Starting phenix.real_space_refine on Fri Jul 19 09:16:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wny_37675/07_2024/8wny_37675.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wny_37675/07_2024/8wny_37675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wny_37675/07_2024/8wny_37675.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wny_37675/07_2024/8wny_37675.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wny_37675/07_2024/8wny_37675.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wny_37675/07_2024/8wny_37675.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.077 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 4713 2.51 5 N 1190 2.21 5 O 1298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7233 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3645 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Chain: "B" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3525 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 23, 'TRANS': 432} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Time building chain proxies: 4.76, per 1000 atoms: 0.66 Number of scatterers: 7233 At special positions: 0 Unit cell: (105.12, 77.745, 122.64, 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 1298 8.00 N 1190 7.00 C 4713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 154 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 366 " " NAG A 702 " - " ASN A 382 " " NAG A 703 " - " ASN A 425 " " NAG A 704 " - " ASN A 507 " Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.3 seconds 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DSN B1001 " Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 5 sheets defined 63.4% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 167 through 175 Processing helix chain 'A' and resid 178 through 207 removed outlier: 3.511A pdb=" N THR A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.693A pdb=" N PHE A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.580A pdb=" N GLY A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 287 through 301 Processing helix chain 'A' and resid 324 through 342 Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.559A pdb=" N ASN A 353 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.780A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 394 removed outlier: 4.219A pdb=" N ILE A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.724A pdb=" N SER A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 removed outlier: 3.975A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 534 removed outlier: 3.596A pdb=" N LEU A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 585 through 589 removed outlier: 4.240A pdb=" N SER A 589 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 54 removed outlier: 3.536A pdb=" N THR B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 59 Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.845A pdb=" N GLY B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 100 removed outlier: 3.765A pdb=" N VAL B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 115 through 129 Processing helix chain 'B' and resid 129 through 148 Processing helix chain 'B' and resid 157 through 179 removed outlier: 3.547A pdb=" N SER B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 211 Processing helix chain 'B' and resid 218 through 223 removed outlier: 3.590A pdb=" N PHE B 223 " --> pdb=" O PRO B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 243 through 246 Processing helix chain 'B' and resid 247 through 258 removed outlier: 3.518A pdb=" N PHE B 250 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 251 " --> pdb=" O TRP B 248 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLU B 256 " --> pdb=" O TYR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 291 removed outlier: 3.506A pdb=" N ASN B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Proline residue: B 266 - end of helix Proline residue: B 274 - end of helix Processing helix chain 'B' and resid 292 through 298 Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 312 through 315 Processing helix chain 'B' and resid 316 through 347 removed outlier: 3.933A pdb=" N VAL B 320 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.588A pdb=" N MET B 356 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 380 removed outlier: 3.727A pdb=" N LEU B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 413 Processing helix chain 'B' and resid 424 through 445 Processing helix chain 'B' and resid 445 through 458 removed outlier: 3.802A pdb=" N CYS B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 removed outlier: 4.190A pdb=" N ILE B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 492 Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403 removed outlier: 3.548A pdb=" N LEU A 400 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL A 305 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N GLN A 347 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 307 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU A 260 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASP A 308 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU A 262 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP A 434 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N SER A 468 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 544 removed outlier: 6.144A pdb=" N ARG A 626 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU A 596 " --> pdb=" O ARG A 626 " (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 357 through 358 425 hydrogen bonds defined for protein. 1218 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: 2.24 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1128 1.31 - 1.44: 2067 1.44 - 1.56: 4174 1.56 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 7419 Sorted by residual: bond pdb=" CA DSN B1001 " pdb=" CB DSN B1001 " ideal model delta sigma weight residual 1.530 1.462 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" N ILE A 367 " pdb=" CA ILE A 367 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.56e+00 bond pdb=" N ASN A 366 " pdb=" CA ASN A 366 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.17e-02 7.31e+03 6.30e+00 bond pdb=" N SER A 505 " pdb=" CA SER A 505 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.23e-02 6.61e+03 6.22e+00 bond pdb=" N THR A 276 " pdb=" CA THR A 276 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.57e+00 ... (remaining 7414 not shown) Histogram of bond angle deviations from ideal: 95.69 - 103.39: 84 103.39 - 111.08: 3013 111.08 - 118.78: 2976 118.78 - 126.48: 3873 126.48 - 134.18: 153 Bond angle restraints: 10099 Sorted by residual: angle pdb=" C ASN A 507 " pdb=" CA ASN A 507 " pdb=" CB ASN A 507 " ideal model delta sigma weight residual 109.16 120.14 -10.98 1.29e+00 6.01e-01 7.25e+01 angle pdb=" N ASN A 507 " pdb=" CA ASN A 507 " pdb=" C ASN A 507 " ideal model delta sigma weight residual 114.75 105.39 9.36 1.26e+00 6.30e-01 5.52e+01 angle pdb=" CA ASN A 507 " pdb=" CB ASN A 507 " pdb=" CG ASN A 507 " ideal model delta sigma weight residual 112.60 118.46 -5.86 1.00e+00 1.00e+00 3.44e+01 angle pdb=" O ASN A 507 " pdb=" C ASN A 507 " pdb=" N MET A 508 " ideal model delta sigma weight residual 121.64 128.12 -6.48 1.23e+00 6.61e-01 2.78e+01 angle pdb=" CA ASN A 507 " pdb=" C ASN A 507 " pdb=" N MET A 508 " ideal model delta sigma weight residual 119.80 113.05 6.75 1.34e+00 5.57e-01 2.54e+01 ... (remaining 10094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 3830 17.60 - 35.20: 397 35.20 - 52.79: 120 52.79 - 70.39: 17 70.39 - 87.99: 8 Dihedral angle restraints: 4372 sinusoidal: 1736 harmonic: 2636 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 154 " pdb=" CB CYS B 154 " ideal model delta sinusoidal sigma weight residual -86.00 -139.09 53.09 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" CA ASN A 366 " pdb=" CB ASN A 366 " pdb=" CG ASN A 366 " pdb=" OD1 ASN A 366 " ideal model delta sinusoidal sigma weight residual 120.00 -166.23 -73.77 2 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CG ARG B 360 " pdb=" CD ARG B 360 " pdb=" NE ARG B 360 " pdb=" CZ ARG B 360 " ideal model delta sinusoidal sigma weight residual 180.00 135.36 44.64 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 4369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.269: 1163 0.269 - 0.538: 1 0.538 - 0.808: 0 0.808 - 1.077: 1 1.077 - 1.346: 1 Chirality restraints: 1166 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 425 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.05 -1.35 2.00e-01 2.50e+01 4.53e+01 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.44 -0.96 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 507 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 1163 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 425 " 0.158 2.00e-02 2.50e+03 1.82e-01 4.15e+02 pdb=" CG ASN A 425 " -0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN A 425 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 425 " -0.295 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.222 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 382 " 0.106 2.00e-02 2.50e+03 1.69e-01 3.56e+02 pdb=" CG ASN A 382 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 382 " 0.055 2.00e-02 2.50e+03 pdb=" ND2 ASN A 382 " -0.298 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " 0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 366 " -0.091 2.00e-02 2.50e+03 1.01e-01 1.27e+02 pdb=" CG ASN A 366 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 366 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 366 " 0.162 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.122 2.00e-02 2.50e+03 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1203 2.76 - 3.29: 6852 3.29 - 3.83: 12011 3.83 - 4.36: 13013 4.36 - 4.90: 23510 Nonbonded interactions: 56589 Sorted by model distance: nonbonded pdb=" O LEU A 456 " pdb=" OG1 THR A 460 " model vdw 2.225 2.440 nonbonded pdb=" O SER A 582 " pdb=" OG SER A 582 " model vdw 2.233 2.440 nonbonded pdb=" OD1 ASP A 493 " pdb=" OG SER A 495 " model vdw 2.238 2.440 nonbonded pdb=" O HIS A 266 " pdb=" OH TYR A 313 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR A 251 " pdb=" OE2 GLU A 472 " model vdw 2.263 2.440 ... (remaining 56584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.240 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 : 0.003 0.068 7419 Z= 0.232 Angle : 0.665 10.980 10099 Z= 0.365 Chirality : 0.064 1.346 1166 Planarity : 0.004 0.072 1258 Dihedral : 15.851 87.990 2681 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.39 % Allowed : 21.29 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.28 (0.28), residues: 920 helix: 2.03 (0.23), residues: 508 sheet: 0.93 (0.70), residues: 57 loop : -0.94 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 316 HIS 0.002 0.000 HIS A 557 PHE 0.014 0.001 PHE A 360 TYR 0.011 0.001 TYR B 385 ARG 0.002 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 96 average time/residue: 0.1759 time to fit residues: 23.8059 Evaluate side-chains 92 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 353 ASN A 539 HIS ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7419 Z= 0.210 Angle : 0.553 7.323 10099 Z= 0.276 Chirality : 0.039 0.152 1166 Planarity : 0.004 0.056 1258 Dihedral : 4.753 58.326 1079 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.45 % Allowed : 19.87 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.69 (0.28), residues: 920 helix: 2.32 (0.23), residues: 520 sheet: 0.88 (0.68), residues: 57 loop : -0.76 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 316 HIS 0.003 0.001 HIS A 557 PHE 0.013 0.001 PHE B 327 TYR 0.014 0.001 TYR B 385 ARG 0.002 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: B 227 MET cc_start: 0.6222 (OUTLIER) cc_final: 0.5820 (ttp) outliers start: 19 outliers final: 11 residues processed: 105 average time/residue: 0.1792 time to fit residues: 26.5872 Evaluate side-chains 98 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 477 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7419 Z= 0.180 Angle : 0.528 9.385 10099 Z= 0.259 Chirality : 0.038 0.159 1166 Planarity : 0.004 0.047 1258 Dihedral : 4.176 59.632 1075 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.10 % Allowed : 20.65 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.91 (0.29), residues: 920 helix: 2.50 (0.23), residues: 521 sheet: 0.84 (0.68), residues: 57 loop : -0.65 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 316 HIS 0.002 0.001 HIS A 557 PHE 0.013 0.001 PHE A 542 TYR 0.012 0.001 TYR B 385 ARG 0.001 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 452 ARG cc_start: 0.7877 (mtt-85) cc_final: 0.6365 (mtt90) REVERT: B 60 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7860 (mt) REVERT: B 227 MET cc_start: 0.6318 (OUTLIER) cc_final: 0.5903 (ttp) REVERT: B 260 ASP cc_start: 0.6780 (t0) cc_final: 0.6554 (t0) outliers start: 24 outliers final: 13 residues processed: 105 average time/residue: 0.1587 time to fit residues: 24.0083 Evaluate side-chains 101 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 477 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 87 optimal weight: 0.0030 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 0.0470 chunk 73 optimal weight: 0.7980 overall best weight: 0.5688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7419 Z= 0.163 Angle : 0.516 8.025 10099 Z= 0.253 Chirality : 0.038 0.222 1166 Planarity : 0.004 0.043 1258 Dihedral : 4.048 58.618 1075 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.35 % Allowed : 21.29 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.00 (0.28), residues: 920 helix: 2.56 (0.23), residues: 521 sheet: 0.88 (0.68), residues: 57 loop : -0.59 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 316 HIS 0.002 0.000 HIS A 557 PHE 0.013 0.001 PHE A 542 TYR 0.011 0.001 TYR B 385 ARG 0.001 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6672 (tpp80) cc_final: 0.6419 (tpp80) REVERT: A 452 ARG cc_start: 0.7871 (mtt-85) cc_final: 0.6358 (mtt90) REVERT: B 60 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7841 (mt) REVERT: B 103 SER cc_start: 0.7811 (OUTLIER) cc_final: 0.7573 (m) REVERT: B 208 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6388 (tt0) REVERT: B 227 MET cc_start: 0.6334 (OUTLIER) cc_final: 0.5938 (ttp) REVERT: B 318 MET cc_start: 0.6412 (ttp) cc_final: 0.5994 (ttp) outliers start: 26 outliers final: 18 residues processed: 108 average time/residue: 0.1816 time to fit residues: 27.7787 Evaluate side-chains 109 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 477 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.0970 chunk 78 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7419 Z= 0.154 Angle : 0.514 13.915 10099 Z= 0.248 Chirality : 0.037 0.162 1166 Planarity : 0.003 0.039 1258 Dihedral : 3.930 56.696 1075 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.00 % Allowed : 19.74 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.09 (0.28), residues: 920 helix: 2.64 (0.23), residues: 521 sheet: 0.94 (0.68), residues: 57 loop : -0.58 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 316 HIS 0.002 0.000 HIS A 557 PHE 0.013 0.001 PHE A 542 TYR 0.011 0.001 TYR B 390 ARG 0.001 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 96 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6685 (tpp80) cc_final: 0.6316 (tpp80) REVERT: A 340 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7358 (mm-40) REVERT: A 452 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.6373 (mtt90) REVERT: B 60 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7814 (mt) REVERT: B 208 GLN cc_start: 0.7216 (mm-40) cc_final: 0.6358 (tt0) REVERT: B 227 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.5937 (ttp) outliers start: 31 outliers final: 21 residues processed: 119 average time/residue: 0.1757 time to fit residues: 29.3698 Evaluate side-chains 114 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 477 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 21 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 0.0040 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7419 Z= 0.140 Angle : 0.514 12.491 10099 Z= 0.245 Chirality : 0.037 0.158 1166 Planarity : 0.003 0.036 1258 Dihedral : 3.821 54.090 1075 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.23 % Allowed : 20.39 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.15 (0.29), residues: 920 helix: 2.70 (0.23), residues: 521 sheet: 0.99 (0.67), residues: 57 loop : -0.57 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 316 HIS 0.002 0.000 HIS A 539 PHE 0.014 0.001 PHE A 542 TYR 0.011 0.001 TYR B 390 ARG 0.001 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6684 (tpp80) cc_final: 0.6306 (tpp80) REVERT: A 290 ASP cc_start: 0.8111 (m-30) cc_final: 0.7606 (t0) REVERT: A 340 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7391 (mm-40) REVERT: A 452 ARG cc_start: 0.7903 (mtt-85) cc_final: 0.6351 (mtt90) REVERT: B 60 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7722 (mt) REVERT: B 208 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6496 (tt0) REVERT: B 227 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.5890 (ttp) outliers start: 25 outliers final: 20 residues processed: 112 average time/residue: 0.1765 time to fit residues: 27.4579 Evaluate side-chains 116 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 477 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7419 Z= 0.219 Angle : 0.551 10.792 10099 Z= 0.267 Chirality : 0.039 0.163 1166 Planarity : 0.003 0.035 1258 Dihedral : 3.844 46.506 1075 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.48 % Allowed : 21.16 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.09 (0.28), residues: 920 helix: 2.62 (0.23), residues: 519 sheet: 1.03 (0.68), residues: 57 loop : -0.52 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 316 HIS 0.003 0.001 HIS A 557 PHE 0.013 0.001 PHE B 440 TYR 0.014 0.001 TYR B 385 ARG 0.002 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5696 (pp) REVERT: A 210 ARG cc_start: 0.6716 (tpp80) cc_final: 0.6425 (tpp80) REVERT: A 290 ASP cc_start: 0.8166 (m-30) cc_final: 0.7669 (t0) REVERT: A 340 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7415 (mm-40) REVERT: A 452 ARG cc_start: 0.7853 (mtt-85) cc_final: 0.6413 (mtt90) REVERT: B 60 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7815 (mt) REVERT: B 170 MET cc_start: 0.8010 (mtt) cc_final: 0.7669 (mtp) REVERT: B 208 GLN cc_start: 0.7328 (mm-40) cc_final: 0.6620 (tt0) REVERT: B 227 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.5978 (ttp) REVERT: B 318 MET cc_start: 0.6460 (ttp) cc_final: 0.6084 (ttp) outliers start: 27 outliers final: 19 residues processed: 117 average time/residue: 0.1916 time to fit residues: 31.1098 Evaluate side-chains 116 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 438 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN B 240 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7419 Z= 0.189 Angle : 0.528 9.867 10099 Z= 0.256 Chirality : 0.038 0.165 1166 Planarity : 0.003 0.035 1258 Dihedral : 3.761 40.050 1075 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.26 % Allowed : 20.90 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.14 (0.28), residues: 920 helix: 2.64 (0.23), residues: 518 sheet: 1.10 (0.68), residues: 57 loop : -0.48 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 316 HIS 0.003 0.001 HIS A 557 PHE 0.014 0.001 PHE A 542 TYR 0.012 0.001 TYR B 385 ARG 0.001 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5792 (pp) REVERT: A 210 ARG cc_start: 0.6738 (tpp80) cc_final: 0.6434 (tpp80) REVERT: A 290 ASP cc_start: 0.8153 (m-30) cc_final: 0.7675 (t0) REVERT: A 340 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7322 (mm-40) REVERT: A 452 ARG cc_start: 0.7861 (mtt-85) cc_final: 0.6412 (mtt90) REVERT: B 60 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7821 (mt) REVERT: B 208 GLN cc_start: 0.7378 (mm-40) cc_final: 0.6686 (tt0) REVERT: B 227 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.6185 (ttp) REVERT: B 318 MET cc_start: 0.6366 (ttp) cc_final: 0.6092 (ttp) outliers start: 33 outliers final: 22 residues processed: 116 average time/residue: 0.1871 time to fit residues: 29.8949 Evaluate side-chains 118 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 477 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 0.0970 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 86 optimal weight: 0.0470 chunk 52 optimal weight: 0.9980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7419 Z= 0.155 Angle : 0.530 9.895 10099 Z= 0.253 Chirality : 0.038 0.164 1166 Planarity : 0.003 0.034 1258 Dihedral : 3.646 34.740 1075 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.10 % Allowed : 22.32 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.20 (0.29), residues: 920 helix: 2.75 (0.23), residues: 520 sheet: 1.17 (0.69), residues: 57 loop : -0.57 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 316 HIS 0.002 0.000 HIS A 539 PHE 0.014 0.001 PHE A 542 TYR 0.010 0.001 TYR B 390 ARG 0.001 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 LEU cc_start: 0.6163 (OUTLIER) cc_final: 0.5719 (pp) REVERT: A 210 ARG cc_start: 0.6707 (tpp80) cc_final: 0.6439 (tpp80) REVERT: A 290 ASP cc_start: 0.8115 (m-30) cc_final: 0.7658 (t0) REVERT: A 340 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7343 (mm-40) REVERT: A 452 ARG cc_start: 0.7821 (mtt-85) cc_final: 0.6391 (mtt90) REVERT: A 534 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7281 (tm-30) REVERT: B 60 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7868 (mt) REVERT: B 208 GLN cc_start: 0.7368 (mm-40) cc_final: 0.6681 (tt0) REVERT: B 227 MET cc_start: 0.6417 (OUTLIER) cc_final: 0.6084 (ttp) REVERT: B 318 MET cc_start: 0.6140 (ttp) cc_final: 0.5932 (ttp) outliers start: 24 outliers final: 17 residues processed: 110 average time/residue: 0.1946 time to fit residues: 29.2236 Evaluate side-chains 113 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 477 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 240 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7419 Z= 0.178 Angle : 0.543 8.921 10099 Z= 0.259 Chirality : 0.039 0.180 1166 Planarity : 0.004 0.034 1258 Dihedral : 3.525 17.635 1072 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.23 % Allowed : 22.45 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.17 (0.29), residues: 920 helix: 2.72 (0.23), residues: 513 sheet: 1.19 (0.70), residues: 57 loop : -0.50 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 316 HIS 0.002 0.000 HIS A 557 PHE 0.013 0.001 PHE A 542 TYR 0.011 0.001 TYR B 385 ARG 0.008 0.000 ARG A 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5788 (pp) REVERT: A 210 ARG cc_start: 0.6736 (tpp80) cc_final: 0.6467 (tpp80) REVERT: A 290 ASP cc_start: 0.8080 (m-30) cc_final: 0.7704 (t0) REVERT: A 340 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7285 (mm-40) REVERT: A 452 ARG cc_start: 0.7855 (mtt-85) cc_final: 0.6406 (mtt90) REVERT: A 534 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7368 (tm-30) REVERT: B 60 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7910 (mt) REVERT: B 170 MET cc_start: 0.7992 (mtt) cc_final: 0.7667 (mtp) REVERT: B 208 GLN cc_start: 0.7379 (mm-40) cc_final: 0.6700 (tt0) REVERT: B 227 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.6201 (ttp) REVERT: B 318 MET cc_start: 0.6239 (ttp) cc_final: 0.5986 (ttp) outliers start: 25 outliers final: 21 residues processed: 109 average time/residue: 0.1922 time to fit residues: 28.5402 Evaluate side-chains 115 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 477 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 0.0070 chunk 52 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 240 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.179989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140297 restraints weight = 9119.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.138719 restraints weight = 8454.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.140277 restraints weight = 8386.906| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7419 Z= 0.173 Angle : 0.540 8.177 10099 Z= 0.257 Chirality : 0.038 0.180 1166 Planarity : 0.003 0.033 1258 Dihedral : 3.500 16.879 1072 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.23 % Allowed : 22.45 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.19 (0.29), residues: 920 helix: 2.74 (0.23), residues: 513 sheet: 1.16 (0.70), residues: 57 loop : -0.51 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 316 HIS 0.002 0.000 HIS A 557 PHE 0.016 0.001 PHE B 440 TYR 0.010 0.001 TYR B 385 ARG 0.008 0.000 ARG A 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1616.15 seconds wall clock time: 29 minutes 45.75 seconds (1785.75 seconds total)