PHE E 132 TYR 0.013 0.002 TYR E 322 ARG 0.006 0.001 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 246 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 GLN cc_start: 0.8907 (pp30) cc_final: 0.8437 (pp30) REVERT: C 175 MET cc_start: 0.4447 (ppp) cc_final: 0.4197 (ppp) REVERT: E 127 SER cc_start: 0.8916 (m) cc_final: 0.8634 (p) REVERT: E 325 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8446 (mm) REVERT: F 131 LYS cc_start: 0.9053 (mtmm) cc_final: 0.8697 (mtmm) REVERT: D 30 PHE cc_start: 0.8196 (t80) cc_final: 0.7977 (t80) REVERT: D 137 HIS cc_start: 0.8292 (p-80) cc_final: 0.7809 (p-80) REVERT: D 142 ARG cc_start: 0.7911 (tpp80) cc_final: 0.7464 (tpp80) REVERT: D 206 LEU cc_start: 0.8583 (tp) cc_final: 0.8377 (tt) REVERT: D 212 MET cc_start: 0.8183 (mmt) cc_final: 0.7713 (tpp) outliers start: 38 outliers final: 23 residues processed: 274 average time/residue: 0.2275 time to fit residues: 84.0442 Evaluate side-chains 233 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 209 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 0.0770 chunk 93 optimal weight: 5.9990 chunk 76 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 0.0370 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 HIS D 97 HIS D 107 ASN ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9804 Z= 0.142 Angle : 0.537 7.147 13262 Z= 0.259 Chirality : 0.041 0.133 1553 Planarity : 0.003 0.039 1698 Dihedral : 5.326 55.206 1394 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.23 % Allowed : 19.57 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.20), residues: 1249 helix: -2.11 (0.21), residues: 447 sheet: -1.52 (0.38), residues: 184 loop : -2.37 (0.21), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 246 HIS 0.010 0.001 HIS D 141 PHE 0.016 0.001 PHE D 68 TYR 0.014 0.001 TYR C 142 ARG 0.004 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 229 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 86 LYS cc_start: 0.8308 (mmtm) cc_final: 0.8073 (mtmm) REVERT: C 153 GLN cc_start: 0.8799 (pp30) cc_final: 0.8385 (pp30) REVERT: C 239 LYS cc_start: 0.8221 (tppt) cc_final: 0.7932 (tptp) REVERT: E 127 SER cc_start: 0.8912 (m) cc_final: 0.8616 (p) REVERT: E 134 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8086 (mp10) REVERT: E 161 LYS cc_start: 0.8257 (mmmm) cc_final: 0.7924 (ptpp) REVERT: E 203 PHE cc_start: 0.7574 (t80) cc_final: 0.7354 (t80) REVERT: E 325 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8435 (mt) REVERT: F 131 LYS cc_start: 0.9042 (mtmm) cc_final: 0.8758 (mtmm) REVERT: D 30 PHE cc_start: 0.8228 (t80) cc_final: 0.7940 (t80) REVERT: D 36 GLU cc_start: 0.6858 (pt0) cc_final: 0.6599 (mp0) REVERT: D 38 MET cc_start: 0.6275 (mtt) cc_final: 0.5800 (mtt) REVERT: D 137 HIS cc_start: 0.8198 (p-80) cc_final: 0.7884 (p-80) REVERT: D 142 ARG cc_start: 0.7958 (tpp80) cc_final: 0.7730 (tpp80) REVERT: D 212 MET cc_start: 0.8214 (mmt) cc_final: 0.7915 (tpp) outliers start: 33 outliers final: 17 residues processed: 251 average time/residue: 0.2247 time to fit residues: 76.9309 Evaluate side-chains 229 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 210 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9804 Z= 0.395 Angle : 0.699 8.977 13262 Z= 0.349 Chirality : 0.046 0.162 1553 Planarity : 0.004 0.037 1698 Dihedral : 6.622 62.323 1394 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 5.77 % Allowed : 19.77 % Favored : 74.46 % 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: -2.80 (0.22), residues: 1249 helix: -1.75 (0.22), residues: 493 sheet: -1.34 (0.44), residues: 136 loop : -2.02 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 246 HIS 0.010 0.002 HIS D 141 PHE 0.036 0.002 PHE F 95 TYR 0.012 0.002 TYR E 322 ARG 0.013 0.001 ARG E 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 220 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 GLN cc_start: 0.8998 (pp30) cc_final: 0.8646 (tm-30) REVERT: E 127 SER cc_start: 0.8905 (m) cc_final: 0.8701 (p) REVERT: E 134 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: F 38 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6481 (tmm) REVERT: F 131 LYS cc_start: 0.9028 (mtmm) cc_final: 0.8730 (mtmm) REVERT: F 199 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.6344 (p90) REVERT: F 212 MET cc_start: 0.8207 (mmm) cc_final: 0.7514 (mmp) REVERT: D 30 PHE cc_start: 0.8279 (t80) cc_final: 0.7943 (t80) REVERT: D 137 HIS cc_start: 0.8267 (p-80) cc_final: 0.7875 (p-80) REVERT: D 142 ARG cc_start: 0.8384 (tpp80) cc_final: 0.7982 (tpp80) REVERT: D 171 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7812 (tm-30) REVERT: D 212 MET cc_start: 0.8390 (mmt) cc_final: 0.8037 (tpp) outliers start: 59 outliers final: 41 residues processed: 258 average time/residue: 0.2242 time to fit residues: 79.7710 Evaluate side-chains 239 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 195 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 199 PHE Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 102 optimal weight: 0.0980 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9804 Z= 0.162 Angle : 0.562 10.235 13262 Z= 0.271 Chirality : 0.042 0.148 1553 Planarity : 0.003 0.029 1698 Dihedral : 5.650 54.562 1394 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.62 % Allowed : 22.70 % Favored : 73.68 % 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: -2.21 (0.22), residues: 1249 helix: -1.08 (0.23), residues: 475 sheet: -1.35 (0.40), residues: 160 loop : -1.76 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 246 HIS 0.008 0.001 HIS D 141 PHE 0.020 0.001 PHE E 13 TYR 0.011 0.001 TYR E 262 ARG 0.006 0.000 ARG E 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 204 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 153 GLN cc_start: 0.8992 (pp30) cc_final: 0.8673 (tm-30) REVERT: C 239 LYS cc_start: 0.8261 (tppt) cc_final: 0.8002 (tptp) REVERT: E 127 SER cc_start: 0.8852 (m) cc_final: 0.8616 (p) REVERT: E 325 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8306 (mm) REVERT: F 212 MET cc_start: 0.8067 (mmm) cc_final: 0.7330 (mmp) REVERT: D 30 PHE cc_start: 0.8184 (t80) cc_final: 0.7875 (t80) REVERT: D 36 GLU cc_start: 0.7528 (pt0) cc_final: 0.7136 (mp0) REVERT: D 38 MET cc_start: 0.6763 (mtt) cc_final: 0.6223 (mtt) REVERT: D 137 HIS cc_start: 0.8146 (p-80) cc_final: 0.7834 (p-80) REVERT: D 142 ARG cc_start: 0.8403 (tpp80) cc_final: 0.8181 (tpp80) REVERT: D 171 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7884 (tm-30) REVERT: D 212 MET cc_start: 0.8401 (mmt) cc_final: 0.8043 (tpp) outliers start: 37 outliers final: 24 residues processed: 230 average time/residue: 0.2105 time to fit residues: 67.7796 Evaluate side-chains 204 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 179 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 99 optimal weight: 0.0970 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 0.0570 overall best weight: 1.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9804 Z= 0.218 Angle : 0.605 11.570 13262 Z= 0.287 Chirality : 0.044 0.205 1553 Planarity : 0.003 0.032 1698 Dihedral : 5.839 56.089 1394 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.89 % Allowed : 22.60 % Favored : 72.50 % 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: -1.89 (0.23), residues: 1249 helix: -0.65 (0.24), residues: 473 sheet: -1.23 (0.42), residues: 156 loop : -1.71 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 138 HIS 0.013 0.001 HIS F 96 PHE 0.018 0.001 PHE E 13 TYR 0.012 0.001 TYR E 262 ARG 0.009 0.000 ARG F 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 194 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 153 GLN cc_start: 0.9036 (pp30) cc_final: 0.8667 (tm-30) REVERT: E 127 SER cc_start: 0.8789 (m) cc_final: 0.8453 (p) REVERT: E 203 PHE cc_start: 0.7931 (t80) cc_final: 0.7652 (t80) REVERT: E 325 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8339 (mm) REVERT: F 38 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6417 (tmm) REVERT: F 212 MET cc_start: 0.8004 (mmm) cc_final: 0.7372 (mmp) REVERT: F 219 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7462 (mmm-85) REVERT: D 30 PHE cc_start: 0.8120 (t80) cc_final: 0.7750 (t80) REVERT: D 137 HIS cc_start: 0.8262 (p-80) cc_final: 0.8047 (p-80) REVERT: D 142 ARG cc_start: 0.8364 (tpp80) cc_final: 0.8084 (tpp80) REVERT: D 170 ASP cc_start: 0.8016 (t0) cc_final: 0.7792 (t0) REVERT: D 212 MET cc_start: 0.8323 (mmt) cc_final: 0.7978 (tpp) outliers start: 50 outliers final: 35 residues processed: 226 average time/residue: 0.2126 time to fit residues: 66.7476 Evaluate side-chains 217 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.2980 chunk 13 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 87 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.6438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9804 Z= 0.152 Angle : 0.582 10.306 13262 Z= 0.275 Chirality : 0.042 0.211 1553 Planarity : 0.003 0.026 1698 Dihedral : 5.700 58.262 1394 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.33 % Allowed : 24.07 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.23), residues: 1249 helix: -0.17 (0.26), residues: 458 sheet: -1.33 (0.40), residues: 168 loop : -1.56 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 246 HIS 0.008 0.001 HIS F 96 PHE 0.047 0.002 PHE F 95 TYR 0.009 0.001 TYR C 142 ARG 0.004 0.000 ARG F 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 198 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 39 MET cc_start: 0.8510 (ttp) cc_final: 0.8193 (ttp) REVERT: C 153 GLN cc_start: 0.9014 (pp30) cc_final: 0.8692 (tm-30) REVERT: E 127 SER cc_start: 0.8774 (m) cc_final: 0.8481 (p) REVERT: E 203 PHE cc_start: 0.7657 (t80) cc_final: 0.7328 (t80) REVERT: E 325 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8233 (mm) REVERT: F 38 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6426 (tmm) REVERT: F 48 LYS cc_start: 0.6988 (ptmm) cc_final: 0.6486 (ptmm) REVERT: F 73 MET cc_start: 0.7764 (ptp) cc_final: 0.7536 (mtm) REVERT: F 185 PHE cc_start: 0.8267 (m-80) cc_final: 0.7760 (m-80) REVERT: F 212 MET cc_start: 0.8003 (mmm) cc_final: 0.7317 (mmp) REVERT: D 38 MET cc_start: 0.6370 (mtt) cc_final: 0.6136 (mtt) REVERT: D 137 HIS cc_start: 0.8249 (p-80) cc_final: 0.8017 (p-80) REVERT: D 142 ARG cc_start: 0.8330 (tpp80) cc_final: 0.8049 (tpp80) REVERT: D 212 MET cc_start: 0.8275 (mmt) cc_final: 0.8038 (tpp) outliers start: 34 outliers final: 28 residues processed: 219 average time/residue: 0.2258 time to fit residues: 68.8922 Evaluate side-chains 212 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 182 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 0.0270 chunk 108 optimal weight: 9.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS F 123 ASN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9804 Z= 0.150 Angle : 0.585 10.345 13262 Z= 0.276 Chirality : 0.042 0.204 1553 Planarity : 0.003 0.028 1698 Dihedral : 5.467 56.462 1394 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.23 % Allowed : 24.85 % Favored : 71.92 % 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: -1.30 (0.24), residues: 1249 helix: 0.12 (0.26), residues: 460 sheet: -1.27 (0.41), residues: 158 loop : -1.49 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 246 HIS 0.007 0.001 HIS D 141 PHE 0.014 0.001 PHE E 13 TYR 0.009 0.001 TYR C 142 ARG 0.007 0.000 ARG F 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 199 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 153 GLN cc_start: 0.8994 (pp30) cc_final: 0.8686 (tm-30) REVERT: E 127 SER cc_start: 0.8837 (m) cc_final: 0.8491 (p) REVERT: E 203 PHE cc_start: 0.7493 (t80) cc_final: 0.7282 (t80) REVERT: E 276 MET cc_start: 0.8629 (mmp) cc_final: 0.8337 (mmp) REVERT: E 325 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8149 (mm) REVERT: F 38 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6356 (tmm) REVERT: F 185 PHE cc_start: 0.8261 (m-80) cc_final: 0.7756 (m-80) REVERT: F 212 MET cc_start: 0.8005 (mmm) cc_final: 0.7333 (mmp) REVERT: D 137 HIS cc_start: 0.8184 (p-80) cc_final: 0.7819 (p-80) REVERT: D 212 MET cc_start: 0.8288 (mmt) cc_final: 0.7655 (mmp) outliers start: 33 outliers final: 27 residues processed: 222 average time/residue: 0.2104 time to fit residues: 65.0401 Evaluate side-chains 221 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 ASN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9804 Z= 0.190 Angle : 0.631 10.874 13262 Z= 0.301 Chirality : 0.043 0.205 1553 Planarity : 0.003 0.028 1698 Dihedral : 5.698 59.231 1394 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.52 % Allowed : 24.36 % Favored : 72.11 % 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: -1.30 (0.24), residues: 1249 helix: 0.15 (0.26), residues: 467 sheet: -1.28 (0.41), residues: 158 loop : -1.52 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 246 HIS 0.010 0.001 HIS F 96 PHE 0.015 0.001 PHE E 13 TYR 0.017 0.001 TYR E 262 ARG 0.007 0.000 ARG F 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 1.086 Fit side-chains REVERT: C 153 GLN cc_start: 0.8999 (pp30) cc_final: 0.8684 (tm-30) REVERT: C 195 GLU cc_start: 0.8452 (pp20) cc_final: 0.7967 (pp20) REVERT: C 291 MET cc_start: 0.8155 (mmp) cc_final: 0.7910 (mmt) REVERT: E 127 SER cc_start: 0.8850 (m) cc_final: 0.8548 (p) REVERT: E 203 PHE cc_start: 0.7543 (t80) cc_final: 0.7295 (t80) REVERT: E 276 MET cc_start: 0.8680 (mmp) cc_final: 0.8327 (mmp) REVERT: E 325 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8225 (mm) REVERT: F 38 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6359 (tmm) REVERT: F 73 MET cc_start: 0.7956 (ptp) cc_final: 0.7500 (mtp) REVERT: F 185 PHE cc_start: 0.8286 (m-80) cc_final: 0.7774 (m-80) REVERT: F 212 MET cc_start: 0.8078 (mmm) cc_final: 0.7467 (mmp) REVERT: D 212 MET cc_start: 0.8300 (mmt) cc_final: 0.7669 (mmp) outliers start: 36 outliers final: 31 residues processed: 213 average time/residue: 0.2082 time to fit residues: 62.2313 Evaluate side-chains 211 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 178 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.0170 chunk 81 optimal weight: 0.7980 chunk 123 optimal weight: 0.0870 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 10 optimal weight: 0.0020 chunk 75 optimal weight: 0.0980 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 ASN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.6715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9804 Z= 0.147 Angle : 0.621 11.067 13262 Z= 0.294 Chirality : 0.042 0.161 1553 Planarity : 0.003 0.030 1698 Dihedral : 5.294 53.196 1394 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.74 % Allowed : 25.34 % Favored : 71.92 % 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: -1.18 (0.24), residues: 1249 helix: 0.38 (0.26), residues: 462 sheet: -1.33 (0.41), residues: 160 loop : -1.53 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 246 HIS 0.012 0.001 HIS F 96 PHE 0.059 0.001 PHE F 95 TYR 0.010 0.001 TYR C 142 ARG 0.004 0.000 ARG E 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 1.033 Fit side-chains REVERT: C 141 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8075 (ptpp) REVERT: C 153 GLN cc_start: 0.9002 (pp30) cc_final: 0.8717 (tm-30) REVERT: C 195 GLU cc_start: 0.8434 (pp20) cc_final: 0.7937 (pp20) REVERT: C 291 MET cc_start: 0.8105 (mmp) cc_final: 0.7637 (mmt) REVERT: E 127 SER cc_start: 0.8847 (m) cc_final: 0.8522 (p) REVERT: E 276 MET cc_start: 0.8639 (mmp) cc_final: 0.8277 (mmp) REVERT: E 325 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8096 (mm) REVERT: F 38 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6356 (tmm) REVERT: F 73 MET cc_start: 0.7923 (ptp) cc_final: 0.7465 (mtp) REVERT: F 185 PHE cc_start: 0.8194 (m-80) cc_final: 0.7771 (m-80) REVERT: F 212 MET cc_start: 0.8069 (mmm) cc_final: 0.7476 (mmp) REVERT: D 137 HIS cc_start: 0.8212 (p-80) cc_final: 0.7880 (p-80) REVERT: D 212 MET cc_start: 0.8262 (mmt) cc_final: 0.7578 (mmp) outliers start: 28 outliers final: 24 residues processed: 207 average time/residue: 0.1887 time to fit residues: 56.1090 Evaluate side-chains 204 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 0.0020 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 ASN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.139314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.095956 restraints weight = 16477.528| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.10 r_work: 0.3162 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.6785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9804 Z= 0.166 Angle : 0.627 13.127 13262 Z= 0.291 Chirality : 0.042 0.177 1553 Planarity : 0.003 0.028 1698 Dihedral : 5.459 57.777 1394 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.54 % Allowed : 25.73 % Favored : 71.72 % 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: -1.13 (0.24), residues: 1249 helix: 0.33 (0.25), residues: 484 sheet: -1.04 (0.40), residues: 166 loop : -1.56 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 246 HIS 0.005 0.001 HIS F 96 PHE 0.016 0.001 PHE E 13 TYR 0.012 0.001 TYR E 262 ARG 0.004 0.000 ARG E 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2460.44 seconds wall clock time: 44 minutes 57.59 seconds (2697.59 seconds total)