Starting phenix.real_space_refine on Tue Feb 13 19:53:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsk_30835/02_2024/7dsk_30835_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsk_30835/02_2024/7dsk_30835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsk_30835/02_2024/7dsk_30835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsk_30835/02_2024/7dsk_30835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsk_30835/02_2024/7dsk_30835_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsk_30835/02_2024/7dsk_30835_neut.pdb" } resolution = 2.9 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= 0.003 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 1 5.49 5 S 27 5.16 5 C 4936 2.51 5 N 1191 2.21 5 O 1369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 348": "NH1" <-> "NH2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B ARG 421": "NH1" <-> "NH2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B GLU 506": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7524 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3670 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 22, 'TRANS': 448} Chain: "B" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3586 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 24, 'TRANS': 439} 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: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 108 Unusual residues: {'HNX': 1, 'Y01': 2} Classifications: {'undetermined': 3, 'water': 12} Link IDs: {None: 14} Time building chain proxies: 6.03, per 1000 atoms: 0.80 Number of scatterers: 7524 At special positions: 0 Unit cell: (83.699, 82.612, 125.005, 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 1 15.00 O 1369 8.00 N 1191 7.00 C 4936 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 164 " 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: 3.07 Conformation dependent library (CDL) restraints added in 1.2 seconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 57.4% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 178 through 206 Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.590A pdb=" N THR A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.893A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.546A pdb=" N LYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 342 removed outlier: 3.848A pdb=" N VAL A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 357 through 372 removed outlier: 3.860A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.871A pdb=" N THR A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.565A pdb=" N SER A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.557A pdb=" N PHE A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.604A pdb=" N LEU A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN A 530 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 71 through 80 Processing helix chain 'B' and resid 81 through 110 Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.701A pdb=" N VAL B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 139 through 157 removed outlier: 3.671A pdb=" N SER B 143 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 189 Processing helix chain 'B' and resid 189 through 220 removed outlier: 3.715A pdb=" N ALA B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 243 through 253 removed outlier: 4.074A pdb=" N ALA B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 274 through 298 Proline residue: B 283 - end of helix removed outlier: 3.503A pdb=" N THR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 325 through 356 removed outlier: 3.716A pdb=" N GLY B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 387 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 396 through 422 removed outlier: 3.505A pdb=" N PHE B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N PHE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 451 Processing helix chain 'B' and resid 454 through 466 removed outlier: 4.269A pdb=" N CYS B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 473 removed outlier: 4.171A pdb=" N VAL B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 501 removed outlier: 4.045A pdb=" N GLN B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY B 488 " --> pdb=" O TRP B 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.482A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLY A 380 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 348 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 removed outlier: 3.676A pdb=" N LYS A 267 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.766A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA5, first strand: chain 'B' and resid 365 through 366 376 hydrogen bonds defined for protein. 1083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1170 1.31 - 1.43: 2057 1.43 - 1.56: 4410 1.56 - 1.68: 23 1.68 - 1.81: 41 Bond restraints: 7701 Sorted by residual: bond pdb=" CAI Y01 B 603 " pdb=" CAZ Y01 B 603 " ideal model delta sigma weight residual 1.332 1.557 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" CAI Y01 B 602 " pdb=" CAZ Y01 B 602 " ideal model delta sigma weight residual 1.332 1.548 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C02 HNX B 601 " pdb=" C07 HNX B 601 " ideal model delta sigma weight residual 1.507 1.707 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C09 HNX B 601 " pdb=" C10 HNX B 601 " ideal model delta sigma weight residual 1.523 1.323 0.200 2.00e-02 2.50e+03 9.97e+01 bond pdb=" C18 HNX B 601 " pdb=" C19 HNX B 601 " ideal model delta sigma weight residual 1.411 1.564 -0.153 2.00e-02 2.50e+03 5.87e+01 ... (remaining 7696 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.51: 243 106.51 - 113.43: 4300 113.43 - 120.35: 2947 120.35 - 127.27: 2894 127.27 - 134.19: 104 Bond angle restraints: 10488 Sorted by residual: angle pdb=" C PRO A 209 " pdb=" N ARG A 210 " pdb=" CA ARG A 210 " ideal model delta sigma weight residual 121.54 133.29 -11.75 1.91e+00 2.74e-01 3.79e+01 angle pdb=" N THR B 71 " pdb=" CA THR B 71 " pdb=" C THR B 71 " ideal model delta sigma weight residual 109.81 121.90 -12.09 2.21e+00 2.05e-01 2.99e+01 angle pdb=" C08 HNX B 601 " pdb=" C09 HNX B 601 " pdb=" C10 HNX B 601 " ideal model delta sigma weight residual 111.98 126.75 -14.77 3.00e+00 1.11e-01 2.42e+01 angle pdb=" N THR B 299 " pdb=" CA THR B 299 " pdb=" C THR B 299 " ideal model delta sigma weight residual 114.62 109.03 5.59 1.14e+00 7.69e-01 2.40e+01 angle pdb=" C VAL B 322 " pdb=" N MET B 323 " pdb=" CA MET B 323 " ideal model delta sigma weight residual 122.74 129.75 -7.01 1.44e+00 4.82e-01 2.37e+01 ... (remaining 10483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 4514 33.93 - 67.86: 141 67.86 - 101.79: 34 101.79 - 135.72: 33 135.72 - 169.66: 11 Dihedral angle restraints: 4733 sinusoidal: 2053 harmonic: 2680 Sorted by residual: dihedral pdb=" CA LEU B 137 " pdb=" C LEU B 137 " pdb=" N LEU B 138 " pdb=" CA LEU B 138 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA PRO A 209 " pdb=" C PRO A 209 " pdb=" N ARG A 210 " pdb=" CA ARG A 210 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CAD Y01 B 603 " pdb=" CAZ Y01 B 603 " pdb=" CBH Y01 B 603 " pdb=" CAV Y01 B 603 " ideal model delta sinusoidal sigma weight residual 288.69 119.03 169.66 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.191: 1223 1.191 - 2.381: 0 2.381 - 3.572: 0 3.572 - 4.763: 0 4.763 - 5.954: 10 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CBI Y01 B 602 " pdb=" CAU Y01 B 602 " pdb=" CBE Y01 B 602 " pdb=" CBG Y01 B 602 " both_signs ideal model delta sigma weight residual False 2.94 -3.02 5.95 2.00e-01 2.50e+01 8.86e+02 chirality pdb=" CBI Y01 B 603 " pdb=" CAU Y01 B 603 " pdb=" CBE Y01 B 603 " pdb=" CBG Y01 B 603 " both_signs ideal model delta sigma weight residual False 2.94 -2.96 5.90 2.00e-01 2.50e+01 8.71e+02 chirality pdb=" CBH Y01 B 602 " pdb=" CAT Y01 B 602 " pdb=" CAZ Y01 B 602 " pdb=" CBF Y01 B 602 " both_signs ideal model delta sigma weight residual False -2.85 2.64 -5.49 2.00e-01 2.50e+01 7.55e+02 ... (remaining 1230 not shown) Planarity restraints: 1285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 137 " 0.020 2.00e-02 2.50e+03 4.01e-02 1.60e+01 pdb=" C LEU B 137 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU B 137 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU B 138 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 282 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO B 283 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 283 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 283 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 469 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO B 470 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.034 5.00e-02 4.00e+02 ... (remaining 1282 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 57 2.56 - 3.14: 5470 3.14 - 3.73: 11392 3.73 - 4.31: 15995 4.31 - 4.90: 26576 Nonbonded interactions: 59490 Sorted by model distance: nonbonded pdb=" OE1 GLU B 506 " pdb=" N THR B 507 " model vdw 1.969 2.520 nonbonded pdb=" O GLY B 67 " pdb=" OG1 THR B 71 " model vdw 2.279 2.440 nonbonded pdb=" O ASP A 325 " pdb=" OG1 THR A 329 " model vdw 2.291 2.440 nonbonded pdb=" O TYR A 251 " pdb=" OG SER A 254 " model vdw 2.300 2.440 nonbonded pdb=" O ILE B 139 " pdb=" OG SER B 143 " model vdw 2.309 2.440 ... (remaining 59485 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.940 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.670 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.011 0.225 7701 Z= 0.663 Angle : 1.122 14.771 10488 Z= 0.580 Chirality : 0.490 5.954 1233 Planarity : 0.007 0.071 1281 Dihedral : 23.271 169.655 3008 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.16 % Favored : 91.30 % Rotamer: Outliers : 0.63 % Allowed : 5.45 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.22), residues: 931 helix: -1.97 (0.18), residues: 485 sheet: -1.34 (0.61), residues: 65 loop : -2.73 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 220 HIS 0.004 0.001 HIS B 367 PHE 0.017 0.002 PHE A 627 TYR 0.014 0.002 TYR B 387 ARG 0.002 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8282 (pttm) cc_final: 0.7927 (mtmt) REVERT: B 77 LYS cc_start: 0.8421 (tppt) cc_final: 0.7895 (mmtm) REVERT: B 81 SER cc_start: 0.8881 (p) cc_final: 0.8660 (p) REVERT: B 238 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5821 (pt) REVERT: B 365 MET cc_start: 0.8943 (mtt) cc_final: 0.8591 (mtt) outliers start: 5 outliers final: 4 residues processed: 122 average time/residue: 0.9821 time to fit residues: 128.2545 Evaluate side-chains 79 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 506 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 340 GLN A 353 ASN A 539 HIS A 557 HIS A 580 GLN B 273 ASN B 358 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7701 Z= 0.224 Angle : 1.234 32.467 10488 Z= 0.486 Chirality : 0.110 1.867 1233 Planarity : 0.005 0.047 1281 Dihedral : 24.295 177.024 1373 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.73 % Favored : 91.84 % Rotamer: Outliers : 2.66 % Allowed : 12.42 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.26), residues: 931 helix: 0.24 (0.22), residues: 490 sheet: -1.31 (0.58), residues: 71 loop : -2.50 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.002 0.001 HIS A 221 PHE 0.019 0.001 PHE B 462 TYR 0.012 0.001 TYR A 629 ARG 0.005 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.811 Fit side-chains REVERT: A 398 ASP cc_start: 0.7084 (t70) cc_final: 0.6828 (t0) REVERT: B 77 LYS cc_start: 0.8318 (tppt) cc_final: 0.8021 (ttpp) REVERT: B 365 MET cc_start: 0.8894 (mtt) cc_final: 0.8470 (mtt) REVERT: B 415 MET cc_start: 0.8207 (tmm) cc_final: 0.8001 (ttt) REVERT: B 451 PHE cc_start: 0.7765 (m-80) cc_final: 0.7524 (m-10) outliers start: 21 outliers final: 10 residues processed: 91 average time/residue: 0.7525 time to fit residues: 75.2925 Evaluate side-chains 82 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 0.0070 chunk 67 optimal weight: 0.9980 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7701 Z= 0.236 Angle : 1.195 31.110 10488 Z= 0.460 Chirality : 0.111 1.848 1233 Planarity : 0.004 0.039 1281 Dihedral : 23.600 179.763 1364 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.52 % Favored : 92.16 % Rotamer: Outliers : 3.55 % Allowed : 13.43 % Favored : 83.02 % 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: -0.40 (0.28), residues: 931 helix: 1.24 (0.24), residues: 489 sheet: -1.17 (0.58), residues: 71 loop : -2.21 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 220 HIS 0.002 0.001 HIS A 557 PHE 0.011 0.001 PHE B 130 TYR 0.018 0.001 TYR A 629 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 81 time to evaluate : 0.878 Fit side-chains REVERT: A 398 ASP cc_start: 0.7126 (t70) cc_final: 0.6842 (t0) REVERT: B 77 LYS cc_start: 0.8272 (tppt) cc_final: 0.8014 (ttpp) REVERT: B 218 GLN cc_start: 0.7952 (tp40) cc_final: 0.7607 (tm-30) REVERT: B 394 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: B 451 PHE cc_start: 0.7731 (m-80) cc_final: 0.7486 (m-10) outliers start: 28 outliers final: 13 residues processed: 99 average time/residue: 0.7245 time to fit residues: 78.8641 Evaluate side-chains 86 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 480 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7701 Z= 0.186 Angle : 1.172 31.008 10488 Z= 0.446 Chirality : 0.111 1.817 1233 Planarity : 0.004 0.037 1281 Dihedral : 23.290 178.617 1364 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.73 % Favored : 92.16 % Rotamer: Outliers : 3.17 % Allowed : 15.46 % Favored : 81.37 % 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: 0.13 (0.29), residues: 931 helix: 1.66 (0.24), residues: 495 sheet: -0.76 (0.59), residues: 72 loop : -2.05 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 134 HIS 0.002 0.000 HIS B 420 PHE 0.020 0.001 PHE B 462 TYR 0.012 0.001 TYR A 629 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 81 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 300 LYS cc_start: 0.8809 (mttp) cc_final: 0.8584 (ttmm) REVERT: A 398 ASP cc_start: 0.7162 (t70) cc_final: 0.6873 (t0) REVERT: B 77 LYS cc_start: 0.8268 (tppt) cc_final: 0.8025 (ttpp) REVERT: B 218 GLN cc_start: 0.7921 (tp40) cc_final: 0.7582 (tm-30) REVERT: B 394 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.6926 (m-80) REVERT: B 451 PHE cc_start: 0.7703 (m-80) cc_final: 0.7502 (m-10) outliers start: 25 outliers final: 12 residues processed: 99 average time/residue: 0.7860 time to fit residues: 85.3239 Evaluate side-chains 91 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 480 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7701 Z= 0.218 Angle : 1.178 31.236 10488 Z= 0.448 Chirality : 0.110 1.824 1233 Planarity : 0.004 0.038 1281 Dihedral : 23.116 179.143 1364 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.94 % Rotamer: Outliers : 3.42 % Allowed : 16.86 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.29), residues: 931 helix: 1.85 (0.24), residues: 495 sheet: -0.74 (0.58), residues: 72 loop : -1.93 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 367 PHE 0.010 0.001 PHE B 95 TYR 0.012 0.001 TYR A 629 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 75 time to evaluate : 0.929 Fit side-chains REVERT: A 300 LYS cc_start: 0.8818 (mttp) cc_final: 0.8585 (ttmm) REVERT: A 398 ASP cc_start: 0.7241 (t70) cc_final: 0.6943 (t0) REVERT: B 77 LYS cc_start: 0.8287 (tppt) cc_final: 0.8045 (ttpp) REVERT: B 218 GLN cc_start: 0.7914 (tp40) cc_final: 0.7568 (tm-30) REVERT: B 394 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: B 451 PHE cc_start: 0.7698 (m-80) cc_final: 0.7496 (m-10) outliers start: 27 outliers final: 11 residues processed: 93 average time/residue: 0.7387 time to fit residues: 75.7189 Evaluate side-chains 89 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 394 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7701 Z= 0.193 Angle : 1.170 31.066 10488 Z= 0.443 Chirality : 0.110 1.823 1233 Planarity : 0.004 0.038 1281 Dihedral : 22.925 178.831 1364 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.94 % Rotamer: Outliers : 2.92 % Allowed : 17.49 % Favored : 79.59 % 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: 0.50 (0.29), residues: 931 helix: 1.96 (0.24), residues: 495 sheet: -0.66 (0.58), residues: 72 loop : -1.87 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 134 HIS 0.002 0.000 HIS B 367 PHE 0.020 0.001 PHE B 462 TYR 0.011 0.001 TYR A 629 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 0.859 Fit side-chains REVERT: A 300 LYS cc_start: 0.8809 (mttp) cc_final: 0.8582 (ttmm) REVERT: A 398 ASP cc_start: 0.7243 (t70) cc_final: 0.6936 (t0) REVERT: B 77 LYS cc_start: 0.8329 (tppt) cc_final: 0.8091 (ttpp) REVERT: B 218 GLN cc_start: 0.7875 (tp40) cc_final: 0.7564 (tm-30) REVERT: B 394 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.6794 (m-80) outliers start: 23 outliers final: 15 residues processed: 97 average time/residue: 0.7218 time to fit residues: 76.9801 Evaluate side-chains 91 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7701 Z= 0.209 Angle : 1.173 31.179 10488 Z= 0.445 Chirality : 0.110 1.825 1233 Planarity : 0.004 0.040 1281 Dihedral : 22.799 179.046 1364 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.84 % Favored : 92.05 % Rotamer: Outliers : 3.30 % Allowed : 17.36 % Favored : 79.34 % 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: 0.55 (0.29), residues: 931 helix: 1.98 (0.24), residues: 496 sheet: -0.69 (0.57), residues: 72 loop : -1.81 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 134 HIS 0.002 0.001 HIS B 367 PHE 0.011 0.001 PHE B 297 TYR 0.010 0.001 TYR A 629 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 75 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8051 (ptpp) REVERT: A 300 LYS cc_start: 0.8811 (mttp) cc_final: 0.8584 (ttmm) REVERT: B 77 LYS cc_start: 0.8301 (tppt) cc_final: 0.8097 (ttpp) REVERT: B 218 GLN cc_start: 0.7894 (tp40) cc_final: 0.7609 (tm-30) REVERT: B 394 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.6760 (m-80) outliers start: 26 outliers final: 16 residues processed: 92 average time/residue: 0.6996 time to fit residues: 71.1763 Evaluate side-chains 91 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 HIS ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7701 Z= 0.177 Angle : 1.159 31.109 10488 Z= 0.437 Chirality : 0.110 1.832 1233 Planarity : 0.004 0.042 1281 Dihedral : 22.662 179.434 1364 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.73 % Favored : 92.16 % Rotamer: Outliers : 2.92 % Allowed : 17.87 % Favored : 79.21 % 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: 0.66 (0.29), residues: 931 helix: 2.13 (0.24), residues: 491 sheet: -0.66 (0.57), residues: 72 loop : -1.79 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 134 HIS 0.002 0.000 HIS B 367 PHE 0.022 0.001 PHE B 462 TYR 0.009 0.001 TYR A 554 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: B 51 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8114 (t) REVERT: B 218 GLN cc_start: 0.7955 (tp40) cc_final: 0.7581 (tm-30) REVERT: B 394 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.6685 (m-80) outliers start: 23 outliers final: 13 residues processed: 94 average time/residue: 0.7544 time to fit residues: 77.9256 Evaluate side-chains 86 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7701 Z= 0.179 Angle : 1.163 31.097 10488 Z= 0.440 Chirality : 0.110 1.832 1233 Planarity : 0.004 0.042 1281 Dihedral : 22.581 179.651 1364 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.84 % Favored : 92.05 % Rotamer: Outliers : 2.41 % Allowed : 19.26 % Favored : 78.33 % 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: 0.71 (0.29), residues: 931 helix: 2.18 (0.24), residues: 490 sheet: -0.60 (0.57), residues: 72 loop : -1.78 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 134 HIS 0.002 0.001 HIS B 367 PHE 0.017 0.001 PHE B 330 TYR 0.009 0.001 TYR A 226 ARG 0.002 0.000 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7709 (ptpp) REVERT: B 218 GLN cc_start: 0.7965 (tp40) cc_final: 0.7606 (tm-30) REVERT: B 394 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.6664 (m-80) outliers start: 19 outliers final: 13 residues processed: 91 average time/residue: 0.6705 time to fit residues: 67.9647 Evaluate side-chains 88 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 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 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7701 Z= 0.273 Angle : 1.197 31.377 10488 Z= 0.463 Chirality : 0.111 1.813 1233 Planarity : 0.004 0.044 1281 Dihedral : 22.564 179.668 1364 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.70 % Favored : 91.19 % Rotamer: Outliers : 1.77 % Allowed : 20.03 % Favored : 78.20 % 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: 0.56 (0.29), residues: 931 helix: 2.06 (0.24), residues: 490 sheet: -0.58 (0.57), residues: 72 loop : -1.88 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.002 0.001 HIS A 221 PHE 0.021 0.001 PHE B 462 TYR 0.014 0.001 TYR A 554 ARG 0.002 0.000 ARG B 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: B 218 GLN cc_start: 0.8031 (tp40) cc_final: 0.7668 (tm-30) REVERT: B 394 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.6698 (m-80) outliers start: 14 outliers final: 13 residues processed: 86 average time/residue: 0.6972 time to fit residues: 66.2196 Evaluate side-chains 86 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.082421 restraints weight = 12723.455| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.92 r_work: 0.2869 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7701 Z= 0.248 Angle : 1.185 31.363 10488 Z= 0.456 Chirality : 0.111 1.813 1233 Planarity : 0.004 0.043 1281 Dihedral : 22.524 179.257 1364 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.16 % Favored : 91.73 % Rotamer: Outliers : 2.15 % Allowed : 20.03 % Favored : 77.82 % 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: 0.64 (0.29), residues: 931 helix: 2.12 (0.24), residues: 489 sheet: -0.54 (0.57), residues: 72 loop : -1.82 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 319 PHE 0.012 0.001 PHE B 330 TYR 0.011 0.001 TYR A 554 ARG 0.002 0.000 ARG A 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2251.26 seconds wall clock time: 41 minutes 8.97 seconds (2468.97 seconds total)