Starting phenix.real_space_refine on Sun Mar 10 22:44:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sde_23517/03_2024/7sde_23517_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sde_23517/03_2024/7sde_23517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sde_23517/03_2024/7sde_23517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sde_23517/03_2024/7sde_23517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sde_23517/03_2024/7sde_23517_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sde_23517/03_2024/7sde_23517_neut.pdb" } resolution = 3.2 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 3748 2.51 5 N 943 2.21 5 O 1011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5734 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3856 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 3 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 232} Chain breaks: 5 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 3.62, per 1000 atoms: 0.63 Number of scatterers: 5734 At special positions: 0 Unit cell: (68.096, 80.864, 105.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1011 8.00 N 943 7.00 C 3748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.1 seconds 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1414 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 61.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 25 through 41 removed outlier: 3.660A pdb=" N LEU A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.793A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.971A pdb=" N VAL A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 removed outlier: 4.030A pdb=" N LEU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 126 through 140 removed outlier: 3.775A pdb=" N ALA A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 229 through 239 removed outlier: 3.502A pdb=" N ILE A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 261 removed outlier: 3.920A pdb=" N CYS A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 292 through 302 removed outlier: 4.036A pdb=" N SER A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 363 removed outlier: 4.481A pdb=" N LEU A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 362 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.936A pdb=" N PHE A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.565A pdb=" N THR A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 442 removed outlier: 3.918A pdb=" N LEU A 442 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.540A pdb=" N PHE A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 removed outlier: 3.950A pdb=" N LEU A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 496 removed outlier: 4.087A pdb=" N ILE A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 518 Processing helix chain 'A' and resid 518 through 529 removed outlier: 4.073A pdb=" N ARG A 522 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 529 " --> pdb=" O TRP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 547 removed outlier: 3.505A pdb=" N GLN A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.513A pdb=" N MET B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 317 removed outlier: 3.541A pdb=" N ARG B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 354 through 366 removed outlier: 4.065A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 removed outlier: 3.663A pdb=" N ARG B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 404 through 416 Processing helix chain 'B' and resid 432 through 441 removed outlier: 3.753A pdb=" N CYS B 436 " --> pdb=" O TYR B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 462 removed outlier: 4.018A pdb=" N LEU B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 738 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: 1.45 Time building geometry restraints manager: 2.41 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: 1785 1.34 - 1.46: 1133 1.46 - 1.58: 2893 1.58 - 1.70: 0 1.70 - 1.82: 45 Bond restraints: 5856 Sorted by residual: bond pdb=" CA GLU A 193 " pdb=" C GLU A 193 " ideal model delta sigma weight residual 1.524 1.556 -0.032 1.24e-02 6.50e+03 6.64e+00 bond pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.25e-02 6.40e+03 3.33e+00 bond pdb=" N TYR A 20 " pdb=" CA TYR A 20 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.31e+00 bond pdb=" C MET A 241 " pdb=" O MET A 241 " ideal model delta sigma weight residual 1.244 1.226 0.018 1.00e-02 1.00e+04 3.15e+00 bond pdb=" CA ALA B 323 " pdb=" C ALA B 323 " ideal model delta sigma weight residual 1.530 1.511 0.020 1.23e-02 6.61e+03 2.58e+00 ... (remaining 5851 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.90: 147 106.90 - 113.71: 3198 113.71 - 120.53: 2246 120.53 - 127.34: 2288 127.34 - 134.16: 41 Bond angle restraints: 7920 Sorted by residual: angle pdb=" N LYS A 146 " pdb=" CA LYS A 146 " pdb=" C LYS A 146 " ideal model delta sigma weight residual 110.24 123.45 -13.21 1.47e+00 4.63e-01 8.07e+01 angle pdb=" N GLN A 194 " pdb=" CA GLN A 194 " pdb=" C GLN A 194 " ideal model delta sigma weight residual 112.57 119.12 -6.55 1.13e+00 7.83e-01 3.36e+01 angle pdb=" N ARG A 364 " pdb=" CA ARG A 364 " pdb=" C ARG A 364 " ideal model delta sigma weight residual 113.12 106.11 7.01 1.25e+00 6.40e-01 3.15e+01 angle pdb=" C ASP A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta sigma weight residual 119.24 124.34 -5.10 1.04e+00 9.25e-01 2.40e+01 angle pdb=" N LYS A 146 " pdb=" CA LYS A 146 " pdb=" CB LYS A 146 " ideal model delta sigma weight residual 109.48 102.06 7.42 1.55e+00 4.16e-01 2.29e+01 ... (remaining 7915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3072 17.64 - 35.28: 307 35.28 - 52.92: 102 52.92 - 70.56: 28 70.56 - 88.20: 7 Dihedral angle restraints: 3516 sinusoidal: 1356 harmonic: 2160 Sorted by residual: dihedral pdb=" N TYR A 20 " pdb=" C TYR A 20 " pdb=" CA TYR A 20 " pdb=" CB TYR A 20 " ideal model delta harmonic sigma weight residual 122.80 135.03 -12.23 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" C TYR A 20 " pdb=" N TYR A 20 " pdb=" CA TYR A 20 " pdb=" CB TYR A 20 " ideal model delta harmonic sigma weight residual -122.60 -134.70 12.10 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" CA GLU B 398 " pdb=" C GLU B 398 " pdb=" N PHE B 399 " pdb=" CA PHE B 399 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 3513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 847 0.098 - 0.195: 52 0.195 - 0.293: 9 0.293 - 0.390: 2 0.390 - 0.488: 1 Chirality restraints: 911 Sorted by residual: chirality pdb=" CA TYR A 20 " pdb=" N TYR A 20 " pdb=" C TYR A 20 " pdb=" CB TYR A 20 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CA ILE A 435 " pdb=" N ILE A 435 " pdb=" C ILE A 435 " pdb=" CB ILE A 435 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA TRP A 240 " pdb=" N TRP A 240 " pdb=" C TRP A 240 " pdb=" CB TRP A 240 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 908 not shown) Planarity restraints: 993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 279 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C SER A 279 " 0.040 2.00e-02 2.50e+03 pdb=" O SER A 279 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO A 280 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 193 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C GLU A 193 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU A 193 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 194 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 411 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C SER A 411 " 0.029 2.00e-02 2.50e+03 pdb=" O SER A 411 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 412 " -0.010 2.00e-02 2.50e+03 ... (remaining 990 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 591 2.74 - 3.28: 5984 3.28 - 3.82: 8827 3.82 - 4.36: 11087 4.36 - 4.90: 18709 Nonbonded interactions: 45198 Sorted by model distance: nonbonded pdb=" O SER A 458 " pdb=" OG SER A 458 " model vdw 2.201 2.440 nonbonded pdb=" O PHE A 461 " pdb=" NH2 ARG A 522 " model vdw 2.213 2.520 nonbonded pdb=" N GLU A 473 " pdb=" OE1 GLU A 473 " model vdw 2.216 2.520 nonbonded pdb=" O PHE A 50 " pdb=" NE2 GLN A 54 " model vdw 2.232 2.520 nonbonded pdb=" CD2 LEU A 438 " pdb=" OE1 GLU A 451 " model vdw 2.278 3.460 ... (remaining 45193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.380 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: 5.030 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.980 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.004 0.032 5856 Z= 0.239 Angle : 0.918 13.208 7920 Z= 0.621 Chirality : 0.057 0.488 911 Planarity : 0.003 0.037 993 Dihedral : 17.029 88.204 2102 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 25.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.62 % Favored : 89.09 % Rotamer: Outliers : 8.60 % Allowed : 16.69 % Favored : 74.71 % Cbeta Deviations : 0.14 % 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: -4.65 (0.25), residues: 706 helix: -2.68 (0.21), residues: 412 sheet: None (None), residues: 0 loop : -3.61 (0.29), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 200 HIS 0.002 0.001 HIS A 46 PHE 0.011 0.001 PHE A 413 TYR 0.009 0.001 TYR A 82 ARG 0.001 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 116 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 146 LYS cc_start: 0.7399 (pttt) cc_final: 0.7085 (mtmm) REVERT: A 300 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.6979 (m-10) REVERT: A 451 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6616 (tt0) REVERT: A 507 GLU cc_start: 0.7163 (mp0) cc_final: 0.6827 (mp0) REVERT: A 508 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7159 (pt0) REVERT: A 545 MET cc_start: 0.7802 (mtp) cc_final: 0.7542 (mtp) outliers start: 52 outliers final: 29 residues processed: 157 average time/residue: 0.1900 time to fit residues: 38.3915 Evaluate side-chains 121 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 89 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 0.0970 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 HIS A 90 ASN A 94 ASN A 134 GLN A 227 GLN A 266 ASN A 274 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN A 345 GLN A 383 GLN A 495 HIS B 201 HIS B 206 ASN B 211 GLN B 389 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5856 Z= 0.175 Angle : 0.587 8.432 7920 Z= 0.298 Chirality : 0.040 0.168 911 Planarity : 0.004 0.045 993 Dihedral : 8.626 58.317 837 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.46 % Allowed : 18.51 % Favored : 77.02 % 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: -2.77 (0.29), residues: 706 helix: -0.96 (0.24), residues: 432 sheet: None (None), residues: 0 loop : -3.27 (0.30), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 200 HIS 0.007 0.001 HIS A 495 PHE 0.011 0.001 PHE B 343 TYR 0.025 0.002 TYR A 257 ARG 0.002 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 0.658 Fit side-chains REVERT: A 447 SER cc_start: 0.7175 (m) cc_final: 0.6667 (t) REVERT: A 516 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7308 (tt0) REVERT: A 525 TRP cc_start: 0.6538 (t-100) cc_final: 0.6301 (t-100) REVERT: A 545 MET cc_start: 0.7612 (mtp) cc_final: 0.7374 (mtp) outliers start: 27 outliers final: 13 residues processed: 135 average time/residue: 0.1617 time to fit residues: 28.9895 Evaluate side-chains 108 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN B 407 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 5856 Z= 0.304 Angle : 0.648 8.526 7920 Z= 0.322 Chirality : 0.043 0.136 911 Planarity : 0.004 0.045 993 Dihedral : 6.578 53.100 786 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.46 % Allowed : 21.32 % Favored : 74.21 % 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: -2.11 (0.30), residues: 706 helix: -0.41 (0.25), residues: 434 sheet: None (None), residues: 0 loop : -3.06 (0.31), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 240 HIS 0.005 0.001 HIS A 261 PHE 0.020 0.002 PHE B 396 TYR 0.019 0.002 TYR A 20 ARG 0.004 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 363 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7741 (tt) REVERT: A 447 SER cc_start: 0.7312 (m) cc_final: 0.6596 (t) REVERT: B 369 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8448 (pp) outliers start: 27 outliers final: 20 residues processed: 114 average time/residue: 0.1607 time to fit residues: 24.6017 Evaluate side-chains 108 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.0670 chunk 61 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5856 Z= 0.157 Angle : 0.556 14.660 7920 Z= 0.272 Chirality : 0.039 0.123 911 Planarity : 0.003 0.044 993 Dihedral : 5.887 51.401 786 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.64 % Allowed : 24.13 % Favored : 73.22 % 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: -1.33 (0.31), residues: 706 helix: 0.19 (0.26), residues: 436 sheet: None (None), residues: 0 loop : -2.73 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 200 HIS 0.003 0.001 HIS A 261 PHE 0.010 0.001 PHE B 343 TYR 0.016 0.001 TYR B 432 ARG 0.004 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 363 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7738 (tt) REVERT: A 447 SER cc_start: 0.7425 (m) cc_final: 0.6954 (t) REVERT: B 369 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8397 (pp) REVERT: B 450 ILE cc_start: 0.6872 (mp) cc_final: 0.6351 (mp) outliers start: 16 outliers final: 11 residues processed: 114 average time/residue: 0.1775 time to fit residues: 26.8340 Evaluate side-chains 104 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 0.0670 chunk 28 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5856 Z= 0.274 Angle : 0.619 11.556 7920 Z= 0.305 Chirality : 0.041 0.126 911 Planarity : 0.004 0.047 993 Dihedral : 6.056 53.315 783 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.97 % Allowed : 22.64 % Favored : 73.39 % 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 (0.31), residues: 706 helix: 0.22 (0.26), residues: 437 sheet: None (None), residues: 0 loop : -2.65 (0.33), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 240 HIS 0.004 0.001 HIS A 261 PHE 0.017 0.002 PHE B 343 TYR 0.020 0.002 TYR A 20 ARG 0.005 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 300 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.7191 (m-10) REVERT: A 363 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7711 (tt) REVERT: A 457 LYS cc_start: 0.6999 (ptpt) cc_final: 0.6726 (ptpp) REVERT: A 497 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6563 (tp) REVERT: B 336 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7147 (mt-10) REVERT: B 369 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8421 (pp) REVERT: B 450 ILE cc_start: 0.6851 (mp) cc_final: 0.6312 (mp) outliers start: 24 outliers final: 15 residues processed: 110 average time/residue: 0.1724 time to fit residues: 25.1788 Evaluate side-chains 110 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5856 Z= 0.197 Angle : 0.570 12.090 7920 Z= 0.280 Chirality : 0.040 0.125 911 Planarity : 0.003 0.047 993 Dihedral : 5.811 51.875 783 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.97 % Allowed : 22.98 % Favored : 73.06 % 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: -0.91 (0.32), residues: 706 helix: 0.49 (0.26), residues: 438 sheet: None (None), residues: 0 loop : -2.50 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 200 HIS 0.003 0.001 HIS A 261 PHE 0.013 0.002 PHE B 343 TYR 0.017 0.001 TYR B 209 ARG 0.005 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6716 (tp) REVERT: B 336 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: B 369 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8373 (pp) REVERT: B 450 ILE cc_start: 0.6901 (mp) cc_final: 0.6370 (mp) outliers start: 24 outliers final: 18 residues processed: 115 average time/residue: 0.1747 time to fit residues: 26.8987 Evaluate side-chains 112 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 31 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.0170 chunk 43 optimal weight: 0.5980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5856 Z= 0.145 Angle : 0.546 11.738 7920 Z= 0.266 Chirality : 0.038 0.125 911 Planarity : 0.003 0.047 993 Dihedral : 5.401 50.110 783 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.98 % Allowed : 24.79 % Favored : 72.23 % 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: -0.57 (0.32), residues: 706 helix: 0.80 (0.26), residues: 436 sheet: None (None), residues: 0 loop : -2.43 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 200 HIS 0.002 0.000 HIS A 261 PHE 0.012 0.001 PHE A 272 TYR 0.020 0.001 TYR B 432 ARG 0.005 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 363 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7748 (tt) REVERT: A 387 ARG cc_start: 0.7720 (ttm110) cc_final: 0.7514 (ttp-110) REVERT: A 477 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6800 (mp) REVERT: B 369 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8388 (pp) REVERT: B 450 ILE cc_start: 0.6905 (mp) cc_final: 0.6383 (mp) outliers start: 18 outliers final: 12 residues processed: 113 average time/residue: 0.1757 time to fit residues: 26.2662 Evaluate side-chains 112 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5856 Z= 0.216 Angle : 0.609 13.197 7920 Z= 0.293 Chirality : 0.040 0.134 911 Planarity : 0.004 0.048 993 Dihedral : 5.353 51.957 781 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.14 % Allowed : 24.79 % Favored : 72.07 % 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: -0.53 (0.32), residues: 706 helix: 0.79 (0.26), residues: 436 sheet: None (None), residues: 0 loop : -2.34 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 240 HIS 0.003 0.001 HIS A 261 PHE 0.017 0.002 PHE B 343 TYR 0.017 0.001 TYR A 20 ARG 0.005 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 363 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7744 (tt) REVERT: A 457 LYS cc_start: 0.7163 (ptpt) cc_final: 0.6917 (pttm) REVERT: A 477 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6856 (mp) REVERT: B 369 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8390 (pp) REVERT: B 450 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6382 (mp) outliers start: 19 outliers final: 15 residues processed: 109 average time/residue: 0.1588 time to fit residues: 23.2856 Evaluate side-chains 112 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 0.0040 chunk 70 optimal weight: 0.0060 chunk 65 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 0.4808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5856 Z= 0.156 Angle : 0.568 13.862 7920 Z= 0.273 Chirality : 0.039 0.126 911 Planarity : 0.003 0.047 993 Dihedral : 5.043 50.392 781 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.98 % Allowed : 25.12 % Favored : 71.90 % 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: -0.29 (0.32), residues: 706 helix: 0.98 (0.26), residues: 436 sheet: None (None), residues: 0 loop : -2.22 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 200 HIS 0.002 0.000 HIS A 261 PHE 0.013 0.001 PHE B 396 TYR 0.019 0.001 TYR B 432 ARG 0.003 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 363 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7778 (tt) REVERT: A 387 ARG cc_start: 0.7810 (ttm110) cc_final: 0.7546 (ttp-110) REVERT: A 477 LEU cc_start: 0.7408 (tp) cc_final: 0.7053 (mp) REVERT: B 369 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8422 (pp) REVERT: B 450 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6395 (mp) outliers start: 18 outliers final: 15 residues processed: 110 average time/residue: 0.1573 time to fit residues: 23.3389 Evaluate side-chains 114 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 51 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5856 Z= 0.163 Angle : 0.579 12.282 7920 Z= 0.281 Chirality : 0.039 0.123 911 Planarity : 0.003 0.047 993 Dihedral : 4.842 50.305 779 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.31 % Allowed : 24.63 % Favored : 72.07 % 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: -0.19 (0.33), residues: 706 helix: 1.05 (0.26), residues: 436 sheet: None (None), residues: 0 loop : -2.17 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 200 HIS 0.004 0.001 HIS A 261 PHE 0.014 0.001 PHE B 396 TYR 0.015 0.001 TYR A 20 ARG 0.002 0.000 ARG A 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 363 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7697 (tt) REVERT: A 387 ARG cc_start: 0.7770 (ttm110) cc_final: 0.7547 (ttp-110) REVERT: A 477 LEU cc_start: 0.7392 (tp) cc_final: 0.7010 (mp) REVERT: B 292 MET cc_start: 0.7058 (ttp) cc_final: 0.6840 (ttt) REVERT: B 369 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8380 (pp) REVERT: B 450 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6443 (mp) outliers start: 20 outliers final: 16 residues processed: 109 average time/residue: 0.1767 time to fit residues: 25.3240 Evaluate side-chains 113 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 40 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** 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 = 0.4283 r_free = 0.4283 target = 0.185470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.158890 restraints weight = 7334.744| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.71 r_work: 0.3890 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5856 Z= 0.156 Angle : 0.563 11.422 7920 Z= 0.274 Chirality : 0.039 0.124 911 Planarity : 0.003 0.047 993 Dihedral : 4.766 50.007 779 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.47 % Allowed : 24.79 % Favored : 71.74 % 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: -0.07 (0.33), residues: 706 helix: 1.14 (0.26), residues: 436 sheet: None (None), residues: 0 loop : -2.10 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 200 HIS 0.002 0.000 HIS A 261 PHE 0.014 0.001 PHE A 272 TYR 0.018 0.001 TYR B 432 ARG 0.006 0.000 ARG A 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1560.61 seconds wall clock time: 28 minutes 52.34 seconds (1732.34 seconds total)