Starting phenix.real_space_refine on Tue Feb 13 19:01:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmh_30406/02_2024/7cmh_30406_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmh_30406/02_2024/7cmh_30406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmh_30406/02_2024/7cmh_30406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmh_30406/02_2024/7cmh_30406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmh_30406/02_2024/7cmh_30406_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmh_30406/02_2024/7cmh_30406_updated.pdb" } resolution = 3.4 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 4830 2.51 5 N 1179 2.21 5 O 1330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B ARG 361": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7368 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain: "B" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3480 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 25, 'TRANS': 432} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 126 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3, 111 Unusual residues: {'3PH': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Conformer: "B" Number of residues, atoms: 3, 111 Unusual residues: {'3PH': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} bond proxies already assigned to first conformer: 94 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP B 601 " occ=0.50 ... (28 atoms not shown) pdb=" OXTBTRP B 601 " occ=0.50 Time building chain proxies: 4.66, per 1000 atoms: 0.63 Number of scatterers: 7368 At special positions: 0 Unit cell: (82.916, 84.007, 127.647, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 1330 8.00 N 1179 7.00 C 4830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 154 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.3 seconds 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1702 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 5 sheets defined 49.7% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.584A pdb=" N VAL A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 207 removed outlier: 3.581A pdb=" N TRP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 195 " --> pdb=" O TRP A 191 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.704A pdb=" N LYS A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASP A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 289 through 300 removed outlier: 3.548A pdb=" N SER A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 341 removed outlier: 3.723A pdb=" N ALA A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 4.313A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.585A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.927A pdb=" N GLN A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 removed outlier: 3.701A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.974A pdb=" N GLU A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 533 removed outlier: 3.501A pdb=" N ARG A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN A 530 " --> pdb=" O ARG A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 538 No H-bonds generated for 'chain 'A' and resid 535 through 538' Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'B' and resid 42 through 53 removed outlier: 3.860A pdb=" N GLY B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 72 through 99 removed outlier: 3.657A pdb=" N ILE B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 96 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.734A pdb=" N VAL B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 removed outlier: 3.554A pdb=" N LEU B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 128 " --> pdb=" O TRP B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 146 removed outlier: 3.634A pdb=" N GLN B 135 " --> pdb=" O TYR B 131 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 138 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 removed outlier: 3.628A pdb=" N TRP B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 187 through 209 removed outlier: 3.592A pdb=" N GLN B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 218 No H-bonds generated for 'chain 'B' and resid 215 through 218' Processing helix chain 'B' and resid 231 through 239 removed outlier: 3.850A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 264 through 288 removed outlier: 3.954A pdb=" N ILE B 271 " --> pdb=" O ARG B 267 " (cutoff:3.500A) Proline residue: B 274 - end of helix removed outlier: 3.521A pdb=" N TYR B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 302 through 308 Processing helix chain 'B' and resid 314 through 317 No H-bonds generated for 'chain 'B' and resid 314 through 317' Processing helix chain 'B' and resid 320 through 335 removed outlier: 4.036A pdb=" N SER B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.660A pdb=" N ALA B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 368 No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 370 through 379 removed outlier: 4.049A pdb=" N THR B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B 378 " --> pdb=" O SER B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 411 removed outlier: 4.025A pdb=" N ASN B 389 " --> pdb=" O TYR B 385 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE B 394 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR B 402 " --> pdb=" O PHE B 398 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 403 " --> pdb=" O TYR B 399 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 444 removed outlier: 3.553A pdb=" N VAL B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 457 removed outlier: 3.836A pdb=" N GLY B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 455 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.506A pdb=" N PHE B 464 " --> pdb=" O VAL B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 490 removed outlier: 3.707A pdb=" N ASP B 478 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 479 " --> pdb=" O CYS B 475 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 480 " --> pdb=" O PHE B 476 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 225 through 227 Processing sheet with id= B, first strand: chain 'A' and resid 259 through 262 removed outlier: 7.224A pdb=" N ARG A 304 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A 262 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 306 " --> pdb=" O LEU A 262 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 346 through 349 removed outlier: 6.525A pdb=" N LEU A 400 " --> pdb=" O ALA A 379 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 432 through 434 Processing sheet with id= E, first strand: chain 'A' and resid 541 through 544 removed outlier: 5.988A pdb=" N ARG A 626 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU A 596 " --> pdb=" O ARG A 626 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 610 " --> pdb=" O ALA A 594 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 705 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: 1.85 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2161 1.34 - 1.45: 1262 1.45 - 1.57: 4079 1.57 - 1.69: 2 1.69 - 1.81: 41 Bond restraints: 7545 Sorted by residual: bond pdb=" C31 3PH B 603 " pdb=" O31 3PH B 603 " ideal model delta sigma weight residual 1.325 1.452 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C21 3PH B 603 " pdb=" O21 3PH B 603 " ideal model delta sigma weight residual 1.328 1.455 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C31 3PH B 602 " pdb=" O31 3PH B 602 " ideal model delta sigma weight residual 1.325 1.451 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C21 3PH B 602 " pdb=" O21 3PH B 602 " ideal model delta sigma weight residual 1.328 1.452 -0.124 2.00e-02 2.50e+03 3.81e+01 bond pdb=" O11 3PH B 602 " pdb=" P 3PH B 602 " ideal model delta sigma weight residual 1.703 1.608 0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 7540 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.68: 237 106.68 - 113.62: 4236 113.62 - 120.56: 3101 120.56 - 127.50: 2591 127.50 - 134.44: 94 Bond angle restraints: 10259 Sorted by residual: angle pdb=" C GLY A 175 " pdb=" N SER A 176 " pdb=" CA SER A 176 " ideal model delta sigma weight residual 122.83 129.01 -6.18 1.08e+00 8.57e-01 3.28e+01 angle pdb=" N ASN B 176 " pdb=" CA ASN B 176 " pdb=" C ASN B 176 " ideal model delta sigma weight residual 111.28 116.28 -5.00 1.09e+00 8.42e-01 2.10e+01 angle pdb=" N SER B 61 " pdb=" CA SER B 61 " pdb=" C SER B 61 " ideal model delta sigma weight residual 113.25 118.96 -5.71 1.30e+00 5.92e-01 1.93e+01 angle pdb=" N SER B 178 " pdb=" CA SER B 178 " pdb=" C SER B 178 " ideal model delta sigma weight residual 110.28 116.55 -6.27 1.48e+00 4.57e-01 1.80e+01 angle pdb=" CA SER A 176 " pdb=" C SER A 176 " pdb=" N PRO A 177 " ideal model delta sigma weight residual 118.09 121.55 -3.46 8.20e-01 1.49e+00 1.78e+01 ... (remaining 10254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 4137 21.77 - 43.54: 342 43.54 - 65.31: 42 65.31 - 87.09: 12 87.09 - 108.86: 8 Dihedral angle restraints: 4541 sinusoidal: 1887 harmonic: 2654 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 154 " pdb=" CB CYS B 154 " ideal model delta sinusoidal sigma weight residual -86.00 -37.22 -48.78 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CA SER A 176 " pdb=" C SER A 176 " pdb=" N PRO A 177 " pdb=" CA PRO A 177 " ideal model delta harmonic sigma weight residual 180.00 153.48 26.52 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA THR B 381 " pdb=" C THR B 381 " pdb=" N SER B 382 " pdb=" CA SER B 382 " ideal model delta harmonic sigma weight residual 180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 4538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1088 0.089 - 0.178: 103 0.178 - 0.267: 8 0.267 - 0.356: 1 0.356 - 0.445: 1 Chirality restraints: 1201 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" CB VAL B 492 " pdb=" CA VAL B 492 " pdb=" CG1 VAL B 492 " pdb=" CG2 VAL B 492 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 425 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1198 not shown) Planarity restraints: 1265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 228 " -0.054 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO B 229 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 131 " -0.041 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO B 132 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 460 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.69e+00 pdb=" N PRO B 461 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 461 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 461 " -0.034 5.00e-02 4.00e+02 ... (remaining 1262 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1087 2.75 - 3.29: 6706 3.29 - 3.83: 11675 3.83 - 4.36: 14043 4.36 - 4.90: 23689 Nonbonded interactions: 57200 Sorted by model distance: nonbonded pdb=" O PHE B 243 " pdb=" CE3ATRP B 601 " model vdw 2.214 3.340 nonbonded pdb=" OD1 ASN B 134 " pdb=" N ATRP B 601 " model vdw 2.224 2.520 nonbonded pdb=" O PHE B 59 " pdb=" OH TYR B 145 " model vdw 2.251 2.440 nonbonded pdb=" O VAL B 129 " pdb=" OG1 THR B 133 " model vdw 2.257 2.440 nonbonded pdb=" O PHE B 243 " pdb=" N BTRP B 601 " model vdw 2.279 2.520 ... (remaining 57195 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.890 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.360 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 0.127 7545 Z= 0.398 Angle : 1.060 10.434 10259 Z= 0.558 Chirality : 0.056 0.445 1201 Planarity : 0.007 0.081 1261 Dihedral : 16.328 108.858 2836 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.56 % Favored : 90.68 % Rotamer: Outliers : 1.18 % Allowed : 10.08 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.98 (0.17), residues: 923 helix: -4.53 (0.10), residues: 463 sheet: -1.57 (0.58), residues: 70 loop : -3.54 (0.22), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 124 HIS 0.006 0.002 HIS B 358 PHE 0.018 0.002 PHE B 335 TYR 0.034 0.002 TYR B 145 ARG 0.004 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 191 time to evaluate : 0.972 Fit side-chains REVERT: A 192 LEU cc_start: 0.8554 (tp) cc_final: 0.8234 (tp) REVERT: A 383 SER cc_start: 0.8874 (m) cc_final: 0.8385 (m) REVERT: A 430 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.8128 (mtm180) REVERT: B 204 MET cc_start: 0.8038 (mmt) cc_final: 0.7653 (mmm) REVERT: B 257 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.5925 (tm-30) REVERT: B 263 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8102 (ptpp) REVERT: B 443 TRP cc_start: 0.5862 (t-100) cc_final: 0.5494 (t60) REVERT: B 479 PHE cc_start: 0.7763 (t80) cc_final: 0.7519 (t80) outliers start: 9 outliers final: 2 residues processed: 197 average time/residue: 0.2009 time to fit residues: 52.7588 Evaluate side-chains 143 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 363 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN A 296 GLN A 317 ASN A 353 ASN A 388 GLN A 560 GLN A 601 GLN A 620 HIS B 284 ASN B 331 ASN B 349 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7545 Z= 0.204 Angle : 0.684 10.086 10259 Z= 0.337 Chirality : 0.044 0.296 1201 Planarity : 0.006 0.064 1261 Dihedral : 11.865 94.654 1253 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.48 % Favored : 92.42 % Rotamer: Outliers : 2.62 % Allowed : 18.06 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.22), residues: 923 helix: -2.72 (0.18), residues: 481 sheet: -0.54 (0.67), residues: 57 loop : -3.02 (0.25), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 124 HIS 0.003 0.001 HIS B 471 PHE 0.011 0.001 PHE A 445 TYR 0.013 0.001 TYR B 495 ARG 0.006 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 0.900 Fit side-chains REVERT: A 192 LEU cc_start: 0.8547 (tp) cc_final: 0.8243 (tp) REVERT: A 451 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9088 (tt) REVERT: B 111 LYS cc_start: 0.8092 (tptm) cc_final: 0.7459 (ttpp) REVERT: B 257 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.5489 (tm-30) REVERT: B 263 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8073 (ptpp) REVERT: B 443 TRP cc_start: 0.5704 (t-100) cc_final: 0.5285 (t60) REVERT: B 469 TRP cc_start: 0.5684 (t-100) cc_final: 0.5052 (t-100) outliers start: 19 outliers final: 8 residues processed: 159 average time/residue: 0.1819 time to fit residues: 39.5009 Evaluate side-chains 141 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 490 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 68 optimal weight: 0.0370 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 89 optimal weight: 0.0670 chunk 73 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN B 208 GLN B 284 ASN B 349 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 7545 Z= 0.159 Angle : 0.605 9.243 10259 Z= 0.293 Chirality : 0.042 0.280 1201 Planarity : 0.004 0.054 1261 Dihedral : 10.603 84.448 1250 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.26 % Favored : 92.63 % Rotamer: Outliers : 3.93 % Allowed : 18.85 % Favored : 77.23 % 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: -2.92 (0.25), residues: 923 helix: -1.58 (0.22), residues: 476 sheet: -0.48 (0.69), residues: 57 loop : -2.55 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 124 HIS 0.002 0.001 HIS B 358 PHE 0.011 0.001 PHE A 627 TYR 0.009 0.001 TYR A 554 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 0.749 Fit side-chains REVERT: A 183 ARG cc_start: 0.8156 (ttm110) cc_final: 0.7060 (mtm110) REVERT: A 451 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9068 (tt) REVERT: A 595 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7784 (p0) REVERT: B 111 LYS cc_start: 0.8119 (tptm) cc_final: 0.7483 (ttpp) REVERT: B 263 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7914 (ptpp) REVERT: B 469 TRP cc_start: 0.5685 (t-100) cc_final: 0.4983 (t-100) outliers start: 29 outliers final: 17 residues processed: 157 average time/residue: 0.1767 time to fit residues: 38.0762 Evaluate side-chains 148 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 490 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.0770 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7545 Z= 0.162 Angle : 0.597 8.785 10259 Z= 0.286 Chirality : 0.042 0.273 1201 Planarity : 0.004 0.050 1261 Dihedral : 9.648 73.804 1247 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.61 % Favored : 93.28 % Rotamer: Outliers : 5.10 % Allowed : 20.03 % Favored : 74.87 % 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: -2.35 (0.26), residues: 923 helix: -1.02 (0.23), residues: 473 sheet: -0.40 (0.68), residues: 57 loop : -2.36 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 124 HIS 0.003 0.001 HIS B 471 PHE 0.021 0.001 PHE A 346 TYR 0.009 0.001 TYR A 554 ARG 0.003 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 139 time to evaluate : 0.802 Fit side-chains REVERT: A 179 TRP cc_start: 0.7894 (m100) cc_final: 0.7553 (m100) REVERT: A 183 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7156 (mtm110) REVERT: A 249 LEU cc_start: 0.8923 (mm) cc_final: 0.8712 (mp) REVERT: A 344 ASP cc_start: 0.7521 (t70) cc_final: 0.7058 (t0) REVERT: A 451 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9046 (tt) REVERT: B 111 LYS cc_start: 0.8136 (tptm) cc_final: 0.7498 (ttpp) REVERT: B 263 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7850 (ptpp) REVERT: B 469 TRP cc_start: 0.5418 (t-100) cc_final: 0.4797 (t-100) outliers start: 38 outliers final: 23 residues processed: 162 average time/residue: 0.1746 time to fit residues: 39.1172 Evaluate side-chains 164 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 490 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 530 GLN B 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7545 Z= 0.208 Angle : 0.609 8.931 10259 Z= 0.292 Chirality : 0.043 0.249 1201 Planarity : 0.004 0.050 1261 Dihedral : 8.929 63.065 1247 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.15 % Favored : 92.74 % Rotamer: Outliers : 5.50 % Allowed : 20.68 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.27), residues: 923 helix: -0.63 (0.24), residues: 473 sheet: -0.35 (0.68), residues: 57 loop : -2.21 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 124 HIS 0.004 0.001 HIS B 471 PHE 0.017 0.001 PHE A 346 TYR 0.011 0.001 TYR B 495 ARG 0.007 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 143 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 179 TRP cc_start: 0.7919 (m100) cc_final: 0.7607 (m100) REVERT: A 183 ARG cc_start: 0.8236 (ttm110) cc_final: 0.7301 (mtm110) REVERT: A 344 ASP cc_start: 0.7571 (t70) cc_final: 0.7063 (t0) REVERT: A 451 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9035 (tt) REVERT: A 595 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7787 (p0) REVERT: B 263 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7825 (ptpp) REVERT: B 469 TRP cc_start: 0.5480 (t-100) cc_final: 0.4802 (t-100) outliers start: 42 outliers final: 23 residues processed: 166 average time/residue: 0.1687 time to fit residues: 38.6960 Evaluate side-chains 162 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 490 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 0.0170 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 601 GLN B 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7545 Z= 0.164 Angle : 0.599 9.271 10259 Z= 0.283 Chirality : 0.042 0.251 1201 Planarity : 0.004 0.049 1261 Dihedral : 8.244 62.590 1247 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.93 % Favored : 92.96 % Rotamer: Outliers : 5.10 % Allowed : 21.86 % Favored : 73.04 % 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: -1.60 (0.27), residues: 923 helix: -0.30 (0.24), residues: 475 sheet: -0.40 (0.68), residues: 57 loop : -2.10 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 124 HIS 0.003 0.001 HIS A 620 PHE 0.025 0.001 PHE A 346 TYR 0.009 0.001 TYR B 495 ARG 0.006 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 179 TRP cc_start: 0.7942 (m100) cc_final: 0.7631 (m100) REVERT: A 183 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7352 (mtm110) REVERT: A 210 ARG cc_start: 0.4870 (mmt180) cc_final: 0.4196 (mmt90) REVERT: A 344 ASP cc_start: 0.7555 (t70) cc_final: 0.7062 (t0) REVERT: A 451 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9041 (tt) REVERT: A 595 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7778 (p0) REVERT: B 111 LYS cc_start: 0.8076 (tptm) cc_final: 0.7493 (ttpp) REVERT: B 263 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7520 (tttt) REVERT: B 469 TRP cc_start: 0.5403 (t-100) cc_final: 0.4746 (t-100) outliers start: 39 outliers final: 24 residues processed: 170 average time/residue: 0.1482 time to fit residues: 34.9136 Evaluate side-chains 165 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 49 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 54 optimal weight: 0.0870 chunk 53 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 601 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7545 Z= 0.147 Angle : 0.590 9.003 10259 Z= 0.279 Chirality : 0.042 0.269 1201 Planarity : 0.004 0.049 1261 Dihedral : 7.860 62.050 1247 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.72 % Favored : 93.17 % Rotamer: Outliers : 5.10 % Allowed : 22.64 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.28), residues: 923 helix: -0.09 (0.24), residues: 474 sheet: -0.50 (0.67), residues: 52 loop : -2.02 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 124 HIS 0.002 0.000 HIS B 358 PHE 0.009 0.001 PHE B 306 TYR 0.008 0.001 TYR A 313 ARG 0.007 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 TRP cc_start: 0.7887 (m100) cc_final: 0.7601 (m100) REVERT: A 183 ARG cc_start: 0.8202 (ttm110) cc_final: 0.7338 (mtm110) REVERT: A 210 ARG cc_start: 0.4850 (mmt180) cc_final: 0.4153 (mmt90) REVERT: A 344 ASP cc_start: 0.7490 (t70) cc_final: 0.7040 (t0) REVERT: A 451 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9006 (tt) REVERT: A 595 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7771 (p0) REVERT: B 263 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7477 (tttt) REVERT: B 458 THR cc_start: 0.8925 (p) cc_final: 0.8631 (t) outliers start: 39 outliers final: 27 residues processed: 167 average time/residue: 0.1734 time to fit residues: 40.1889 Evaluate side-chains 169 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 0.0670 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7545 Z= 0.168 Angle : 0.592 9.470 10259 Z= 0.280 Chirality : 0.042 0.307 1201 Planarity : 0.004 0.067 1261 Dihedral : 7.581 62.267 1247 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.37 % Favored : 92.52 % Rotamer: Outliers : 4.45 % Allowed : 23.56 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.28), residues: 923 helix: 0.03 (0.25), residues: 485 sheet: -0.44 (0.68), residues: 52 loop : -2.01 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 124 HIS 0.003 0.001 HIS B 471 PHE 0.009 0.001 PHE A 542 TYR 0.009 0.001 TYR A 313 ARG 0.007 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7319 (mtm110) REVERT: A 210 ARG cc_start: 0.4751 (mmt180) cc_final: 0.4155 (mmt90) REVERT: A 344 ASP cc_start: 0.7638 (t70) cc_final: 0.7121 (t0) REVERT: A 451 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8989 (tt) REVERT: A 595 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7765 (p0) REVERT: B 263 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7494 (tttt) REVERT: B 406 GLN cc_start: 0.9241 (tm-30) cc_final: 0.8930 (tm-30) REVERT: B 458 THR cc_start: 0.8933 (p) cc_final: 0.8645 (t) outliers start: 34 outliers final: 24 residues processed: 167 average time/residue: 0.1655 time to fit residues: 38.7378 Evaluate side-chains 168 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7545 Z= 0.187 Angle : 0.603 9.685 10259 Z= 0.285 Chirality : 0.043 0.326 1201 Planarity : 0.004 0.064 1261 Dihedral : 7.436 62.902 1247 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.85 % Rotamer: Outliers : 4.19 % Allowed : 24.48 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.28), residues: 923 helix: 0.16 (0.25), residues: 485 sheet: -0.36 (0.69), residues: 52 loop : -1.96 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 124 HIS 0.003 0.001 HIS B 471 PHE 0.014 0.001 PHE A 346 TYR 0.008 0.001 TYR A 554 ARG 0.007 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 TRP cc_start: 0.7784 (m100) cc_final: 0.7419 (m100) REVERT: A 183 ARG cc_start: 0.8203 (ttm110) cc_final: 0.7359 (mtm110) REVERT: A 188 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8236 (mm) REVERT: A 210 ARG cc_start: 0.4822 (mmt180) cc_final: 0.4240 (mmt90) REVERT: A 344 ASP cc_start: 0.7483 (t70) cc_final: 0.6976 (t0) REVERT: A 451 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8998 (tt) REVERT: A 595 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7780 (p0) REVERT: B 263 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7508 (tttt) REVERT: B 406 GLN cc_start: 0.9238 (tm-30) cc_final: 0.8942 (tm-30) REVERT: B 458 THR cc_start: 0.8977 (p) cc_final: 0.8696 (t) outliers start: 32 outliers final: 25 residues processed: 163 average time/residue: 0.1721 time to fit residues: 38.7923 Evaluate side-chains 172 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 480 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 chunk 57 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7545 Z= 0.149 Angle : 0.588 9.142 10259 Z= 0.278 Chirality : 0.042 0.332 1201 Planarity : 0.004 0.053 1261 Dihedral : 7.267 62.975 1247 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.83 % Favored : 93.07 % Rotamer: Outliers : 3.53 % Allowed : 24.87 % Favored : 71.60 % 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: -0.94 (0.29), residues: 923 helix: 0.31 (0.25), residues: 488 sheet: -0.27 (0.69), residues: 52 loop : -1.90 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 124 HIS 0.002 0.001 HIS B 471 PHE 0.011 0.001 PHE A 346 TYR 0.009 0.001 TYR A 313 ARG 0.007 0.000 ARG A 440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: 0.8443 (mm) cc_final: 0.8240 (mm) REVERT: A 210 ARG cc_start: 0.4440 (mmt180) cc_final: 0.3978 (mmt90) REVERT: A 344 ASP cc_start: 0.7505 (t70) cc_final: 0.7015 (t0) REVERT: A 451 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8966 (tt) REVERT: A 595 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7738 (p0) REVERT: B 406 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8905 (tm-30) REVERT: B 458 THR cc_start: 0.8931 (p) cc_final: 0.8666 (t) outliers start: 27 outliers final: 20 residues processed: 164 average time/residue: 0.1724 time to fit residues: 39.1765 Evaluate side-chains 160 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 52 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: A 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.108222 restraints weight = 11821.718| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.82 r_work: 0.3163 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7545 Z= 0.181 Angle : 0.598 9.360 10259 Z= 0.285 Chirality : 0.043 0.343 1201 Planarity : 0.004 0.055 1261 Dihedral : 7.147 63.130 1243 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.26 % Favored : 92.63 % Rotamer: Outliers : 3.53 % Allowed : 25.13 % Favored : 71.34 % 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: -0.87 (0.29), residues: 923 helix: 0.36 (0.25), residues: 489 sheet: -0.28 (0.69), residues: 52 loop : -1.87 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 124 HIS 0.003 0.001 HIS B 471 PHE 0.010 0.001 PHE A 542 TYR 0.009 0.001 TYR A 313 ARG 0.007 0.001 ARG A 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1940.88 seconds wall clock time: 35 minutes 53.18 seconds (2153.18 seconds total)