Starting phenix.real_space_refine on Sat Mar 16 06:10:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpq_22419/03_2024/7jpq_22419_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpq_22419/03_2024/7jpq_22419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpq_22419/03_2024/7jpq_22419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpq_22419/03_2024/7jpq_22419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpq_22419/03_2024/7jpq_22419_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpq_22419/03_2024/7jpq_22419_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 65 5.16 5 C 8911 2.51 5 N 2339 2.21 5 O 2540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "B ASP 396": "OD1" <-> "OD2" Residue "B TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 562": "OD1" <-> "OD2" Residue "B GLU 571": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C GLU 377": "OE1" <-> "OE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C ASP 449": "OD1" <-> "OD2" Residue "C PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 589": "OE1" <-> "OE2" Residue "C GLU 638": "OE1" <-> "OE2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C GLU 674": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C GLU 686": "OE1" <-> "OE2" Residue "C PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 701": "OD1" <-> "OD2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "D TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D GLU 368": "OE1" <-> "OE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D ASP 407": "OD1" <-> "OD2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E ASP 117": "OD1" <-> "OD2" Residue "E TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 271": "NH1" <-> "NH2" Residue "E ASP 287": "OD1" <-> "OD2" Residue "E TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 399": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13863 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2436 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain breaks: 2 Chain: "C" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4788 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 24, 'TRANS': 562} Chain breaks: 9 Chain: "D" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3281 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 2 Chain: "E" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3294 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 19, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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} Chain: "E" 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: 7.56, per 1000 atoms: 0.55 Number of scatterers: 13863 At special positions: 0 Unit cell: (92.02, 113.42, 162.64, 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 65 16.00 P 6 15.00 Mg 2 11.99 O 2540 8.00 N 2339 7.00 C 8911 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: 5.01 Conformation dependent library (CDL) restraints added in 2.3 seconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3286 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 6 sheets defined 53.6% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 296 through 306 removed outlier: 4.162A pdb=" N HIS B 299 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 303 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 304 " --> pdb=" O TRP B 301 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 305 " --> pdb=" O MET B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 329 Processing helix chain 'B' and resid 348 through 358 Processing helix chain 'B' and resid 369 through 378 Processing helix chain 'B' and resid 403 through 413 Processing helix chain 'B' and resid 429 through 432 Processing helix chain 'B' and resid 435 through 441 Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 486 through 501 removed outlier: 3.816A pdb=" N LEU B 495 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 521 Processing helix chain 'B' and resid 529 through 542 removed outlier: 3.692A pdb=" N GLU B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 539 " --> pdb=" O GLN B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 569 Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 40 through 65 removed outlier: 3.555A pdb=" N TYR C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 87 removed outlier: 3.776A pdb=" N ASN C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.606A pdb=" N GLN C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 157 removed outlier: 3.529A pdb=" N LEU C 148 " --> pdb=" O MET C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 191 Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.812A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.587A pdb=" N SER C 269 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 270' Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 321 through 337 Processing helix chain 'C' and resid 340 through 344 removed outlier: 3.707A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 356 removed outlier: 3.619A pdb=" N ARG C 353 " --> pdb=" O PRO C 349 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 367 Processing helix chain 'C' and resid 370 through 377 Processing helix chain 'C' and resid 383 through 389 Processing helix chain 'C' and resid 391 through 425 removed outlier: 3.707A pdb=" N CYS C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 451 through 461 Processing helix chain 'C' and resid 465 through 481 removed outlier: 4.248A pdb=" N THR C 470 " --> pdb=" O ASP C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 497 removed outlier: 3.721A pdb=" N GLU C 495 " --> pdb=" O ALA C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 566 removed outlier: 3.796A pdb=" N ASN C 554 " --> pdb=" O VAL C 550 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' Processing helix chain 'C' and resid 576 through 578 No H-bonds generated for 'chain 'C' and resid 576 through 578' Processing helix chain 'C' and resid 584 through 591 Processing helix chain 'C' and resid 600 through 603 No H-bonds generated for 'chain 'C' and resid 600 through 603' Processing helix chain 'C' and resid 606 through 608 No H-bonds generated for 'chain 'C' and resid 606 through 608' Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.979A pdb=" N GLU C 638 " --> pdb=" O LYS C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 656 removed outlier: 4.048A pdb=" N VAL C 655 " --> pdb=" O ALA C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 689 Processing helix chain 'D' and resid 19 through 28 Processing helix chain 'D' and resid 41 through 56 Processing helix chain 'D' and resid 73 through 85 Processing helix chain 'D' and resid 88 through 91 No H-bonds generated for 'chain 'D' and resid 88 through 91' Processing helix chain 'D' and resid 107 through 117 Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 161 through 166 removed outlier: 3.583A pdb=" N ALA D 165 " --> pdb=" O PHE D 161 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N HIS D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 166' Processing helix chain 'D' and resid 171 through 180 Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 243 through 257 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 276 through 289 removed outlier: 4.461A pdb=" N ARG D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 309 Processing helix chain 'D' and resid 313 through 320 Processing helix chain 'D' and resid 323 through 339 removed outlier: 3.713A pdb=" N ILE D 338 " --> pdb=" O HIS D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 357 Processing helix chain 'D' and resid 369 through 381 removed outlier: 3.769A pdb=" N HIS D 378 " --> pdb=" O LYS D 374 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D 380 " --> pdb=" O PHE D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 423 through 430 Processing helix chain 'E' and resid 12 through 22 Processing helix chain 'E' and resid 43 through 54 removed outlier: 3.736A pdb=" N THR E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 83 removed outlier: 4.043A pdb=" N LEU E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 109 Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 135 through 142 Proline residue: E 139 - end of helix Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 162 through 165 No H-bonds generated for 'chain 'E' and resid 162 through 165' Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 201 through 215 removed outlier: 3.777A pdb=" N VAL E 214 " --> pdb=" O ILE E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 233 through 241 Proline residue: E 239 - end of helix Processing helix chain 'E' and resid 250 through 266 Proline residue: E 259 - end of helix removed outlier: 3.786A pdb=" N GLN E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 284 removed outlier: 4.031A pdb=" N ASP E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 317 Processing helix chain 'E' and resid 321 through 327 removed outlier: 3.753A pdb=" N ASP E 324 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS E 325 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE E 327 " --> pdb=" O ASP E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 369 Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.605A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 422 Processing helix chain 'E' and resid 427 through 430 No H-bonds generated for 'chain 'E' and resid 427 through 430' Processing sheet with id= A, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.215A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 311 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 388 " --> pdb=" O TYR B 419 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ILE B 421 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 390 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N SER B 423 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE B 392 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 272 through 277 removed outlier: 7.125A pdb=" N LEU C 246 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N ALA C 103 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 248 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU C 105 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE C 250 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 215 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE C 249 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 217 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLY C 251 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU C 219 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 214 through 216 removed outlier: 7.743A pdb=" N ILE D 215 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU D 64 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL D 154 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ILE D 190 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE D 156 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LEU D 192 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU D 158 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU D 95 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE D 157 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL D 97 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASP D 159 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU D 99 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 385 through 387 Processing sheet with id= E, first strand: chain 'E' and resid 175 through 178 removed outlier: 3.501A pdb=" N PHE E 175 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ILE E 33 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL E 154 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE E 35 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE E 156 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL E 120 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU E 155 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE E 122 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU E 157 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU E 124 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 393 through 395 553 hydrogen bonds defined for protein. 1614 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: 4.31 Time building geometry restraints manager: 5.45 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: 3333 1.33 - 1.45: 2766 1.45 - 1.57: 7948 1.57 - 1.69: 11 1.69 - 1.81: 97 Bond restraints: 14155 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.94e+01 bond pdb=" C5 ATP D 901 " pdb=" C6 ATP D 901 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.13e+01 bond pdb=" C5 ATP E 501 " pdb=" C6 ATP E 501 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.82e+01 bond pdb=" C4 ATP E 501 " pdb=" N9 ATP E 501 " ideal model delta sigma weight residual 1.374 1.325 0.049 1.00e-02 1.00e+04 2.44e+01 ... (remaining 14150 not shown) Histogram of bond angle deviations from ideal: 96.80 - 104.61: 208 104.61 - 112.42: 7060 112.42 - 120.23: 6257 120.23 - 128.05: 5499 128.05 - 135.86: 135 Bond angle restraints: 19159 Sorted by residual: angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.27 18.60 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 119.61 17.22 1.00e+00 1.00e+00 2.97e+02 angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 123.07 16.80 1.00e+00 1.00e+00 2.82e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 122.14 14.69 1.00e+00 1.00e+00 2.16e+02 angle pdb=" C5 ATP E 501 " pdb=" C4 ATP E 501 " pdb=" N3 ATP E 501 " ideal model delta sigma weight residual 126.80 119.11 7.69 1.00e+00 1.00e+00 5.92e+01 ... (remaining 19154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.45: 7769 18.45 - 36.90: 678 36.90 - 55.35: 104 55.35 - 73.80: 25 73.80 - 92.24: 16 Dihedral angle restraints: 8592 sinusoidal: 3574 harmonic: 5018 Sorted by residual: dihedral pdb=" CA HIS D 34 " pdb=" C HIS D 34 " pdb=" N SER D 35 " pdb=" CA SER D 35 " ideal model delta harmonic sigma weight residual -180.00 -150.99 -29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASN B 378 " pdb=" C ASN B 378 " pdb=" N LYS B 379 " pdb=" CA LYS B 379 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ARG D 397 " pdb=" C ARG D 397 " pdb=" N GLU D 398 " pdb=" CA GLU D 398 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 8589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1787 0.078 - 0.156: 339 0.156 - 0.234: 54 0.234 - 0.312: 7 0.312 - 0.389: 1 Chirality restraints: 2188 Sorted by residual: chirality pdb=" CB ILE B 421 " pdb=" CA ILE B 421 " pdb=" CG1 ILE B 421 " pdb=" CG2 ILE B 421 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB THR B 449 " pdb=" CA THR B 449 " pdb=" OG1 THR B 449 " pdb=" CG2 THR B 449 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE C 447 " pdb=" CA ILE C 447 " pdb=" CG1 ILE C 447 " pdb=" CG2 ILE C 447 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2185 not shown) Planarity restraints: 2410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 418 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO D 419 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO D 419 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 419 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 443 " 0.019 2.00e-02 2.50e+03 2.48e-02 1.54e+01 pdb=" CG TRP B 443 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP B 443 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP B 443 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 443 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP B 443 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 443 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 443 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 443 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 443 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 240 " -0.010 2.00e-02 2.50e+03 2.40e-02 1.01e+01 pdb=" CG PHE D 240 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE D 240 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE D 240 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE D 240 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 240 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE D 240 " -0.001 2.00e-02 2.50e+03 ... (remaining 2407 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 98 2.65 - 3.21: 12267 3.21 - 3.78: 20463 3.78 - 4.34: 27696 4.34 - 4.90: 45536 Nonbonded interactions: 106060 Sorted by model distance: nonbonded pdb=" OG1 THR D 74 " pdb="MG MG D 902 " model vdw 2.088 2.170 nonbonded pdb=" O3B ATP D 901 " pdb="MG MG D 902 " model vdw 2.097 2.170 nonbonded pdb=" OD1 ASN C 644 " pdb=" N THR C 700 " model vdw 2.319 2.520 nonbonded pdb=" O PHE B 380 " pdb=" ND2 ASN B 417 " model vdw 2.355 2.520 nonbonded pdb=" O THR B 448 " pdb=" OG1 THR B 448 " model vdw 2.356 2.440 ... (remaining 106055 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 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: 1.740 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: 0.010 Extract box with map and model: 7.670 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 38.230 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 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 : 0.008 0.077 14155 Z= 0.502 Angle : 1.138 18.604 19159 Z= 0.665 Chirality : 0.063 0.389 2188 Planarity : 0.007 0.113 2410 Dihedral : 14.611 92.245 5306 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.18), residues: 1653 helix: -1.00 (0.15), residues: 928 sheet: -1.07 (0.41), residues: 146 loop : -1.80 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP B 443 HIS 0.013 0.003 HIS C 114 PHE 0.052 0.004 PHE D 138 TYR 0.044 0.003 TYR E 204 ARG 0.019 0.002 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.647 Fit side-chains REVERT: B 454 TYR cc_start: 0.8961 (m-80) cc_final: 0.8625 (m-80) REVERT: B 474 LEU cc_start: 0.4687 (mm) cc_final: 0.3908 (pt) REVERT: B 475 SER cc_start: 0.8036 (p) cc_final: 0.7820 (p) REVERT: B 497 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7831 (mtmm) REVERT: B 498 TYR cc_start: 0.8132 (t80) cc_final: 0.7906 (t80) REVERT: C 189 MET cc_start: 0.7405 (mtp) cc_final: 0.7085 (ttp) REVERT: C 281 CYS cc_start: 0.7745 (m) cc_final: 0.7374 (m) REVERT: C 304 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7470 (pm20) REVERT: C 686 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6434 (mt-10) REVERT: D 137 SER cc_start: 0.8633 (t) cc_final: 0.8278 (p) REVERT: E 6 ASN cc_start: 0.6643 (m-40) cc_final: 0.6377 (p0) REVERT: E 119 THR cc_start: 0.8286 (m) cc_final: 0.8038 (p) REVERT: E 189 LYS cc_start: 0.8373 (ttmt) cc_final: 0.7963 (tttp) REVERT: E 248 ARG cc_start: 0.6810 (tpp-160) cc_final: 0.5730 (ttt-90) REVERT: E 263 LYS cc_start: 0.7064 (mmtm) cc_final: 0.6713 (ttmm) REVERT: E 280 LYS cc_start: 0.6695 (tmtt) cc_final: 0.6440 (mptt) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2747 time to fit residues: 87.2396 Evaluate side-chains 124 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN B 393 HIS C 62 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 HIS C 500 GLN C 576 HIS D 19 GLN D 36 ASN D 212 HIS D 250 ASN D 288 ASN D 420 ASN E 195 HIS E 256 ASN E 260 HIS E 398 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14155 Z= 0.177 Angle : 0.531 5.605 19159 Z= 0.280 Chirality : 0.040 0.149 2188 Planarity : 0.004 0.065 2410 Dihedral : 7.666 78.670 1875 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.89 % Allowed : 5.75 % Favored : 93.36 % 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: -0.90 (0.19), residues: 1653 helix: 0.13 (0.16), residues: 947 sheet: -0.77 (0.42), residues: 136 loop : -1.69 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 443 HIS 0.007 0.001 HIS C 576 PHE 0.021 0.002 PHE C 548 TYR 0.019 0.001 TYR E 204 ARG 0.005 0.001 ARG D 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.495 Fit side-chains REVERT: C 182 ASP cc_start: 0.7682 (t0) cc_final: 0.7435 (t0) REVERT: C 189 MET cc_start: 0.7283 (mtp) cc_final: 0.7038 (ttp) REVERT: C 560 ASP cc_start: 0.7923 (t0) cc_final: 0.7380 (t0) REVERT: C 686 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6463 (mt-10) REVERT: D 137 SER cc_start: 0.8648 (t) cc_final: 0.8297 (p) REVERT: E 6 ASN cc_start: 0.6735 (m-40) cc_final: 0.6498 (p0) REVERT: E 119 THR cc_start: 0.8275 (m) cc_final: 0.8038 (p) REVERT: E 189 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8009 (tttp) REVERT: E 248 ARG cc_start: 0.6765 (tpp-160) cc_final: 0.5945 (ttm-80) REVERT: E 263 LYS cc_start: 0.6841 (mmtm) cc_final: 0.6559 (ttmm) REVERT: E 398 HIS cc_start: 0.6243 (OUTLIER) cc_final: 0.5676 (t70) outliers start: 14 outliers final: 12 residues processed: 147 average time/residue: 0.2423 time to fit residues: 53.7608 Evaluate side-chains 131 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 398 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 121 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 110 ASN C 260 HIS C 677 HIS D 36 ASN D 212 HIS D 420 ASN E 195 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14155 Z= 0.207 Angle : 0.501 5.402 19159 Z= 0.263 Chirality : 0.040 0.165 2188 Planarity : 0.004 0.050 2410 Dihedral : 7.155 70.133 1875 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.53 % Allowed : 7.02 % Favored : 91.44 % 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: -0.42 (0.20), residues: 1653 helix: 0.59 (0.17), residues: 948 sheet: -0.55 (0.43), residues: 136 loop : -1.62 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 51 HIS 0.013 0.001 HIS E 195 PHE 0.015 0.001 PHE C 652 TYR 0.017 0.001 TYR E 204 ARG 0.005 0.000 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.685 Fit side-chains REVERT: C 182 ASP cc_start: 0.7769 (t0) cc_final: 0.7436 (t0) REVERT: C 686 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6366 (mt-10) REVERT: D 111 LEU cc_start: 0.8898 (tp) cc_final: 0.8508 (tp) REVERT: D 137 SER cc_start: 0.8679 (t) cc_final: 0.8336 (p) REVERT: E 6 ASN cc_start: 0.6935 (m-40) cc_final: 0.6558 (p0) REVERT: E 119 THR cc_start: 0.8389 (m) cc_final: 0.8139 (p) REVERT: E 189 LYS cc_start: 0.8427 (ttmt) cc_final: 0.7968 (tttp) REVERT: E 248 ARG cc_start: 0.6776 (tpp-160) cc_final: 0.5946 (ttm-80) REVERT: E 263 LYS cc_start: 0.6841 (mmtm) cc_final: 0.6602 (ttmm) outliers start: 24 outliers final: 16 residues processed: 141 average time/residue: 0.2342 time to fit residues: 50.4848 Evaluate side-chains 130 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 282 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 161 optimal weight: 0.0010 chunk 79 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN C 110 ASN C 260 HIS D 358 GLN D 420 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14155 Z= 0.175 Angle : 0.469 5.301 19159 Z= 0.247 Chirality : 0.039 0.172 2188 Planarity : 0.003 0.046 2410 Dihedral : 6.841 69.049 1875 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.53 % Allowed : 8.30 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1653 helix: 0.87 (0.17), residues: 952 sheet: -0.26 (0.44), residues: 130 loop : -1.52 (0.23), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 51 HIS 0.004 0.001 HIS D 34 PHE 0.020 0.001 PHE C 548 TYR 0.014 0.001 TYR E 204 ARG 0.004 0.000 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 1.677 Fit side-chains REVERT: C 182 ASP cc_start: 0.7796 (t0) cc_final: 0.7510 (t0) REVERT: C 422 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6252 (t80) REVERT: C 589 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7792 (mm-30) REVERT: C 686 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6419 (mt-10) REVERT: D 111 LEU cc_start: 0.8882 (tp) cc_final: 0.8480 (tp) REVERT: D 137 SER cc_start: 0.8676 (t) cc_final: 0.8324 (p) REVERT: E 6 ASN cc_start: 0.6969 (m-40) cc_final: 0.6667 (p0) REVERT: E 119 THR cc_start: 0.8364 (m) cc_final: 0.8143 (p) REVERT: E 189 LYS cc_start: 0.8452 (ttmt) cc_final: 0.7970 (tttt) REVERT: E 248 ARG cc_start: 0.6787 (tpp-160) cc_final: 0.5948 (ttm-80) outliers start: 24 outliers final: 17 residues processed: 138 average time/residue: 0.2537 time to fit residues: 52.8329 Evaluate side-chains 132 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 282 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 120 optimal weight: 0.0770 chunk 66 optimal weight: 0.0270 chunk 137 optimal weight: 0.0030 chunk 111 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN C 636 HIS D 420 ASN E 232 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14155 Z= 0.117 Angle : 0.429 5.087 19159 Z= 0.226 Chirality : 0.037 0.167 2188 Planarity : 0.003 0.046 2410 Dihedral : 6.479 67.742 1875 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.40 % Allowed : 9.13 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1653 helix: 1.20 (0.17), residues: 962 sheet: -0.06 (0.45), residues: 130 loop : -1.37 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 51 HIS 0.003 0.000 HIS D 34 PHE 0.027 0.001 PHE D 38 TYR 0.014 0.001 TYR C 429 ARG 0.005 0.000 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 1.759 Fit side-chains REVERT: B 465 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7228 (tt) REVERT: C 59 GLU cc_start: 0.7277 (pt0) cc_final: 0.6926 (mt-10) REVERT: C 182 ASP cc_start: 0.7706 (t0) cc_final: 0.7449 (t0) REVERT: C 422 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.6110 (t80) REVERT: D 111 LEU cc_start: 0.8799 (tp) cc_final: 0.8361 (tp) REVERT: D 137 SER cc_start: 0.8685 (t) cc_final: 0.8338 (p) REVERT: D 287 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8100 (tp) REVERT: E 101 ASP cc_start: 0.7704 (m-30) cc_final: 0.7489 (m-30) REVERT: E 189 LYS cc_start: 0.8426 (ttmt) cc_final: 0.7970 (tttp) REVERT: E 248 ARG cc_start: 0.6779 (tpp-160) cc_final: 0.5943 (ttm-80) REVERT: E 256 ASN cc_start: 0.8425 (t0) cc_final: 0.8134 (t0) outliers start: 22 outliers final: 15 residues processed: 140 average time/residue: 0.2590 time to fit residues: 55.2600 Evaluate side-chains 130 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 282 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN D 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14155 Z= 0.231 Angle : 0.481 6.470 19159 Z= 0.252 Chirality : 0.039 0.156 2188 Planarity : 0.003 0.045 2410 Dihedral : 6.601 69.087 1875 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.98 % Allowed : 9.83 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1653 helix: 1.19 (0.17), residues: 961 sheet: 0.16 (0.46), residues: 123 loop : -1.46 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 51 HIS 0.005 0.001 HIS D 34 PHE 0.023 0.002 PHE B 569 TYR 0.013 0.001 TYR C 429 ARG 0.003 0.000 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.627 Fit side-chains REVERT: B 465 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7304 (tt) REVERT: C 182 ASP cc_start: 0.7864 (t0) cc_final: 0.7597 (t0) REVERT: C 422 PHE cc_start: 0.6757 (OUTLIER) cc_final: 0.6144 (t80) REVERT: D 111 LEU cc_start: 0.8873 (tp) cc_final: 0.8444 (tp) REVERT: D 137 SER cc_start: 0.8707 (t) cc_final: 0.8349 (p) REVERT: D 287 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8141 (tp) REVERT: E 189 LYS cc_start: 0.8476 (ttmt) cc_final: 0.7956 (tttp) REVERT: E 248 ARG cc_start: 0.6844 (tpp-160) cc_final: 0.5997 (ttm-80) REVERT: E 256 ASN cc_start: 0.8532 (t0) cc_final: 0.8226 (t0) outliers start: 31 outliers final: 22 residues processed: 136 average time/residue: 0.2365 time to fit residues: 49.6118 Evaluate side-chains 135 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 282 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 8.9990 chunk 18 optimal weight: 0.0980 chunk 92 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN D 358 GLN D 420 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14155 Z= 0.141 Angle : 0.436 5.283 19159 Z= 0.229 Chirality : 0.037 0.144 2188 Planarity : 0.003 0.043 2410 Dihedral : 6.413 69.476 1875 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.66 % Allowed : 10.73 % Favored : 87.61 % 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 (0.21), residues: 1653 helix: 1.33 (0.17), residues: 963 sheet: 0.38 (0.47), residues: 123 loop : -1.42 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 51 HIS 0.003 0.001 HIS D 34 PHE 0.026 0.001 PHE B 569 TYR 0.012 0.001 TYR D 174 ARG 0.004 0.000 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.309 Fit side-chains REVERT: B 465 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7328 (tt) REVERT: C 26 ILE cc_start: 0.7838 (mt) cc_final: 0.7591 (mt) REVERT: C 59 GLU cc_start: 0.7243 (pt0) cc_final: 0.6818 (mt-10) REVERT: C 182 ASP cc_start: 0.7810 (t0) cc_final: 0.7560 (t0) REVERT: C 422 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6244 (t80) REVERT: D 111 LEU cc_start: 0.8852 (tp) cc_final: 0.8418 (tp) REVERT: D 137 SER cc_start: 0.8703 (t) cc_final: 0.8338 (p) REVERT: D 287 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8099 (tp) REVERT: E 101 ASP cc_start: 0.7746 (m-30) cc_final: 0.7532 (m-30) REVERT: E 189 LYS cc_start: 0.8454 (ttmt) cc_final: 0.7938 (tttp) REVERT: E 248 ARG cc_start: 0.6846 (tpp-160) cc_final: 0.6000 (ttm-80) REVERT: E 256 ASN cc_start: 0.8478 (t0) cc_final: 0.8143 (t0) outliers start: 26 outliers final: 17 residues processed: 136 average time/residue: 0.2506 time to fit residues: 50.6767 Evaluate side-chains 132 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 282 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN C 62 GLN D 420 ASN E 277 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14155 Z= 0.275 Angle : 0.512 5.433 19159 Z= 0.268 Chirality : 0.040 0.149 2188 Planarity : 0.004 0.044 2410 Dihedral : 6.705 71.827 1875 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.11 % Allowed : 10.92 % Favored : 86.97 % 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: 0.27 (0.21), residues: 1653 helix: 1.13 (0.17), residues: 961 sheet: 0.37 (0.46), residues: 123 loop : -1.50 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 51 HIS 0.006 0.001 HIS D 34 PHE 0.026 0.002 PHE B 569 TYR 0.015 0.002 TYR C 429 ARG 0.008 0.000 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 107 time to evaluate : 1.577 Fit side-chains REVERT: B 465 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7403 (tt) REVERT: C 26 ILE cc_start: 0.7873 (mt) cc_final: 0.7639 (mt) REVERT: C 182 ASP cc_start: 0.7890 (t0) cc_final: 0.7649 (t0) REVERT: C 422 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6359 (t80) REVERT: D 111 LEU cc_start: 0.8902 (tp) cc_final: 0.8494 (tp) REVERT: D 137 SER cc_start: 0.8722 (t) cc_final: 0.8358 (p) REVERT: D 287 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8151 (tp) REVERT: E 189 LYS cc_start: 0.8502 (ttmt) cc_final: 0.7972 (tttp) REVERT: E 248 ARG cc_start: 0.6897 (tpp-160) cc_final: 0.5998 (ttm-80) outliers start: 33 outliers final: 22 residues processed: 129 average time/residue: 0.2314 time to fit residues: 46.2702 Evaluate side-chains 127 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 282 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN C 62 GLN D 420 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14155 Z= 0.172 Angle : 0.457 5.379 19159 Z= 0.239 Chirality : 0.038 0.137 2188 Planarity : 0.003 0.043 2410 Dihedral : 6.509 71.812 1875 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.66 % Allowed : 11.30 % Favored : 87.04 % 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: 0.44 (0.21), residues: 1653 helix: 1.27 (0.17), residues: 962 sheet: 0.46 (0.47), residues: 123 loop : -1.46 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 51 HIS 0.004 0.001 HIS D 34 PHE 0.026 0.001 PHE B 569 TYR 0.012 0.001 TYR D 174 ARG 0.006 0.000 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 1.801 Fit side-chains REVERT: B 465 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7346 (tt) REVERT: C 26 ILE cc_start: 0.7866 (mt) cc_final: 0.7619 (mt) REVERT: C 182 ASP cc_start: 0.7817 (t0) cc_final: 0.7583 (t0) REVERT: C 304 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7757 (tm-30) REVERT: C 422 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.6298 (t80) REVERT: D 111 LEU cc_start: 0.8876 (tp) cc_final: 0.8460 (tp) REVERT: D 137 SER cc_start: 0.8715 (t) cc_final: 0.8345 (p) REVERT: D 287 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8128 (tp) REVERT: E 189 LYS cc_start: 0.8492 (ttmt) cc_final: 0.7977 (tttp) REVERT: E 248 ARG cc_start: 0.6894 (tpp-160) cc_final: 0.5983 (ttm-80) REVERT: E 256 ASN cc_start: 0.8558 (t0) cc_final: 0.8262 (t0) outliers start: 26 outliers final: 21 residues processed: 131 average time/residue: 0.2592 time to fit residues: 51.7382 Evaluate side-chains 131 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN D 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14155 Z= 0.145 Angle : 0.437 5.325 19159 Z= 0.227 Chirality : 0.037 0.133 2188 Planarity : 0.003 0.042 2410 Dihedral : 6.292 69.843 1875 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.53 % Allowed : 11.56 % Favored : 86.91 % 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: 0.62 (0.21), residues: 1653 helix: 1.41 (0.18), residues: 963 sheet: 0.58 (0.48), residues: 123 loop : -1.40 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 51 HIS 0.003 0.001 HIS D 34 PHE 0.027 0.001 PHE B 569 TYR 0.012 0.001 TYR D 174 ARG 0.007 0.000 ARG D 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.468 Fit side-chains REVERT: C 26 ILE cc_start: 0.7854 (mt) cc_final: 0.7606 (mt) REVERT: C 59 GLU cc_start: 0.7272 (pt0) cc_final: 0.7049 (mm-30) REVERT: C 182 ASP cc_start: 0.7791 (t0) cc_final: 0.7586 (t0) REVERT: C 304 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7711 (tm-30) REVERT: C 422 PHE cc_start: 0.6829 (OUTLIER) cc_final: 0.6430 (t80) REVERT: D 111 LEU cc_start: 0.8881 (tp) cc_final: 0.8447 (tp) REVERT: D 137 SER cc_start: 0.8713 (t) cc_final: 0.8337 (p) REVERT: D 218 MET cc_start: 0.7728 (mmt) cc_final: 0.7489 (mmt) REVERT: D 287 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8079 (tp) REVERT: E 189 LYS cc_start: 0.8480 (ttmt) cc_final: 0.7985 (tttp) REVERT: E 248 ARG cc_start: 0.6832 (tpp-160) cc_final: 0.6032 (ttm-80) REVERT: E 256 ASN cc_start: 0.8475 (t0) cc_final: 0.8130 (t0) outliers start: 24 outliers final: 17 residues processed: 131 average time/residue: 0.2127 time to fit residues: 42.3154 Evaluate side-chains 129 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 420 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108775 restraints weight = 20171.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110601 restraints weight = 16684.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111364 restraints weight = 13655.423| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14155 Z= 0.148 Angle : 0.441 5.363 19159 Z= 0.229 Chirality : 0.037 0.135 2188 Planarity : 0.003 0.043 2410 Dihedral : 6.254 69.229 1875 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.34 % Allowed : 11.75 % Favored : 86.91 % 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 (0.21), residues: 1653 helix: 1.46 (0.18), residues: 962 sheet: 0.68 (0.48), residues: 123 loop : -1.39 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 51 HIS 0.003 0.001 HIS D 34 PHE 0.027 0.001 PHE B 569 TYR 0.014 0.001 TYR D 174 ARG 0.006 0.000 ARG D 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2269.12 seconds wall clock time: 43 minutes 16.05 seconds (2596.05 seconds total)