Starting phenix.real_space_refine on Wed Feb 14 10:30:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zda_14639/02_2024/7zda_14639_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zda_14639/02_2024/7zda_14639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zda_14639/02_2024/7zda_14639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zda_14639/02_2024/7zda_14639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zda_14639/02_2024/7zda_14639_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zda_14639/02_2024/7zda_14639_neut_updated.pdb" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 29 5.16 5 C 5781 2.51 5 N 1592 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 2": "NH1" <-> "NH2" Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ASP 126": "OD1" <-> "OD2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 316": "OD1" <-> "OD2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C ASP 335": "OD1" <-> "OD2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 374": "NH1" <-> "NH2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C ASP 461": "OD1" <-> "OD2" Residue "C ARG 481": "NH1" <-> "NH2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C GLU 519": "OE1" <-> "OE2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C GLU 523": "OE1" <-> "OE2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 552": "OE1" <-> "OE2" Residue "C TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D ASP 135": "OD1" <-> "OD2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ASP 207": "OD1" <-> "OD2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 282": "OD1" <-> "OD2" Residue "D PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ASP 306": "OD1" <-> "OD2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D GLU 354": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D GLU 452": "OE1" <-> "OE2" Residue "D PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 493": "NH1" <-> "NH2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "D ARG 566": "NH1" <-> "NH2" Residue "D TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 569": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9052 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4425 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 18, 'TRANS': 553} Chain: "D" Number of atoms: 4563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4563 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 27, 'TRANS': 559} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'PO3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.61, per 1000 atoms: 0.62 Number of scatterers: 9052 At special positions: 0 Unit cell: (119.691, 80.352, 111.321, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 P 6 15.00 Mg 2 11.99 O 1642 8.00 N 1592 7.00 C 5781 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=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.6 seconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 4 sheets defined 60.6% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'C' and resid 8 through 12 Processing helix chain 'C' and resid 15 through 49 removed outlier: 3.609A pdb=" N LEU C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 106 removed outlier: 3.598A pdb=" N ARG C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) Proline residue: C 105 - end of helix Processing helix chain 'C' and resid 116 through 131 removed outlier: 3.655A pdb=" N LEU C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 136 No H-bonds generated for 'chain 'C' and resid 133 through 136' Processing helix chain 'C' and resid 138 through 156 removed outlier: 3.531A pdb=" N VAL C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 184 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 186 through 215 removed outlier: 3.584A pdb=" N GLY C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLU C 212 " --> pdb=" O GLN C 208 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 264 removed outlier: 3.540A pdb=" N GLN C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 4.412A pdb=" N PHE C 285 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS C 286 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 287 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA C 290 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE C 291 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 292 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 318 removed outlier: 4.850A pdb=" N PHE C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS C 303 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 304 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C 305 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 308 " --> pdb=" O GLY C 305 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE C 314 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP C 316 " --> pdb=" O ARG C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 386 removed outlier: 3.586A pdb=" N GLN C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 409 through 415 removed outlier: 3.883A pdb=" N GLN C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 443 through 452 removed outlier: 3.685A pdb=" N ILE C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 477 through 490 Processing helix chain 'C' and resid 507 through 520 Processing helix chain 'C' and resid 556 through 561 Processing helix chain 'C' and resid 565 through 570 removed outlier: 3.647A pdb=" N LYS C 570 " --> pdb=" O TYR C 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 18 removed outlier: 3.536A pdb=" N GLU D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 53 removed outlier: 3.613A pdb=" N ARG D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 63 through 109 removed outlier: 3.634A pdb=" N ILE D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 116 removed outlier: 4.549A pdb=" N GLY D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.593A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 138 removed outlier: 4.334A pdb=" N MET D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N HIS D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 159 removed outlier: 4.003A pdb=" N VAL D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix Processing helix chain 'D' and resid 165 through 193 removed outlier: 3.549A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Proline residue: D 174 - end of helix Proline residue: D 177 - end of helix removed outlier: 3.565A pdb=" N GLY D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 202 Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 225 through 273 removed outlier: 3.694A pdb=" N ASP D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 329 removed outlier: 3.709A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 4.002A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 3.678A pdb=" N GLY D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N HIS D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ALA D 313 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS D 314 " --> pdb=" O PHE D 310 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 397 removed outlier: 3.570A pdb=" N LEU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 418 through 424 removed outlier: 4.219A pdb=" N LYS D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 452 through 461 Processing helix chain 'D' and resid 488 through 499 Processing helix chain 'D' and resid 518 through 529 Processing helix chain 'D' and resid 567 through 572 Processing helix chain 'D' and resid 576 through 582 Processing sheet with id= A, first strand: chain 'C' and resid 360 through 363 Processing sheet with id= B, first strand: chain 'C' and resid 550 through 554 removed outlier: 7.035A pdb=" N VAL C 544 " --> pdb=" O ILE C 551 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C 542 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN C 541 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL C 526 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE C 371 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N MET C 528 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 371 through 373 Processing sheet with id= D, first strand: chain 'D' and resid 537 through 540 removed outlier: 6.864A pdb=" N VAL D 552 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL D 382 " --> pdb=" O VAL D 552 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TRP D 554 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU D 563 " --> pdb=" O VAL D 555 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLN D 557 " --> pdb=" O ILE D 561 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE D 561 " --> pdb=" O GLN D 557 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1344 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: 2.75 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2075 1.33 - 1.45: 1851 1.45 - 1.57: 5242 1.57 - 1.69: 8 1.69 - 1.81: 55 Bond restraints: 9231 Sorted by residual: bond pdb=" C4 ATP D 602 " pdb=" C5 ATP D 602 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.56e+01 bond pdb=" C5 ATP D 602 " pdb=" C6 ATP D 602 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.53e+01 bond pdb=" O2 PO3 C 603 " pdb=" P PO3 C 603 " ideal model delta sigma weight residual 1.604 1.506 0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" O1 PO3 C 603 " pdb=" P PO3 C 603 " ideal model delta sigma weight residual 1.604 1.506 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" O3 PO3 C 603 " pdb=" P PO3 C 603 " ideal model delta sigma weight residual 1.601 1.506 0.095 2.00e-02 2.50e+03 2.26e+01 ... (remaining 9226 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.86: 265 106.86 - 114.21: 5390 114.21 - 121.55: 4877 121.55 - 128.90: 1942 128.90 - 136.25: 79 Bond angle restraints: 12553 Sorted by residual: angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 119.13 20.74 1.00e+00 1.00e+00 4.30e+02 angle pdb=" PA ATP D 602 " pdb=" O3A ATP D 602 " pdb=" PB ATP D 602 " ideal model delta sigma weight residual 136.83 121.55 15.28 1.00e+00 1.00e+00 2.34e+02 angle pdb=" C5 ATP D 602 " pdb=" C4 ATP D 602 " pdb=" N3 ATP D 602 " ideal model delta sigma weight residual 126.80 118.92 7.88 1.00e+00 1.00e+00 6.22e+01 angle pdb=" N3 ATP D 602 " pdb=" C4 ATP D 602 " pdb=" N9 ATP D 602 " ideal model delta sigma weight residual 127.04 134.87 -7.83 1.15e+00 7.59e-01 4.66e+01 angle pdb=" N1 ATP D 602 " pdb=" C2 ATP D 602 " pdb=" N3 ATP D 602 " ideal model delta sigma weight residual 128.69 123.59 5.10 1.00e+00 1.00e+00 2.60e+01 ... (remaining 12548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 5156 24.08 - 48.16: 327 48.16 - 72.24: 19 72.24 - 96.32: 14 96.32 - 120.40: 2 Dihedral angle restraints: 5518 sinusoidal: 2193 harmonic: 3325 Sorted by residual: dihedral pdb=" O1B ADP C 602 " pdb=" O3A ADP C 602 " pdb=" PB ADP C 602 " pdb=" PA ADP C 602 " ideal model delta sinusoidal sigma weight residual 300.00 179.60 120.40 1 2.00e+01 2.50e-03 3.61e+01 dihedral pdb=" C5' ADP C 602 " pdb=" O5' ADP C 602 " pdb=" PA ADP C 602 " pdb=" O2A ADP C 602 " ideal model delta sinusoidal sigma weight residual -60.00 -179.38 119.38 1 2.00e+01 2.50e-03 3.58e+01 dihedral pdb=" C ASP D 282 " pdb=" N ASP D 282 " pdb=" CA ASP D 282 " pdb=" CB ASP D 282 " ideal model delta harmonic sigma weight residual -122.60 -132.62 10.02 0 2.50e+00 1.60e-01 1.61e+01 ... (remaining 5515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1309 0.069 - 0.139: 135 0.139 - 0.208: 9 0.208 - 0.277: 3 0.277 - 0.347: 1 Chirality restraints: 1457 Sorted by residual: chirality pdb=" CA ASP D 282 " pdb=" N ASP D 282 " pdb=" C ASP D 282 " pdb=" CB ASP D 282 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA ARG C 13 " pdb=" N ARG C 13 " pdb=" C ARG C 13 " pdb=" CB ARG C 13 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA LEU D 509 " pdb=" N LEU D 509 " pdb=" C LEU D 509 " pdb=" CB LEU D 509 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1454 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O1 PO3 C 603 " -0.127 2.00e-02 2.50e+03 2.20e-01 4.82e+02 pdb=" O2 PO3 C 603 " -0.126 2.00e-02 2.50e+03 pdb=" O3 PO3 C 603 " -0.127 2.00e-02 2.50e+03 pdb=" P PO3 C 603 " 0.380 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 281 " -0.024 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C TYR D 281 " 0.086 2.00e-02 2.50e+03 pdb=" O TYR D 281 " -0.032 2.00e-02 2.50e+03 pdb=" N ASP D 282 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 348 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO C 349 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 349 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 349 " -0.035 5.00e-02 4.00e+02 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 54 2.53 - 3.12: 6756 3.12 - 3.72: 14252 3.72 - 4.31: 20839 4.31 - 4.90: 34396 Nonbonded interactions: 76297 Sorted by model distance: nonbonded pdb=" OG SER D 390 " pdb="MG MG D 601 " model vdw 1.941 2.170 nonbonded pdb=" OE1 GLN C 421 " pdb="MG MG C 601 " model vdw 2.127 2.170 nonbonded pdb="MG MG D 601 " pdb=" O1B ATP D 602 " model vdw 2.138 2.170 nonbonded pdb=" OG SER C 380 " pdb="MG MG C 601 " model vdw 2.185 2.170 nonbonded pdb="MG MG D 601 " pdb=" O1G ATP D 602 " model vdw 2.222 2.170 ... (remaining 76292 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.240 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 27.260 Find NCS groups from input model: 0.300 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.006 0.098 9231 Z= 0.393 Angle : 0.772 20.737 12553 Z= 0.508 Chirality : 0.046 0.347 1457 Planarity : 0.007 0.220 1599 Dihedral : 15.048 120.400 3374 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.11 % Allowed : 0.53 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.23), residues: 1155 helix: -1.58 (0.18), residues: 721 sheet: 0.83 (0.71), residues: 52 loop : -0.90 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 427 HIS 0.005 0.001 HIS C 14 PHE 0.015 0.002 PHE C 291 TYR 0.010 0.002 TYR C 7 ARG 0.011 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.008 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 179 average time/residue: 0.2895 time to fit residues: 66.2032 Evaluate side-chains 127 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 332 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN C 208 GLN C 302 GLN C 306 GLN C 424 HIS C 541 GLN C 553 GLN D 50 GLN D 430 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9231 Z= 0.210 Angle : 0.635 13.356 12553 Z= 0.311 Chirality : 0.041 0.186 1457 Planarity : 0.005 0.053 1599 Dihedral : 8.478 102.190 1309 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.50 % Allowed : 7.59 % Favored : 90.92 % 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: -0.72 (0.24), residues: 1155 helix: -0.13 (0.19), residues: 720 sheet: 1.16 (0.78), residues: 42 loop : -1.13 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 427 HIS 0.004 0.001 HIS D 89 PHE 0.014 0.001 PHE D 371 TYR 0.009 0.001 TYR D 272 ARG 0.004 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: D 154 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8299 (mp) outliers start: 14 outliers final: 6 residues processed: 147 average time/residue: 0.2514 time to fit residues: 49.2664 Evaluate side-chains 124 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 372 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 0.0370 chunk 103 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 194 ASN D 482 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9231 Z= 0.281 Angle : 0.628 13.526 12553 Z= 0.304 Chirality : 0.042 0.147 1457 Planarity : 0.004 0.048 1599 Dihedral : 8.019 94.651 1309 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.71 % Allowed : 10.79 % Favored : 87.50 % 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: -0.14 (0.24), residues: 1155 helix: 0.43 (0.20), residues: 722 sheet: 1.24 (0.81), residues: 42 loop : -1.09 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 427 HIS 0.004 0.001 HIS D 134 PHE 0.016 0.002 PHE D 278 TYR 0.013 0.001 TYR C 59 ARG 0.003 0.000 ARG C 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 262 MET cc_start: 0.8376 (mmt) cc_final: 0.7937 (mmp) outliers start: 16 outliers final: 10 residues processed: 131 average time/residue: 0.2556 time to fit residues: 44.7290 Evaluate side-chains 119 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 0.0050 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9231 Z= 0.213 Angle : 0.589 13.430 12553 Z= 0.281 Chirality : 0.040 0.143 1457 Planarity : 0.004 0.046 1599 Dihedral : 7.553 90.145 1309 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.82 % Allowed : 12.39 % Favored : 85.79 % 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: 0.26 (0.24), residues: 1155 helix: 0.76 (0.20), residues: 722 sheet: 1.46 (0.82), residues: 42 loop : -1.00 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 427 HIS 0.003 0.001 HIS D 134 PHE 0.018 0.001 PHE C 164 TYR 0.012 0.001 TYR D 88 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: C 262 MET cc_start: 0.8342 (mmp) cc_final: 0.7922 (mmp) REVERT: C 500 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6760 (mp0) outliers start: 17 outliers final: 12 residues processed: 132 average time/residue: 0.2626 time to fit residues: 45.9881 Evaluate side-chains 122 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 337 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9231 Z= 0.215 Angle : 0.586 13.432 12553 Z= 0.278 Chirality : 0.040 0.141 1457 Planarity : 0.004 0.045 1599 Dihedral : 7.241 87.302 1309 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.24 % Allowed : 13.03 % Favored : 84.72 % 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: 0.51 (0.25), residues: 1155 helix: 0.99 (0.20), residues: 729 sheet: 1.58 (0.83), residues: 42 loop : -1.01 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 427 HIS 0.003 0.001 HIS D 134 PHE 0.018 0.001 PHE C 164 TYR 0.013 0.001 TYR C 59 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 262 MET cc_start: 0.8349 (mmp) cc_final: 0.7976 (mmp) REVERT: C 500 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6850 (mp0) outliers start: 21 outliers final: 15 residues processed: 135 average time/residue: 0.2634 time to fit residues: 46.9828 Evaluate side-chains 128 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 337 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9231 Z= 0.278 Angle : 0.628 13.483 12553 Z= 0.295 Chirality : 0.042 0.176 1457 Planarity : 0.004 0.044 1599 Dihedral : 7.177 86.377 1309 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.21 % Allowed : 13.78 % Favored : 83.01 % 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: 0.51 (0.25), residues: 1155 helix: 1.01 (0.20), residues: 719 sheet: 1.66 (0.85), residues: 42 loop : -1.00 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 427 HIS 0.004 0.001 HIS D 134 PHE 0.019 0.002 PHE C 164 TYR 0.014 0.001 TYR C 567 ARG 0.005 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: C 262 MET cc_start: 0.8456 (mmp) cc_final: 0.8165 (mmp) REVERT: C 500 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6908 (mp0) outliers start: 30 outliers final: 19 residues processed: 136 average time/residue: 0.2533 time to fit residues: 46.0194 Evaluate side-chains 127 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 540 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9231 Z= 0.221 Angle : 0.607 13.410 12553 Z= 0.284 Chirality : 0.041 0.141 1457 Planarity : 0.004 0.044 1599 Dihedral : 7.057 84.185 1309 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.46 % Allowed : 14.53 % Favored : 83.01 % 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: 0.67 (0.25), residues: 1155 helix: 1.14 (0.20), residues: 719 sheet: 1.65 (0.86), residues: 42 loop : -0.95 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 427 HIS 0.003 0.001 HIS D 134 PHE 0.021 0.001 PHE C 164 TYR 0.020 0.001 TYR C 567 ARG 0.005 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: C 262 MET cc_start: 0.8448 (mmp) cc_final: 0.8102 (mmp) REVERT: C 500 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6893 (mp0) outliers start: 23 outliers final: 14 residues processed: 129 average time/residue: 0.2640 time to fit residues: 45.2288 Evaluate side-chains 120 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 540 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 87 optimal weight: 0.7980 chunk 100 optimal weight: 0.4980 chunk 106 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9231 Z= 0.189 Angle : 0.598 13.540 12553 Z= 0.279 Chirality : 0.040 0.140 1457 Planarity : 0.004 0.044 1599 Dihedral : 6.978 81.966 1309 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.92 % Allowed : 15.60 % Favored : 82.48 % 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: 0.81 (0.25), residues: 1155 helix: 1.27 (0.20), residues: 719 sheet: 1.68 (0.85), residues: 42 loop : -0.92 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 427 HIS 0.002 0.000 HIS D 134 PHE 0.012 0.001 PHE D 577 TYR 0.016 0.001 TYR C 567 ARG 0.010 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: C 500 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6799 (mp0) outliers start: 18 outliers final: 10 residues processed: 127 average time/residue: 0.2571 time to fit residues: 43.6370 Evaluate side-chains 116 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9231 Z= 0.287 Angle : 0.634 13.458 12553 Z= 0.299 Chirality : 0.042 0.180 1457 Planarity : 0.004 0.043 1599 Dihedral : 7.066 82.830 1309 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.03 % Allowed : 15.81 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1155 helix: 1.25 (0.20), residues: 711 sheet: 1.72 (0.84), residues: 42 loop : -0.96 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 427 HIS 0.004 0.001 HIS D 134 PHE 0.014 0.002 PHE C 164 TYR 0.013 0.001 TYR C 567 ARG 0.007 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: C 500 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: D 306 ASP cc_start: 0.7815 (m-30) cc_final: 0.7612 (m-30) outliers start: 19 outliers final: 15 residues processed: 123 average time/residue: 0.2527 time to fit residues: 41.5117 Evaluate side-chains 126 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9231 Z= 0.211 Angle : 0.618 14.251 12553 Z= 0.287 Chirality : 0.040 0.140 1457 Planarity : 0.004 0.044 1599 Dihedral : 7.021 81.029 1309 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.60 % Allowed : 16.45 % Favored : 81.94 % 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: 0.92 (0.25), residues: 1155 helix: 1.35 (0.20), residues: 710 sheet: 1.81 (0.84), residues: 42 loop : -0.82 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 427 HIS 0.002 0.001 HIS D 134 PHE 0.015 0.001 PHE C 164 TYR 0.014 0.001 TYR C 567 ARG 0.007 0.000 ARG C 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: C 500 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6797 (mp0) outliers start: 15 outliers final: 13 residues processed: 121 average time/residue: 0.2726 time to fit residues: 43.8512 Evaluate side-chains 120 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.145926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.110750 restraints weight = 12006.482| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.63 r_work: 0.3112 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9231 Z= 0.280 Angle : 0.635 13.988 12553 Z= 0.298 Chirality : 0.042 0.178 1457 Planarity : 0.004 0.043 1599 Dihedral : 7.081 80.418 1309 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.92 % Allowed : 16.45 % Favored : 81.62 % 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: 0.84 (0.25), residues: 1155 helix: 1.28 (0.20), residues: 711 sheet: 1.88 (0.85), residues: 42 loop : -0.86 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 427 HIS 0.003 0.001 HIS D 134 PHE 0.015 0.002 PHE C 164 TYR 0.013 0.001 TYR C 567 ARG 0.006 0.000 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2218.27 seconds wall clock time: 40 minutes 59.35 seconds (2459.35 seconds total)