Starting phenix.real_space_refine on Fri Aug 9 21:39:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5l_19739/08_2024/8s5l_19739_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5l_19739/08_2024/8s5l_19739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5l_19739/08_2024/8s5l_19739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5l_19739/08_2024/8s5l_19739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5l_19739/08_2024/8s5l_19739_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5l_19739/08_2024/8s5l_19739_trim.cif" } resolution = 3.8 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= 0.012 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 4 5.49 5 S 78 5.16 5 C 8650 2.51 5 N 2372 2.21 5 O 2578 1.98 5 H 13603 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 86": "OD1" <-> "OD2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 477": "OD1" <-> "OD2" Residue "B ASP 506": "OD1" <-> "OD2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 281": "OD1" <-> "OD2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C ASP 538": "OD1" <-> "OD2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D ASP 376": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27289 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5636 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 7904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7904 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Chain: "C" Number of atoms: 7909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7909 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Chain: "D" Number of atoms: 5636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5636 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'HEM': 1, 'PLP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'HEM': 1, 'PLP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 177 SG CYS A 52 79.352 132.334 41.782 1.00 56.77 S ATOM 21626 SG CYS D 52 47.665 28.331 41.717 1.00 56.13 S Time building chain proxies: 13.39, per 1000 atoms: 0.49 Number of scatterers: 27289 At special positions: 0 Unit cell: (127.958, 159.714, 83.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 78 16.00 P 4 15.00 O 2578 8.00 N 2372 7.00 C 8650 6.00 H 13603 1.00 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.14 Conformation dependent library (CDL) restraints added in 3.1 seconds 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3196 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 14 sheets defined 45.6% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 118 through 133 removed outlier: 4.463A pdb=" N ILE A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 162 Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.875A pdb=" N VAL A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.535A pdb=" N LEU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 Processing helix chain 'A' and resid 258 through 272 removed outlier: 3.813A pdb=" N ILE A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 328 through 343 removed outlier: 3.708A pdb=" N GLY A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 361 removed outlier: 3.709A pdb=" N LYS A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 378 through 382 removed outlier: 3.735A pdb=" N MET A 382 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 99 removed outlier: 4.044A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 148 through 162 Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 226 through 235 removed outlier: 3.832A pdb=" N HIS B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 261 through 272 Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.832A pdb=" N GLN B 295 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 343 removed outlier: 3.570A pdb=" N ALA B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 361 removed outlier: 4.268A pdb=" N LYS B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.894A pdb=" N ASN B 380 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET B 382 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 394 Processing helix chain 'B' and resid 398 through 405 removed outlier: 4.338A pdb=" N LYS B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 4.076A pdb=" N HIS B 411 " --> pdb=" O TRP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 430 through 441 removed outlier: 3.647A pdb=" N GLU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 470 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 535 through 548 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 93 through 99 removed outlier: 4.030A pdb=" N LYS C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 133 Processing helix chain 'C' and resid 148 through 162 Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.826A pdb=" N HIS C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 258 through 272 removed outlier: 3.542A pdb=" N LYS C 267 " --> pdb=" O GLY C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 removed outlier: 3.697A pdb=" N GLN C 295 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.771A pdb=" N VAL C 320 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 343 removed outlier: 3.655A pdb=" N ALA C 331 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 336 " --> pdb=" O PHE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 361 removed outlier: 4.218A pdb=" N LYS C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.853A pdb=" N ASN C 380 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET C 382 " --> pdb=" O ARG C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 395 Processing helix chain 'C' and resid 398 through 405 removed outlier: 4.288A pdb=" N LYS C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 removed outlier: 4.025A pdb=" N HIS C 411 " --> pdb=" O TRP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 430 through 442 removed outlier: 3.708A pdb=" N LYS C 441 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 470 Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.621A pdb=" N LYS C 481 " --> pdb=" O GLN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 535 through 548 Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 93 through 99 removed outlier: 3.559A pdb=" N LYS D 97 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 133 removed outlier: 4.478A pdb=" N ILE D 122 " --> pdb=" O VAL D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 162 Processing helix chain 'D' and resid 174 through 184 removed outlier: 3.864A pdb=" N VAL D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 214 Processing helix chain 'D' and resid 226 through 235 removed outlier: 3.517A pdb=" N LEU D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 245 Processing helix chain 'D' and resid 258 through 272 removed outlier: 3.856A pdb=" N LYS D 267 " --> pdb=" O GLY D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 328 through 343 removed outlier: 3.647A pdb=" N GLY D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 361 removed outlier: 3.715A pdb=" N LYS D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 378 through 382 removed outlier: 3.817A pdb=" N MET D 382 " --> pdb=" O ARG D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 394 Processing helix chain 'D' and resid 399 through 404 removed outlier: 3.905A pdb=" N GLU D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.680A pdb=" N LEU A 374 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 250 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER A 254 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU A 251 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL A 280 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ALA A 253 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 281 " --> pdb=" O PHE A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 191 removed outlier: 3.675A pdb=" N THR A 191 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE A 142 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL A 168 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU A 144 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR A 141 " --> pdb=" O HIS A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.684A pdb=" N MET B 250 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N SER B 254 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU B 251 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL B 280 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA B 253 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 322 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 187 through 190 removed outlier: 3.538A pdb=" N VAL B 168 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 423 through 425 removed outlier: 3.527A pdb=" N TYR C 518 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS C 488 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL C 512 " --> pdb=" O LYS C 488 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE C 490 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLU C 514 " --> pdb=" O ILE C 490 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 423 through 425 removed outlier: 3.527A pdb=" N TYR C 518 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA C 509 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL C 533 " --> pdb=" O ALA C 509 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL C 511 " --> pdb=" O PHE C 531 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 448 through 449 removed outlier: 3.662A pdb=" N GLY B 457 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 488 through 491 removed outlier: 6.653A pdb=" N ALA B 509 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL B 533 " --> pdb=" O ALA B 509 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL B 511 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 525 " --> pdb=" O GLN B 517 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 488 through 491 removed outlier: 7.698A pdb=" N THR C 424 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE B 516 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 89 through 91 removed outlier: 6.253A pdb=" N MET C 250 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE C 373 " --> pdb=" O MET C 250 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL C 252 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU C 251 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL C 280 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA C 253 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N SER C 326 " --> pdb=" O GLY C 279 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP C 281 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 187 through 190 Processing sheet with id=AB3, first strand: chain 'C' and resid 448 through 449 removed outlier: 6.736A pdb=" N VAL C 448 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 89 through 91 removed outlier: 6.274A pdb=" N GLU D 104 " --> pdb=" O CYS D 370 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL D 372 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU D 106 " --> pdb=" O VAL D 372 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU D 374 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS D 108 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N SER D 254 " --> pdb=" O ILE D 373 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU D 251 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL D 280 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA D 253 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 322 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 187 through 191 removed outlier: 3.648A pdb=" N THR D 191 " --> pdb=" O MET D 169 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE D 142 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL D 168 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU D 144 " --> pdb=" O VAL D 168 " (cutoff:3.500A) 545 hydrogen bonds defined for protein. 1479 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: 10.40 Time building geometry restraints manager: 23.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 13533 1.08 - 1.32: 2459 1.32 - 1.56: 11441 1.56 - 1.81: 113 1.81 - 2.05: 25 Bond restraints: 27571 Sorted by residual: bond pdb=" C4' LLP A 119 " pdb="H4'1 LLP A 119 " ideal model delta sigma weight residual 0.930 1.084 -0.154 2.00e-02 2.50e+03 5.91e+01 bond pdb=" C4' LLP D 119 " pdb="H4'1 LLP D 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.84e+01 bond pdb=" C6 LLP D 119 " pdb=" H6 LLP D 119 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" C6 LLP A 119 " pdb=" H6 LLP A 119 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.81e+01 bond pdb=" N LLP D 119 " pdb=" H LLP D 119 " ideal model delta sigma weight residual 0.860 1.004 -0.144 2.00e-02 2.50e+03 5.17e+01 ... (remaining 27566 not shown) Histogram of bond angle deviations from ideal: 86.08 - 104.53: 279 104.53 - 122.97: 46680 122.97 - 141.42: 3053 141.42 - 159.87: 0 159.87 - 178.32: 8 Bond angle restraints: 50020 Sorted by residual: angle pdb=" O LLP A 119 " pdb=" C LLP A 119 " pdb=" N ASP A 120 " ideal model delta sigma weight residual 123.00 86.08 36.92 1.60e+00 3.91e-01 5.33e+02 angle pdb=" O LLP D 119 " pdb=" C LLP D 119 " pdb=" N ASP D 120 " ideal model delta sigma weight residual 123.00 87.69 35.31 1.60e+00 3.91e-01 4.87e+02 angle pdb=" OP1 LLP A 119 " pdb=" P LLP A 119 " pdb=" OP4 LLP A 119 " ideal model delta sigma weight residual 100.47 110.60 -10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" OP1 LLP D 119 " pdb=" P LLP D 119 " pdb=" OP4 LLP D 119 " ideal model delta sigma weight residual 100.47 110.28 -9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C LYS B 384 " pdb=" CA LYS B 384 " pdb=" CB LYS B 384 " ideal model delta sigma weight residual 110.42 115.84 -5.42 1.99e+00 2.53e-01 7.41e+00 ... (remaining 50015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 12326 35.03 - 70.05: 408 70.05 - 105.08: 40 105.08 - 140.10: 2 140.10 - 175.13: 1 Dihedral angle restraints: 12777 sinusoidal: 7191 harmonic: 5586 Sorted by residual: dihedral pdb=" C5A PLP C 602 " pdb=" O4P PLP C 602 " pdb=" P PLP C 602 " pdb=" O1P PLP C 602 " ideal model delta sinusoidal sigma weight residual 76.43 -98.70 175.13 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5 PLP B 602 " pdb=" C4 PLP B 602 " pdb=" C4A PLP B 602 " pdb=" O4A PLP B 602 " ideal model delta sinusoidal sigma weight residual 0.00 -137.31 137.31 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" C5A PLP B 602 " pdb=" O4P PLP B 602 " pdb=" P PLP B 602 " pdb=" O1P PLP B 602 " ideal model delta sinusoidal sigma weight residual 76.43 -58.43 134.86 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 12774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1405 0.036 - 0.073: 519 0.073 - 0.109: 131 0.109 - 0.146: 53 0.146 - 0.182: 4 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CA PRO A 375 " pdb=" N PRO A 375 " pdb=" C PRO A 375 " pdb=" CB PRO A 375 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CA PRO B 375 " pdb=" N PRO B 375 " pdb=" C PRO B 375 " pdb=" CB PRO B 375 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA PRO C 375 " pdb=" N PRO C 375 " pdb=" C PRO C 375 " pdb=" CB PRO C 375 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 2109 not shown) Planarity restraints: 4077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LLP A 119 " 0.137 2.00e-02 2.50e+03 2.22e-01 4.92e+02 pdb=" C LLP A 119 " -0.384 2.00e-02 2.50e+03 pdb=" O LLP A 119 " 0.135 2.00e-02 2.50e+03 pdb=" N ASP A 120 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP D 119 " -0.132 2.00e-02 2.50e+03 2.16e-01 4.66e+02 pdb=" C LLP D 119 " 0.374 2.00e-02 2.50e+03 pdb=" O LLP D 119 " -0.131 2.00e-02 2.50e+03 pdb=" N ASP D 120 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 374 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.12e+00 pdb=" N PRO A 375 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.025 5.00e-02 4.00e+02 ... (remaining 4074 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 914 2.14 - 2.75: 52195 2.75 - 3.37: 78159 3.37 - 3.98: 98302 3.98 - 4.60: 156215 Nonbonded interactions: 385785 Sorted by model distance: nonbonded pdb=" OD2 ASP C 249 " pdb=" H ARG C 369 " model vdw 1.525 2.450 nonbonded pdb=" OD2 ASP B 249 " pdb=" H ARG B 369 " model vdw 1.536 2.450 nonbonded pdb=" OE1 GLU D 201 " pdb=" H GLU D 201 " model vdw 1.546 2.450 nonbonded pdb=" OE1 GLU B 399 " pdb=" H GLU B 399 " model vdw 1.546 2.450 nonbonded pdb=" OE1 GLU A 201 " pdb=" H GLU A 201 " model vdw 1.550 2.450 ... (remaining 385780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 42 through 118 or (resid 119 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 120 through 548 or resid 601 through 602)) } 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: 6.510 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: 0.420 Extract box with map and model: 0.980 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 87.240 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 13968 Z= 0.387 Angle : 0.782 36.925 18972 Z= 0.430 Chirality : 0.043 0.182 2112 Planarity : 0.007 0.222 2432 Dihedral : 15.676 175.125 5214 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.56 % Favored : 94.21 % Rotamer: Outliers : 0.14 % Allowed : 12.70 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.18 (0.21), residues: 1726 helix: 0.05 (0.20), residues: 656 sheet: -1.07 (0.29), residues: 262 loop : 0.30 (0.24), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 323 HIS 0.005 0.001 HIS D 203 PHE 0.012 0.002 PHE A 324 TYR 0.015 0.002 TYR D 233 ARG 0.005 0.001 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 1.951 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 outliers start: 2 outliers final: 2 residues processed: 119 average time/residue: 0.5640 time to fit residues: 102.1631 Evaluate side-chains 113 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 387 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 HIS D 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 13968 Z= 0.377 Angle : 0.625 6.771 18972 Z= 0.318 Chirality : 0.043 0.162 2112 Planarity : 0.004 0.034 2432 Dihedral : 9.727 136.300 1916 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.08 % Rotamer: Outliers : 0.96 % Allowed : 13.11 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1726 helix: 0.12 (0.20), residues: 654 sheet: -1.13 (0.29), residues: 266 loop : 0.03 (0.24), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 409 HIS 0.005 0.001 HIS A 203 PHE 0.010 0.001 PHE A 324 TYR 0.011 0.002 TYR D 233 ARG 0.004 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.990 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: C 234 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7670 (t0) outliers start: 14 outliers final: 10 residues processed: 122 average time/residue: 0.5236 time to fit residues: 98.7806 Evaluate side-chains 123 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 316 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 0.0060 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13968 Z= 0.202 Angle : 0.540 6.359 18972 Z= 0.268 Chirality : 0.042 0.152 2112 Planarity : 0.004 0.032 2432 Dihedral : 9.018 118.688 1915 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.02 % Allowed : 13.32 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.01 (0.21), residues: 1726 helix: 0.51 (0.21), residues: 642 sheet: -0.91 (0.30), residues: 262 loop : 0.10 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 323 HIS 0.010 0.001 HIS C 501 PHE 0.008 0.001 PHE C 443 TYR 0.007 0.001 TYR B 233 ARG 0.003 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.917 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: A 86 ASP cc_start: 0.7336 (t0) cc_final: 0.7119 (t0) REVERT: C 234 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7609 (t0) REVERT: C 387 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8583 (p) REVERT: D 184 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8730 (mp) outliers start: 15 outliers final: 9 residues processed: 138 average time/residue: 0.4883 time to fit residues: 103.6962 Evaluate side-chains 129 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 316 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 ASN C 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 13968 Z= 0.324 Angle : 0.574 7.341 18972 Z= 0.288 Chirality : 0.042 0.164 2112 Planarity : 0.004 0.035 2432 Dihedral : 8.914 109.031 1914 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.21 % Favored : 94.73 % Rotamer: Outliers : 1.50 % Allowed : 13.93 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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 (0.21), residues: 1726 helix: 0.52 (0.21), residues: 638 sheet: -1.09 (0.29), residues: 264 loop : -0.07 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 323 HIS 0.004 0.001 HIS D 203 PHE 0.010 0.001 PHE A 324 TYR 0.011 0.001 TYR D 163 ARG 0.004 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 2.167 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: A 184 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8905 (mp) REVERT: C 387 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8679 (p) REVERT: D 86 ASP cc_start: 0.7682 (t0) cc_final: 0.7464 (t0) REVERT: D 184 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8722 (mp) outliers start: 22 outliers final: 15 residues processed: 135 average time/residue: 0.5123 time to fit residues: 106.5376 Evaluate side-chains 133 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 316 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 ASN C 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13968 Z= 0.291 Angle : 0.562 7.479 18972 Z= 0.281 Chirality : 0.042 0.165 2112 Planarity : 0.004 0.036 2432 Dihedral : 8.763 104.392 1914 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.04 % Favored : 94.84 % Rotamer: Outliers : 1.91 % Allowed : 14.28 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1726 helix: 0.42 (0.21), residues: 652 sheet: -1.17 (0.29), residues: 268 loop : -0.25 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 408 HIS 0.005 0.001 HIS D 203 PHE 0.011 0.001 PHE C 443 TYR 0.012 0.001 TYR D 163 ARG 0.003 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 2.164 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: A 184 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8908 (mp) REVERT: C 387 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8704 (p) REVERT: D 86 ASP cc_start: 0.7658 (t0) cc_final: 0.7457 (t0) REVERT: D 184 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8694 (mp) outliers start: 28 outliers final: 19 residues processed: 141 average time/residue: 0.5148 time to fit residues: 113.0713 Evaluate side-chains 137 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13968 Z= 0.367 Angle : 0.593 7.553 18972 Z= 0.299 Chirality : 0.043 0.173 2112 Planarity : 0.004 0.039 2432 Dihedral : 8.815 102.681 1914 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.79 % Favored : 94.09 % Rotamer: Outliers : 1.84 % Allowed : 14.75 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.56 (0.21), residues: 1726 helix: 0.28 (0.21), residues: 664 sheet: -1.31 (0.29), residues: 268 loop : -0.43 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 408 HIS 0.005 0.001 HIS D 203 PHE 0.011 0.002 PHE A 324 TYR 0.013 0.002 TYR D 163 ARG 0.004 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 2.393 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: A 184 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8917 (mp) REVERT: C 387 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8710 (p) REVERT: D 184 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8701 (mp) outliers start: 27 outliers final: 20 residues processed: 134 average time/residue: 0.5268 time to fit residues: 108.7295 Evaluate side-chains 136 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 316 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13968 Z= 0.276 Angle : 0.557 7.147 18972 Z= 0.277 Chirality : 0.042 0.162 2112 Planarity : 0.004 0.035 2432 Dihedral : 8.638 101.263 1914 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.04 % Favored : 94.84 % Rotamer: Outliers : 1.84 % Allowed : 15.16 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.45 (0.21), residues: 1726 helix: 0.37 (0.21), residues: 664 sheet: -1.29 (0.29), residues: 264 loop : -0.36 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 408 HIS 0.006 0.001 HIS A 203 PHE 0.008 0.001 PHE A 324 TYR 0.011 0.001 TYR D 163 ARG 0.003 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 1.962 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: A 184 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8891 (mp) REVERT: C 387 SER cc_start: 0.9141 (OUTLIER) cc_final: 0.8744 (p) REVERT: D 184 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8695 (mp) outliers start: 27 outliers final: 21 residues processed: 139 average time/residue: 0.5020 time to fit residues: 108.4412 Evaluate side-chains 139 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 ASN ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13968 Z= 0.315 Angle : 0.574 7.334 18972 Z= 0.287 Chirality : 0.042 0.169 2112 Planarity : 0.004 0.037 2432 Dihedral : 8.604 98.836 1914 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.08 % Favored : 93.86 % Rotamer: Outliers : 1.98 % Allowed : 15.57 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.52 (0.21), residues: 1726 helix: 0.34 (0.21), residues: 664 sheet: -1.30 (0.30), residues: 260 loop : -0.45 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 408 HIS 0.006 0.001 HIS D 203 PHE 0.010 0.001 PHE A 324 TYR 0.012 0.001 TYR C 381 ARG 0.004 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 2.239 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: A 184 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8900 (mp) REVERT: C 382 MET cc_start: 0.8858 (mmt) cc_final: 0.8640 (mmt) REVERT: C 387 SER cc_start: 0.9134 (OUTLIER) cc_final: 0.8733 (p) REVERT: D 184 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8708 (mp) outliers start: 29 outliers final: 24 residues processed: 137 average time/residue: 0.5100 time to fit residues: 108.4202 Evaluate side-chains 137 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 163 optimal weight: 0.3980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13968 Z= 0.206 Angle : 0.530 6.788 18972 Z= 0.261 Chirality : 0.042 0.160 2112 Planarity : 0.004 0.037 2432 Dihedral : 8.305 96.591 1914 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.71 % Allowed : 16.19 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.29 (0.21), residues: 1726 helix: 0.49 (0.21), residues: 668 sheet: -1.12 (0.30), residues: 260 loop : -0.31 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 408 HIS 0.005 0.001 HIS D 203 PHE 0.006 0.001 PHE A 324 TYR 0.011 0.001 TYR C 381 ARG 0.002 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 2.091 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: C 278 ILE cc_start: 0.9205 (mm) cc_final: 0.8993 (mt) REVERT: C 382 MET cc_start: 0.8864 (mmt) cc_final: 0.8656 (mmt) REVERT: C 387 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8751 (p) REVERT: D 184 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8709 (mp) outliers start: 25 outliers final: 19 residues processed: 140 average time/residue: 0.5059 time to fit residues: 109.9378 Evaluate side-chains 135 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 113 optimal weight: 0.0670 chunk 171 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 105 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13968 Z= 0.160 Angle : 0.522 6.954 18972 Z= 0.254 Chirality : 0.041 0.161 2112 Planarity : 0.004 0.038 2432 Dihedral : 8.134 94.811 1914 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.43 % Allowed : 16.33 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.04 (0.21), residues: 1726 helix: 0.65 (0.21), residues: 660 sheet: -0.96 (0.30), residues: 260 loop : -0.13 (0.24), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 408 HIS 0.004 0.001 HIS D 203 PHE 0.004 0.001 PHE C 443 TYR 0.017 0.001 TYR B 518 ARG 0.002 0.000 ARG A 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 2.279 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: C 169 MET cc_start: 0.6682 (mtt) cc_final: 0.6168 (ttm) REVERT: C 387 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8784 (p) REVERT: D 184 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8700 (mp) outliers start: 21 outliers final: 18 residues processed: 133 average time/residue: 0.5266 time to fit residues: 106.6908 Evaluate side-chains 133 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.0870 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.107160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.089869 restraints weight = 85322.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.093865 restraints weight = 41199.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096581 restraints weight = 25513.258| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13968 Z= 0.238 Angle : 0.545 7.197 18972 Z= 0.268 Chirality : 0.042 0.159 2112 Planarity : 0.004 0.042 2432 Dihedral : 8.109 91.798 1914 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.50 % Allowed : 16.53 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.15 (0.21), residues: 1726 helix: 0.60 (0.21), residues: 672 sheet: -0.99 (0.30), residues: 260 loop : -0.25 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 408 HIS 0.005 0.001 HIS D 203 PHE 0.007 0.001 PHE D 310 TYR 0.015 0.001 TYR B 518 ARG 0.003 0.000 ARG A 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5063.02 seconds wall clock time: 90 minutes 7.74 seconds (5407.74 seconds total)