Starting phenix.real_space_refine on Sat Dec 28 01:26:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wny_37675/12_2024/8wny_37675.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wny_37675/12_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/cci-nas-00/data/ceres_data/8wny_37675/12_2024/8wny_37675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wny_37675/12_2024/8wny_37675.map" model { file = "/net/cci-nas-00/data/ceres_data/8wny_37675/12_2024/8wny_37675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wny_37675/12_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. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.83, per 1000 atoms: 0.67 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 - 3.00 Amino acid : True - 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: 2.18 Conformation dependent library (CDL) restraints added in 1.2 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: 0.84 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: 2.03 Time building geometry restraints manager: 2.16 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: 0.00 - 2.20: 9944 2.20 - 4.39: 122 4.39 - 6.59: 23 6.59 - 8.78: 5 8.78 - 10.98: 5 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 3.040 nonbonded pdb=" O SER A 582 " pdb=" OG SER A 582 " model vdw 2.233 3.040 nonbonded pdb=" OD1 ASP A 493 " pdb=" OG SER A 495 " model vdw 2.238 3.040 nonbonded pdb=" O HIS A 266 " pdb=" OH TYR A 313 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR A 251 " pdb=" OE2 GLU A 472 " model vdw 2.263 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.190 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.640 Find NCS groups from input model: 0.100 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.310 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 96 average time/residue: 0.1741 time to fit residues: 23.5680 Evaluate side-chains 92 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7419 Z= 0.233 Angle : 0.573 7.262 10099 Z= 0.289 Chirality : 0.040 0.141 1166 Planarity : 0.004 0.060 1258 Dihedral : 4.866 59.754 1079 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.10 % Allowed : 18.97 % Favored : 77.94 % 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: 1.57 (0.28), residues: 920 helix: 2.26 (0.23), residues: 515 sheet: 0.78 (0.68), residues: 57 loop : -0.82 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 316 HIS 0.003 0.001 HIS A 557 PHE 0.014 0.001 PHE B 327 TYR 0.015 0.002 TYR B 385 ARG 0.004 0.000 ARG A 227 *********************** 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 124 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 310 THR cc_start: 0.8750 (m) cc_final: 0.8263 (t) REVERT: A 452 ARG cc_start: 0.7899 (mtt-85) cc_final: 0.6448 (mtt90) REVERT: B 170 MET cc_start: 0.8002 (mtt) cc_final: 0.7665 (mtp) REVERT: B 227 MET cc_start: 0.6322 (OUTLIER) cc_final: 0.5914 (ttp) REVERT: B 260 ASP cc_start: 0.7228 (t0) cc_final: 0.7012 (t0) outliers start: 24 outliers final: 18 residues processed: 115 average time/residue: 0.1834 time to fit residues: 29.6748 Evaluate side-chains 112 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL 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 504 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 522 SER 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 295 GLU Chi-restraints excluded: chain B residue 297 LEU 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 467 VAL 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: 7.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 89 optimal weight: 0.0670 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1245 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= 0.156 Angle : 0.512 8.038 10099 Z= 0.254 Chirality : 0.038 0.166 1166 Planarity : 0.004 0.051 1258 Dihedral : 4.095 56.676 1075 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.58 % Allowed : 20.26 % Favored : 77.16 % 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: 1.87 (0.28), residues: 920 helix: 2.58 (0.23), residues: 509 sheet: 0.86 (0.67), residues: 57 loop : -0.75 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 316 HIS 0.002 0.000 HIS B 358 PHE 0.014 0.001 PHE A 542 TYR 0.011 0.001 TYR B 390 ARG 0.002 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 124 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7791 (mmtm) REVERT: A 210 ARG cc_start: 0.6615 (tpp80) cc_final: 0.6370 (tpp80) REVERT: A 310 THR cc_start: 0.8708 (m) cc_final: 0.8226 (t) REVERT: A 452 ARG cc_start: 0.8016 (mtt-85) cc_final: 0.6423 (mtt90) REVERT: B 60 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7809 (mt) REVERT: B 208 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6381 (tt0) REVERT: B 227 MET cc_start: 0.6255 (OUTLIER) cc_final: 0.5846 (ttp) REVERT: B 318 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.6251 (ttp) outliers start: 20 outliers final: 9 residues processed: 118 average time/residue: 0.1772 time to fit residues: 28.7820 Evaluate side-chains 107 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 412 THR 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 B residue 60 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 438 LEU 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: 6.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7419 Z= 0.162 Angle : 0.506 7.141 10099 Z= 0.251 Chirality : 0.038 0.158 1166 Planarity : 0.004 0.045 1258 Dihedral : 3.967 56.566 1075 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.23 % Allowed : 20.13 % Favored : 76.65 % 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: 1.92 (0.28), residues: 920 helix: 2.56 (0.23), residues: 515 sheet: 0.94 (0.67), residues: 57 loop : -0.70 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 316 HIS 0.002 0.001 HIS B 358 PHE 0.014 0.001 PHE A 542 TYR 0.011 0.001 TYR B 385 ARG 0.002 0.000 ARG A 227 *********************** 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 126 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8059 (mmtm) cc_final: 0.7840 (mmtm) REVERT: A 210 ARG cc_start: 0.6620 (tpp80) cc_final: 0.6235 (tpp80) REVERT: A 267 LYS cc_start: 0.7646 (tppt) cc_final: 0.7444 (tppt) REVERT: A 310 THR cc_start: 0.8714 (m) cc_final: 0.8222 (t) REVERT: A 340 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7376 (mm-40) REVERT: A 452 ARG cc_start: 0.7950 (mtt-85) cc_final: 0.6448 (mtt90) REVERT: B 60 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7806 (mt) REVERT: B 208 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6498 (tt0) REVERT: B 227 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5903 (ttp) REVERT: B 318 MET cc_start: 0.6250 (OUTLIER) cc_final: 0.5807 (ttp) outliers start: 25 outliers final: 16 residues processed: 118 average time/residue: 0.1893 time to fit residues: 30.9266 Evaluate side-chains 117 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 412 THR 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 B residue 43 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 168 CYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 318 MET 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: 3.9990 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.0050 chunk 78 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7419 Z= 0.176 Angle : 0.539 13.415 10099 Z= 0.260 Chirality : 0.039 0.219 1166 Planarity : 0.003 0.042 1258 Dihedral : 3.917 53.877 1075 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.48 % Allowed : 19.87 % Favored : 76.65 % 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: 1.96 (0.28), residues: 920 helix: 2.58 (0.23), residues: 516 sheet: 0.99 (0.68), residues: 57 loop : -0.68 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 316 HIS 0.002 0.001 HIS A 557 PHE 0.014 0.001 PHE A 542 TYR 0.012 0.001 TYR A 313 ARG 0.002 0.000 ARG A 227 *********************** 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 to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.842 Fit side-chains REVERT: A 167 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7856 (mmtm) REVERT: A 210 ARG cc_start: 0.6658 (tpp80) cc_final: 0.6254 (tpp80) REVERT: A 290 ASP cc_start: 0.8132 (m-30) cc_final: 0.7622 (t0) REVERT: A 310 THR cc_start: 0.8739 (m) cc_final: 0.8233 (t) REVERT: A 340 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7396 (mm-40) REVERT: A 452 ARG cc_start: 0.7954 (mtt-85) cc_final: 0.6442 (mtt90) REVERT: B 60 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7833 (mt) REVERT: B 196 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.5973 (mm) REVERT: B 208 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6524 (tt0) REVERT: B 227 MET cc_start: 0.6275 (OUTLIER) cc_final: 0.5875 (ttp) REVERT: B 318 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.5999 (ttp) REVERT: B 481 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7755 (mt-10) outliers start: 27 outliers final: 19 residues processed: 117 average time/residue: 0.1875 time to fit residues: 30.6853 Evaluate side-chains 123 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 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 43 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 168 CYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 318 MET 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: 1.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7419 Z= 0.198 Angle : 0.535 7.777 10099 Z= 0.264 Chirality : 0.039 0.161 1166 Planarity : 0.004 0.040 1258 Dihedral : 3.879 49.271 1075 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.00 % Allowed : 20.52 % Favored : 75.48 % 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: 1.96 (0.28), residues: 920 helix: 2.56 (0.23), residues: 515 sheet: 0.96 (0.68), residues: 57 loop : -0.62 (0.33), residues: 348 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 0.016 0.001 PHE B 440 TYR 0.013 0.001 TYR B 385 ARG 0.002 0.000 ARG B 418 *********************** 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 129 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8140 (mmtm) cc_final: 0.7857 (mmtm) REVERT: A 290 ASP cc_start: 0.8161 (m-30) cc_final: 0.7668 (t0) REVERT: A 310 THR cc_start: 0.8738 (m) cc_final: 0.8238 (t) REVERT: A 340 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7394 (mm-40) REVERT: A 452 ARG cc_start: 0.7951 (mtt-85) cc_final: 0.6382 (mtt90) REVERT: B 60 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7849 (mt) REVERT: B 208 GLN cc_start: 0.7354 (mm-40) cc_final: 0.6611 (tt0) REVERT: B 227 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.5928 (ttp) outliers start: 31 outliers final: 21 residues processed: 119 average time/residue: 0.1836 time to fit residues: 30.5722 Evaluate side-chains 116 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 203 VAL 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 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 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 281 THR Chi-restraints excluded: chain B residue 297 LEU 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: 0.0270 chunk 49 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7419 Z= 0.173 Angle : 0.533 7.692 10099 Z= 0.262 Chirality : 0.038 0.162 1166 Planarity : 0.003 0.037 1258 Dihedral : 3.830 43.820 1075 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.35 % Allowed : 21.42 % Favored : 75.23 % 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: 2.60 (0.23), residues: 515 sheet: 1.04 (0.68), residues: 57 loop : -0.63 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 316 HIS 0.002 0.000 HIS A 557 PHE 0.014 0.001 PHE A 542 TYR 0.038 0.002 TYR A 251 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 122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 ASP cc_start: 0.8146 (m-30) cc_final: 0.7666 (t0) REVERT: A 310 THR cc_start: 0.8689 (m) cc_final: 0.8167 (t) REVERT: A 340 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7465 (mm-40) REVERT: A 452 ARG cc_start: 0.7957 (mtt-85) cc_final: 0.6405 (mtt90) REVERT: B 60 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7831 (mt) REVERT: B 196 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.6034 (mm) REVERT: B 208 GLN cc_start: 0.7351 (mm-40) cc_final: 0.6669 (tt0) REVERT: B 227 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.6029 (ttp) outliers start: 26 outliers final: 19 residues processed: 114 average time/residue: 0.1692 time to fit residues: 27.0453 Evaluate side-chains 116 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 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 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 48 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 477 HIS Chi-restraints excluded: chain B residue 488 GLN 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: 0.8980 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 0.0980 chunk 76 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7419 Z= 0.180 Angle : 0.535 8.046 10099 Z= 0.262 Chirality : 0.038 0.163 1166 Planarity : 0.003 0.036 1258 Dihedral : 3.759 40.143 1075 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.74 % Allowed : 21.29 % Favored : 74.97 % 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: 2.08 (0.28), residues: 920 helix: 2.63 (0.23), residues: 514 sheet: 1.73 (0.70), residues: 51 loop : -0.61 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 316 HIS 0.002 0.000 HIS A 557 PHE 0.014 0.001 PHE A 542 TYR 0.040 0.002 TYR A 251 ARG 0.002 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 121 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 290 ASP cc_start: 0.8151 (m-30) cc_final: 0.7674 (t0) REVERT: A 340 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7412 (mm-40) REVERT: A 452 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.6404 (mtt90) REVERT: B 60 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7849 (mt) REVERT: B 196 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.6044 (mm) REVERT: B 208 GLN cc_start: 0.7373 (mm-40) cc_final: 0.6687 (tt0) REVERT: B 227 MET cc_start: 0.6407 (OUTLIER) cc_final: 0.6049 (ttp) outliers start: 29 outliers final: 22 residues processed: 111 average time/residue: 0.1726 time to fit residues: 27.0636 Evaluate side-chains 114 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 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 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 48 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 196 LEU 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 438 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 477 HIS Chi-restraints excluded: chain B residue 488 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 0.0970 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7419 Z= 0.164 Angle : 0.555 14.296 10099 Z= 0.265 Chirality : 0.039 0.186 1166 Planarity : 0.003 0.035 1258 Dihedral : 3.718 36.619 1075 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.23 % Allowed : 21.81 % Favored : 74.97 % 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: 2.01 (0.28), residues: 920 helix: 2.57 (0.23), residues: 515 sheet: 1.78 (0.70), residues: 51 loop : -0.66 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 316 HIS 0.002 0.000 HIS B 485 PHE 0.014 0.001 PHE A 542 TYR 0.033 0.001 TYR A 251 ARG 0.002 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 116 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 290 ASP cc_start: 0.8111 (m-30) cc_final: 0.7691 (t0) REVERT: A 340 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7326 (mm-40) REVERT: A 452 ARG cc_start: 0.7965 (mtt-85) cc_final: 0.6437 (mtt90) REVERT: B 60 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7842 (mt) REVERT: B 196 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6034 (mm) REVERT: B 208 GLN cc_start: 0.7364 (mm-40) cc_final: 0.6685 (tt0) outliers start: 25 outliers final: 21 residues processed: 110 average time/residue: 0.1671 time to fit residues: 26.2019 Evaluate side-chains 112 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 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 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 154 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 477 HIS Chi-restraints excluded: chain B residue 488 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7419 Z= 0.183 Angle : 0.567 13.957 10099 Z= 0.271 Chirality : 0.039 0.191 1166 Planarity : 0.003 0.035 1258 Dihedral : 3.523 15.379 1072 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.61 % Allowed : 21.81 % 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: 2.03 (0.28), residues: 920 helix: 2.56 (0.23), residues: 514 sheet: 1.76 (0.70), residues: 51 loop : -0.61 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 316 HIS 0.002 0.000 HIS A 557 PHE 0.014 0.001 PHE A 542 TYR 0.030 0.001 TYR A 251 ARG 0.002 0.000 ARG B 418 ********************** 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 118 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.797 Fit side-chains REVERT: A 251 TYR cc_start: 0.7719 (t80) cc_final: 0.7421 (t80) REVERT: A 290 ASP cc_start: 0.8118 (m-30) cc_final: 0.7700 (t0) REVERT: A 340 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7375 (mm-40) REVERT: A 452 ARG cc_start: 0.7965 (mtt-85) cc_final: 0.6416 (mtt90) REVERT: B 60 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7857 (mt) REVERT: B 196 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6036 (mm) REVERT: B 208 GLN cc_start: 0.7373 (mm-40) cc_final: 0.6697 (tt0) REVERT: B 227 MET cc_start: 0.6412 (OUTLIER) cc_final: 0.6077 (ttp) outliers start: 28 outliers final: 22 residues processed: 109 average time/residue: 0.1654 time to fit residues: 25.7082 Evaluate side-chains 113 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 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 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 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 154 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 196 LEU 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 438 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 477 HIS Chi-restraints excluded: chain B residue 488 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.0370 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.180438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.139960 restraints weight = 9099.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138760 restraints weight = 9148.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.140264 restraints weight = 8977.551| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7419 Z= 0.169 Angle : 0.564 13.714 10099 Z= 0.268 Chirality : 0.039 0.189 1166 Planarity : 0.003 0.034 1258 Dihedral : 3.507 15.277 1072 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.35 % Allowed : 21.68 % Favored : 74.97 % 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: 2.05 (0.29), residues: 920 helix: 2.58 (0.23), residues: 514 sheet: 1.79 (0.71), residues: 51 loop : -0.61 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 316 HIS 0.002 0.000 HIS A 557 PHE 0.014 0.001 PHE A 542 TYR 0.027 0.001 TYR A 251 ARG 0.002 0.000 ARG B 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1581.98 seconds wall clock time: 33 minutes 29.33 seconds (2009.33 seconds total)