Starting phenix.real_space_refine (version: dev) on Wed Dec 14 02:39:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m2y_23637/12_2022/7m2y_23637_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m2y_23637/12_2022/7m2y_23637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m2y_23637/12_2022/7m2y_23637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m2y_23637/12_2022/7m2y_23637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m2y_23637/12_2022/7m2y_23637_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m2y_23637/12_2022/7m2y_23637_updated.pdb" } resolution = 4.03 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= 0.005 sd= 0.822 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 205": "OD1" <-> "OD2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 324": "OD1" <-> "OD2" Residue "C TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 128": "OD1" <-> "OD2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 18560 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3447 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 1 Chain: "B" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3491 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 20, 'TRANS': 426} Chain breaks: 1 Chain: "C" Number of atoms: 5435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5435 Classifications: {'peptide': 656} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 636} Chain breaks: 2 Chain: "D" Number of atoms: 5868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5868 Classifications: {'peptide': 703} Link IDs: {'PTRANS': 25, 'TRANS': 677} Chain breaks: 5 Chain: "U" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 263 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.66, per 1000 atoms: 0.57 Number of scatterers: 18560 At special positions: 0 Unit cell: (136.157, 144.667, 168.778, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 4 15.00 O 3542 8.00 N 3115 7.00 C 11819 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: 8.13 Conformation dependent library (CDL) restraints added in 3.2 seconds 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4370 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 12 sheets defined 56.8% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 11 through 28 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.675A pdb=" N SER A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 178 through 197 removed outlier: 5.213A pdb=" N SER A 184 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 187 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP A 197 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 240 through 243 No H-bonds generated for 'chain 'A' and resid 240 through 243' Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.212A pdb=" N SER A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N THR A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.651A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 328 through 339 removed outlier: 4.266A pdb=" N THR A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LYS A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 400 removed outlier: 3.855A pdb=" N THR A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP A 395 " --> pdb=" O CYS A 391 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.695A pdb=" N GLN A 414 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 441 removed outlier: 3.818A pdb=" N GLU A 441 " --> pdb=" O TYR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 451 removed outlier: 4.098A pdb=" N ASP A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 28 removed outlier: 3.606A pdb=" N HIS B 16 " --> pdb=" O CYS B 13 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL B 17 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP B 22 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 98 through 101 No H-bonds generated for 'chain 'B' and resid 98 through 101' Processing helix chain 'B' and resid 104 through 114 removed outlier: 3.971A pdb=" N THR B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.594A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 Processing helix chain 'B' and resid 186 through 196 removed outlier: 4.438A pdb=" N GLU B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.577A pdb=" N ASN B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 228 through 243 removed outlier: 3.807A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 291 through 299 removed outlier: 4.112A pdb=" N MET B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.538A pdb=" N ALA B 334 " --> pdb=" O GLN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.623A pdb=" N VAL B 384 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 400 removed outlier: 4.195A pdb=" N LYS B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 441 removed outlier: 3.603A pdb=" N GLU B 441 " --> pdb=" O TYR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'C' and resid 167 through 174 Proline residue: C 173 - end of helix Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.852A pdb=" N SER C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 242 removed outlier: 4.494A pdb=" N ALA C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 273 Processing helix chain 'C' and resid 280 through 300 removed outlier: 4.734A pdb=" N GLU C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASN C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 309 through 321 removed outlier: 3.938A pdb=" N SER C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 352 removed outlier: 3.886A pdb=" N LEU C 341 " --> pdb=" O SER C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 396 through 415 Processing helix chain 'C' and resid 419 through 436 removed outlier: 3.646A pdb=" N ASN C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 466 removed outlier: 3.722A pdb=" N ASN C 465 " --> pdb=" O ASN C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 481 Processing helix chain 'C' and resid 486 through 495 Processing helix chain 'C' and resid 497 through 501 Processing helix chain 'C' and resid 509 through 522 Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'C' and resid 536 through 540 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 568 through 572 removed outlier: 4.274A pdb=" N LEU C 572 " --> pdb=" O SER C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 616 removed outlier: 3.650A pdb=" N ILE C 586 " --> pdb=" O TYR C 583 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 587 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR C 600 " --> pdb=" O ASN C 597 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 602 " --> pdb=" O PHE C 599 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS C 615 " --> pdb=" O ARG C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 628 through 654 removed outlier: 3.784A pdb=" N SER C 632 " --> pdb=" O ASN C 629 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 633 " --> pdb=" O LYS C 630 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 638 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 643 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 647 " --> pdb=" O PHE C 644 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN C 654 " --> pdb=" O TYR C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 669 removed outlier: 3.723A pdb=" N GLN C 669 " --> pdb=" O THR C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 736 Processing helix chain 'C' and resid 759 through 791 removed outlier: 3.603A pdb=" N VAL C 763 " --> pdb=" O PRO C 759 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN C 791 " --> pdb=" O PHE C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 831 Processing helix chain 'C' and resid 836 through 844 Processing helix chain 'D' and resid 44 through 46 No H-bonds generated for 'chain 'D' and resid 44 through 46' Processing helix chain 'D' and resid 52 through 68 removed outlier: 3.972A pdb=" N ILE D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 127 removed outlier: 4.441A pdb=" N TYR D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 148 Processing helix chain 'D' and resid 150 through 156 Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 170 through 179 Processing helix chain 'D' and resid 182 through 205 Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 244 through 258 removed outlier: 3.701A pdb=" N LYS D 249 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 289 removed outlier: 3.925A pdb=" N GLN D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASP D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 330 No H-bonds generated for 'chain 'D' and resid 328 through 330' Processing helix chain 'D' and resid 338 through 361 Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 389 through 411 Processing helix chain 'D' and resid 415 through 426 Processing helix chain 'D' and resid 432 through 451 removed outlier: 5.319A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN D 442 " --> pdb=" O PHE D 438 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY D 444 " --> pdb=" O THR D 440 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LYS D 448 " --> pdb=" O GLY D 444 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG D 451 " --> pdb=" O THR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 Processing helix chain 'D' and resid 477 through 480 No H-bonds generated for 'chain 'D' and resid 477 through 480' Processing helix chain 'D' and resid 491 through 497 removed outlier: 3.672A pdb=" N SER D 496 " --> pdb=" O PRO D 492 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N HIS D 497 " --> pdb=" O GLN D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 571 No H-bonds generated for 'chain 'D' and resid 568 through 571' Processing helix chain 'D' and resid 576 through 606 Processing helix chain 'D' and resid 610 through 613 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 626 through 650 Processing helix chain 'D' and resid 652 through 663 Processing helix chain 'D' and resid 669 through 684 Processing helix chain 'D' and resid 687 through 690 No H-bonds generated for 'chain 'D' and resid 687 through 690' Processing helix chain 'D' and resid 693 through 720 removed outlier: 5.038A pdb=" N GLN D 698 " --> pdb=" O PRO D 694 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG D 714 " --> pdb=" O ILE D 710 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA D 715 " --> pdb=" O LYS D 711 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N CYS D 718 " --> pdb=" O ARG D 714 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN D 719 " --> pdb=" O ALA D 715 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU D 720 " --> pdb=" O LYS D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 724 No H-bonds generated for 'chain 'D' and resid 722 through 724' Processing helix chain 'D' and resid 754 through 787 Processing helix chain 'D' and resid 802 through 811 Processing helix chain 'U' and resid 119 through 139 Processing sheet with id= A, first strand: chain 'A' and resid 66 through 68 removed outlier: 6.351A pdb=" N THR A 7 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN A 137 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 54 through 56 Processing sheet with id= C, first strand: chain 'A' and resid 269 through 272 removed outlier: 6.715A pdb=" N HIS A 353 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE A 322 " --> pdb=" O HIS A 353 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASN A 355 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N GLY A 324 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.464A pdb=" N TRP B 93 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N MET B 68 " --> pdb=" O TRP B 93 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ILE B 67 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR B 7 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N MET B 69 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLN B 9 " --> pdb=" O MET B 69 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE B 6 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE B 136 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU B 8 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU B 138 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA B 10 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N HIS B 140 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 166 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU B 138 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR B 168 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS B 140 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR B 170 " --> pdb=" O HIS B 140 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 54 through 56 Processing sheet with id= F, first strand: chain 'B' and resid 269 through 272 removed outlier: 6.490A pdb=" N HIS B 353 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE B 322 " --> pdb=" O HIS B 353 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN B 355 " --> pdb=" O ILE B 322 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 364 through 366 Processing sheet with id= H, first strand: chain 'C' and resid 541 through 545 Processing sheet with id= I, first strand: chain 'C' and resid 681 through 683 Processing sheet with id= J, first strand: chain 'D' and resid 75 through 77 Processing sheet with id= K, first strand: chain 'D' and resid 232 through 235 removed outlier: 6.456A pdb=" N TYR D 324 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASP D 235 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE D 326 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 482 through 486 886 hydrogen bonds defined for protein. 2370 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: 6.00 Time building geometry restraints manager: 8.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3170 1.30 - 1.44: 5553 1.44 - 1.57: 10016 1.57 - 1.71: 65 1.71 - 1.85: 138 Bond restraints: 18942 Sorted by residual: bond pdb=" CB HIS A 29 " pdb=" CG HIS A 29 " ideal model delta sigma weight residual 1.497 1.372 0.125 1.40e-02 5.10e+03 7.99e+01 bond pdb=" CB TYR D 190 " pdb=" CG TYR D 190 " ideal model delta sigma weight residual 1.512 1.338 0.174 2.20e-02 2.07e+03 6.28e+01 bond pdb=" CB TYR C 288 " pdb=" CG TYR C 288 " ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.56e+01 bond pdb=" CB PHE D 78 " pdb=" CG PHE D 78 " ideal model delta sigma weight residual 1.502 1.339 0.163 2.30e-02 1.89e+03 5.03e+01 bond pdb=" CB PHE C 267 " pdb=" CG PHE C 267 " ideal model delta sigma weight residual 1.502 1.352 0.150 2.30e-02 1.89e+03 4.24e+01 ... (remaining 18937 not shown) Histogram of bond angle deviations from ideal: 92.59 - 101.54: 42 101.54 - 110.49: 5697 110.49 - 119.44: 10790 119.44 - 128.39: 9016 128.39 - 137.35: 94 Bond angle restraints: 25639 Sorted by residual: angle pdb=" N THR B 201 " pdb=" CA THR B 201 " pdb=" C THR B 201 " ideal model delta sigma weight residual 108.79 127.10 -18.31 1.53e+00 4.27e-01 1.43e+02 angle pdb=" N ASP A 70 " pdb=" CA ASP A 70 " pdb=" C ASP A 70 " ideal model delta sigma weight residual 111.71 124.32 -12.61 1.15e+00 7.56e-01 1.20e+02 angle pdb=" N GLN D 51 " pdb=" CA GLN D 51 " pdb=" C GLN D 51 " ideal model delta sigma weight residual 113.88 101.33 12.55 1.23e+00 6.61e-01 1.04e+02 angle pdb=" N LEU C 792 " pdb=" CA LEU C 792 " pdb=" C LEU C 792 " ideal model delta sigma weight residual 113.41 101.32 12.09 1.22e+00 6.72e-01 9.82e+01 angle pdb=" N ILE D 804 " pdb=" CA ILE D 804 " pdb=" C ILE D 804 " ideal model delta sigma weight residual 111.00 101.30 9.70 1.09e+00 8.42e-01 7.93e+01 ... (remaining 25634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11015 17.98 - 35.96: 314 35.96 - 53.94: 78 53.94 - 71.92: 47 71.92 - 89.90: 8 Dihedral angle restraints: 11462 sinusoidal: 4722 harmonic: 6740 Sorted by residual: dihedral pdb=" C5' GDP B 501 " pdb=" O5' GDP B 501 " pdb=" PA GDP B 501 " pdb=" O3A GDP B 501 " ideal model delta sinusoidal sigma weight residual 179.98 -102.97 -77.05 1 2.00e+01 2.50e-03 1.86e+01 dihedral pdb=" C5' GDP A 501 " pdb=" O5' GDP A 501 " pdb=" PA GDP A 501 " pdb=" O3A GDP A 501 " ideal model delta sinusoidal sigma weight residual 179.98 -103.00 -77.02 1 2.00e+01 2.50e-03 1.86e+01 dihedral pdb=" C ASP B 97 " pdb=" N ASP B 97 " pdb=" CA ASP B 97 " pdb=" CB ASP B 97 " ideal model delta harmonic sigma weight residual -122.60 -112.18 -10.42 0 2.50e+00 1.60e-01 1.74e+01 ... (remaining 11459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1619 0.082 - 0.164: 895 0.164 - 0.246: 266 0.246 - 0.328: 67 0.328 - 0.410: 9 Chirality restraints: 2856 Sorted by residual: chirality pdb=" CA THR B 201 " pdb=" N THR B 201 " pdb=" C THR B 201 " pdb=" CB THR B 201 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CG LEU B 150 " pdb=" CB LEU B 150 " pdb=" CD1 LEU B 150 " pdb=" CD2 LEU B 150 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CB VAL B 419 " pdb=" CA VAL B 419 " pdb=" CG1 VAL B 419 " pdb=" CG2 VAL B 419 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 2853 not shown) Planarity restraints: 3297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 185 " 0.103 2.00e-02 2.50e+03 5.34e-02 5.70e+01 pdb=" CG TYR A 185 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 185 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 185 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR A 185 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 185 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 185 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 185 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 297 " -0.084 2.00e-02 2.50e+03 4.67e-02 4.37e+01 pdb=" CG TYR C 297 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR C 297 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR C 297 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR C 297 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR C 297 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR C 297 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 297 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 93 " 0.066 2.00e-02 2.50e+03 3.49e-02 3.05e+01 pdb=" CG TRP A 93 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP A 93 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 93 " -0.030 2.00e-02 2.50e+03 pdb=" NE1 TRP A 93 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP A 93 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 93 " -0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 93 " 0.033 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 93 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A 93 " 0.045 2.00e-02 2.50e+03 ... (remaining 3294 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 119 2.55 - 3.14: 16760 3.14 - 3.72: 31251 3.72 - 4.31: 46018 4.31 - 4.90: 69873 Nonbonded interactions: 164021 Sorted by model distance: nonbonded pdb=" OG1 THR A 146 " pdb=" O1B GDP A 501 " model vdw 1.961 2.440 nonbonded pdb=" CB ASN C 621 " pdb=" CD PRO C 622 " model vdw 2.086 3.840 nonbonded pdb=" OG SER A 141 " pdb=" C4' GDP A 501 " model vdw 2.242 3.470 nonbonded pdb=" CA GLY B 144 " pdb=" O5' GDP B 501 " model vdw 2.246 3.440 nonbonded pdb=" OH TYR C 288 " pdb=" OH TYR D 123 " model vdw 2.256 2.440 ... (remaining 164016 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 'A' selection = (chain 'B' and (resid 3 through 277 or resid 288 through 453 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 80 5.16 5 C 11819 2.51 5 N 3115 2.21 5 O 3542 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 5.480 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: 0.020 Extract box with map and model: 21.330 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.170 Process input model: 50.160 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 : 0.022 0.179 18942 Z= 1.421 Angle : 1.803 18.309 25639 Z= 1.236 Chirality : 0.107 0.410 2856 Planarity : 0.010 0.053 3297 Dihedral : 10.989 89.903 7092 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.18 % Favored : 97.56 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.03 (0.17), residues: 2250 helix: -0.11 (0.13), residues: 1248 sheet: -0.07 (0.46), residues: 137 loop : 0.56 (0.22), residues: 865 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 803 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 804 average time/residue: 0.3310 time to fit residues: 386.7538 Evaluate side-chains 455 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 455 time to evaluate : 2.282 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN B 81 ASN B 137 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN B 385 ASN B 418 ASN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN C 290 ASN ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN D 185 GLN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 464 ASN D 565 ASN ** D 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 HIS D 637 ASN D 649 GLN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 117 GLN U 122 GLN ** U 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 18942 Z= 0.292 Angle : 0.794 13.055 25639 Z= 0.426 Chirality : 0.047 0.308 2856 Planarity : 0.006 0.072 3297 Dihedral : 6.491 75.104 2505 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.11 % Favored : 96.67 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.06 (0.17), residues: 2250 helix: 0.30 (0.14), residues: 1225 sheet: -0.59 (0.38), residues: 153 loop : 0.03 (0.22), residues: 872 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 601 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 604 average time/residue: 0.3168 time to fit residues: 284.7981 Evaluate side-chains 429 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 2.235 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 222 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 137 GLN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 565 ASN D 589 GLN D 593 GLN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 117 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 18942 Z= 0.258 Angle : 0.717 9.408 25639 Z= 0.383 Chirality : 0.046 0.225 2856 Planarity : 0.005 0.053 3297 Dihedral : 6.299 64.593 2505 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.04 % Favored : 95.73 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.20 (0.17), residues: 2250 helix: 0.19 (0.14), residues: 1254 sheet: -0.95 (0.36), residues: 163 loop : -0.20 (0.22), residues: 833 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 551 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 552 average time/residue: 0.3050 time to fit residues: 255.7421 Evaluate side-chains 400 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 2.534 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 195 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN B 140 HIS ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN D 65 ASN ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 485 GLN ** D 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 18942 Z= 0.281 Angle : 0.699 10.750 25639 Z= 0.374 Chirality : 0.045 0.192 2856 Planarity : 0.005 0.053 3297 Dihedral : 6.168 62.655 2505 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.80 % Favored : 95.02 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.28 (0.17), residues: 2250 helix: 0.18 (0.14), residues: 1247 sheet: -0.91 (0.38), residues: 149 loop : -0.37 (0.22), residues: 854 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 507 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 509 average time/residue: 0.2989 time to fit residues: 232.9527 Evaluate side-chains 392 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 2.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS B 81 ASN B 137 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN B 418 ASN C 269 ASN C 380 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN D 442 ASN D 480 GLN D 559 HIS ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 18942 Z= 0.199 Angle : 0.644 9.485 25639 Z= 0.340 Chirality : 0.044 0.190 2856 Planarity : 0.005 0.053 3297 Dihedral : 5.966 64.228 2505 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.18 % Favored : 95.64 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.23 (0.17), residues: 2250 helix: 0.30 (0.14), residues: 1245 sheet: -1.16 (0.36), residues: 154 loop : -0.43 (0.22), residues: 851 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 516 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 516 average time/residue: 0.3006 time to fit residues: 236.9570 Evaluate side-chains 395 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 394 time to evaluate : 2.341 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2448 time to fit residues: 3.5547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 20.0000 chunk 196 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 53 optimal weight: 0.0570 chunk 218 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 330 GLN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN D 227 HIS D 442 ASN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 18942 Z= 0.199 Angle : 0.644 8.608 25639 Z= 0.342 Chirality : 0.044 0.198 2856 Planarity : 0.005 0.052 3297 Dihedral : 5.853 65.773 2505 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.67 % Favored : 95.16 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.23 (0.17), residues: 2250 helix: 0.30 (0.14), residues: 1258 sheet: -0.99 (0.40), residues: 139 loop : -0.49 (0.21), residues: 853 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 512 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 512 average time/residue: 0.3075 time to fit residues: 242.1506 Evaluate side-chains 405 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 2.202 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 217 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 100 optimal weight: 0.3980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN C 380 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN D 258 ASN D 442 ASN D 480 GLN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 127 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 18942 Z= 0.202 Angle : 0.643 8.950 25639 Z= 0.339 Chirality : 0.043 0.210 2856 Planarity : 0.004 0.051 3297 Dihedral : 5.744 65.212 2505 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.58 % Favored : 95.24 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.20 (0.17), residues: 2250 helix: 0.36 (0.14), residues: 1260 sheet: -1.23 (0.38), residues: 154 loop : -0.48 (0.22), residues: 836 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 504 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 504 average time/residue: 0.3043 time to fit residues: 234.2298 Evaluate side-chains 392 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 391 time to evaluate : 2.389 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2188 time to fit residues: 3.6011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 148 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 682 ASN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 127 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 18942 Z= 0.216 Angle : 0.654 8.471 25639 Z= 0.346 Chirality : 0.044 0.197 2856 Planarity : 0.004 0.052 3297 Dihedral : 5.707 64.247 2505 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.93 % Favored : 94.89 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 (0.17), residues: 2250 helix: 0.39 (0.14), residues: 1244 sheet: -0.95 (0.41), residues: 139 loop : -0.50 (0.21), residues: 867 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 491 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 491 average time/residue: 0.2981 time to fit residues: 225.8594 Evaluate side-chains 402 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 2.178 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 10.0000 chunk 190 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 chunk 88 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 ASN C 550 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN D 389 ASN ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 127 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 18942 Z= 0.290 Angle : 0.706 9.068 25639 Z= 0.376 Chirality : 0.045 0.201 2856 Planarity : 0.005 0.055 3297 Dihedral : 5.839 65.251 2505 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.47 % Favored : 94.36 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.30 (0.18), residues: 2250 helix: 0.26 (0.14), residues: 1251 sheet: -1.09 (0.40), residues: 151 loop : -0.54 (0.22), residues: 848 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 474 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 474 average time/residue: 0.2996 time to fit residues: 219.0477 Evaluate side-chains 378 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2174 time to fit residues: 3.5633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 190 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 GLN C 380 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS D 442 ASN D 682 ASN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 127 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.7099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 18942 Z= 0.205 Angle : 0.698 9.988 25639 Z= 0.366 Chirality : 0.046 0.187 2856 Planarity : 0.005 0.052 3297 Dihedral : 5.755 64.275 2505 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.80 % Favored : 94.98 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.38 (0.17), residues: 2250 helix: 0.23 (0.14), residues: 1262 sheet: -1.01 (0.40), residues: 146 loop : -0.65 (0.22), residues: 842 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 481 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 481 average time/residue: 0.2986 time to fit residues: 222.0507 Evaluate side-chains 395 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 394 time to evaluate : 2.411 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2147 time to fit residues: 3.6292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 26 optimal weight: 0.0070 chunk 49 optimal weight: 8.9990 chunk 179 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 0.0170 chunk 157 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 355 ASN ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 GLN C 269 ASN C 380 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 HIS ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 127 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.109606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.084172 restraints weight = 71562.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.087147 restraints weight = 36012.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.089042 restraints weight = 21633.300| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.7254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 18942 Z= 0.218 Angle : 0.682 10.745 25639 Z= 0.358 Chirality : 0.045 0.185 2856 Planarity : 0.005 0.051 3297 Dihedral : 5.738 65.049 2505 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.64 % Favored : 94.18 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.32 (0.18), residues: 2250 helix: 0.28 (0.14), residues: 1264 sheet: -0.91 (0.41), residues: 146 loop : -0.66 (0.22), residues: 840 =============================================================================== Job complete usr+sys time: 4748.25 seconds wall clock time: 88 minutes 4.79 seconds (5284.79 seconds total)