Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 11:29:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arh_11882/07_2023/7arh_11882_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arh_11882/07_2023/7arh_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_11882/07_2023/7arh_11882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arh_11882/07_2023/7arh_11882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arh_11882/07_2023/7arh_11882_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arh_11882/07_2023/7arh_11882_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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-1.21rc1-5013/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 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: 5.24, per 1000 atoms: 0.54 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: 3.62 Conformation dependent library (CDL) restraints added in 1.7 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: 0.92 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: 2.17 Time building geometry restraints manager: 3.92 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: 5490 17.79 - 35.57: 386 35.57 - 53.35: 60 53.35 - 71.14: 5 71.14 - 88.92: 8 Dihedral angle restraints: 5949 sinusoidal: 2364 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 5946 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 3.810 Check model and map are aligned: 0.160 Set scattering table: 0.080 Process input model: 26.560 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.550 ------------------------------------------------------------------------------- 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 : 12.261 88.925 3641 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 % 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 *********************** 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 : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 361 average time/residue: 0.2528 time to fit residues: 120.2981 Evaluate side-chains 235 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5447 ------------------------------------------------------------------------------- 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: 7.9990 chunk 93 optimal weight: 0.1980 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: 1.4542 ------------------------------------------------------------------------------- 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 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 97 HIS D 141 HIS D 152 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9804 Z= 0.246 Angle : 0.634 9.557 13262 Z= 0.314 Chirality : 0.043 0.146 1553 Planarity : 0.004 0.049 1698 Dihedral : 4.976 57.012 1388 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 3.72 % 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: -4.22 (0.18), residues: 1249 helix: -3.52 (0.15), residues: 437 sheet: -1.59 (0.38), residues: 189 loop : -2.60 (0.20), residues: 623 *********************** 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 280 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 242 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 26 residues processed: 269 average time/residue: 0.2412 time to fit residues: 87.8766 Evaluate side-chains 221 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 195 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1047 time to fit residues: 6.3640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 0.0670 chunk 121 optimal weight: 0.0020 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.5730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 GLN C 317 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 9804 Z= 0.235 Angle : 0.621 10.346 13262 Z= 0.303 Chirality : 0.043 0.128 1553 Planarity : 0.004 0.040 1698 Dihedral : 5.272 50.359 1388 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 2.94 % 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: -3.06 (0.21), residues: 1249 helix: -1.97 (0.22), residues: 435 sheet: -1.45 (0.38), residues: 184 loop : -2.21 (0.21), residues: 630 *********************** 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 257 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 227 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 248 average time/residue: 0.2245 time to fit residues: 76.5661 Evaluate side-chains 214 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 201 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1214 time to fit residues: 4.1459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.1980 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 0.0030 chunk 32 optimal weight: 4.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 9804 Z= 0.154 Angle : 0.562 11.999 13262 Z= 0.267 Chirality : 0.042 0.169 1553 Planarity : 0.003 0.034 1698 Dihedral : 4.934 55.287 1388 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 1.96 % 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: -2.49 (0.22), residues: 1249 helix: -1.28 (0.23), residues: 455 sheet: -1.31 (0.40), residues: 174 loop : -2.01 (0.22), residues: 620 *********************** 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 236 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 216 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 226 average time/residue: 0.2179 time to fit residues: 68.6862 Evaluate side-chains 202 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 196 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0891 time to fit residues: 2.5481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 0.0570 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 0.0050 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.4112 ------------------------------------------------------------------------------- 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** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9804 Z= 0.137 Angle : 0.557 12.360 13262 Z= 0.261 Chirality : 0.041 0.153 1553 Planarity : 0.003 0.035 1698 Dihedral : 4.764 57.952 1388 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 1.66 % 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: -2.03 (0.23), residues: 1249 helix: -0.75 (0.25), residues: 460 sheet: -0.84 (0.41), residues: 162 loop : -1.94 (0.23), residues: 627 *********************** 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 228 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 211 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 221 average time/residue: 0.2232 time to fit residues: 68.4199 Evaluate side-chains 204 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 196 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0938 time to fit residues: 2.8315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 0.2980 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** E 233 ASN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN D 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 9804 Z= 0.235 Angle : 0.609 15.055 13262 Z= 0.291 Chirality : 0.043 0.156 1553 Planarity : 0.003 0.031 1698 Dihedral : 5.363 56.403 1388 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer Outliers : 2.25 % 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: -1.86 (0.23), residues: 1249 helix: -0.50 (0.25), residues: 470 sheet: -1.03 (0.47), residues: 134 loop : -1.84 (0.23), residues: 645 *********************** 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 228 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 218 average time/residue: 0.2226 time to fit residues: 67.3300 Evaluate side-chains 197 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 184 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0954 time to fit residues: 3.7759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 68 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 chunk 72 optimal weight: 0.1980 chunk 55 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** F 123 ASN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 9804 Z= 0.149 Angle : 0.561 10.134 13262 Z= 0.268 Chirality : 0.042 0.156 1553 Planarity : 0.003 0.028 1698 Dihedral : 4.867 56.353 1388 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.78 % 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: -1.51 (0.24), residues: 1249 helix: -0.12 (0.26), residues: 466 sheet: -0.99 (0.42), residues: 162 loop : -1.69 (0.23), residues: 621 *********************** 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 204 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 196 time to evaluate : 1.125 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 201 average time/residue: 0.2151 time to fit residues: 60.8149 Evaluate side-chains 192 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1066 time to fit residues: 2.2903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 59 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 9804 Z= 0.154 Angle : 0.565 13.007 13262 Z= 0.271 Chirality : 0.042 0.152 1553 Planarity : 0.003 0.027 1698 Dihedral : 4.855 59.517 1388 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 1.17 % 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: -1.32 (0.24), residues: 1249 helix: 0.16 (0.26), residues: 467 sheet: -0.95 (0.42), residues: 162 loop : -1.68 (0.23), residues: 620 *********************** 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 209 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 1.123 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 205 average time/residue: 0.2148 time to fit residues: 61.8494 Evaluate side-chains 191 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0916 time to fit residues: 2.5815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 111 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 105 optimal weight: 0.0770 chunk 110 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.6311 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= 0.147 Angle : 0.570 13.464 13262 Z= 0.269 Chirality : 0.042 0.155 1553 Planarity : 0.003 0.027 1698 Dihedral : 4.728 56.033 1388 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.59 % 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: 0.34 (0.26), residues: 466 sheet: -1.02 (0.41), residues: 164 loop : -1.60 (0.24), residues: 619 *********************** 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 198 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 192 time to evaluate : 1.094 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 194 average time/residue: 0.2137 time to fit residues: 59.2324 Evaluate side-chains 192 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1902 time to fit residues: 3.1264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 7.9990 chunk 71 optimal weight: 0.0470 chunk 55 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.0060 chunk 60 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.8896 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.6511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9804 Z= 0.178 Angle : 0.597 12.692 13262 Z= 0.286 Chirality : 0.042 0.149 1553 Planarity : 0.003 0.027 1698 Dihedral : 4.936 57.428 1388 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.29 % 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: -1.08 (0.24), residues: 1249 helix: 0.53 (0.26), residues: 458 sheet: -0.87 (0.45), residues: 142 loop : -1.64 (0.23), residues: 649 ********************** 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 189 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 1.170 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 187 average time/residue: 0.2092 time to fit residues: 55.5168 Evaluate side-chains 184 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 20.0000 chunk 30 optimal weight: 0.0370 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 GLN E 114 GLN ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.137083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092327 restraints weight = 16529.014| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.10 r_work: 0.3106 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.6876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 9804 Z= 0.266 Angle : 0.661 12.788 13262 Z= 0.316 Chirality : 0.045 0.262 1553 Planarity : 0.003 0.027 1698 Dihedral : 5.630 59.961 1388 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 0.78 % 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: -1.19 (0.24), residues: 1249 helix: 0.26 (0.25), residues: 476 sheet: -0.86 (0.44), residues: 139 loop : -1.62 (0.24), residues: 634 =============================================================================== Job complete usr+sys time: 2352.16 seconds wall clock time: 42 minutes 58.16 seconds (2578.16 seconds total)