Starting phenix.real_space_refine on Sat Jul 20 12:49:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyp_36729/07_2024/8jyp_36729.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyp_36729/07_2024/8jyp_36729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyp_36729/07_2024/8jyp_36729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyp_36729/07_2024/8jyp_36729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyp_36729/07_2024/8jyp_36729.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyp_36729/07_2024/8jyp_36729.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4890 atoms to isotropic. 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 37 5.16 5 C 4235 2.51 5 N 1081 2.21 5 O 1274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6627 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1581 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 14, 'TRANS': 184} Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.97, per 1000 atoms: 0.75 Number of scatterers: 6627 At special positions: 0 Unit cell: (99.495, 80.4, 124.62, 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 37 16.00 O 1274 8.00 N 1081 7.00 C 4235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG B 1 " - " ASN D 546 " " NAG C 1 " - " ASN D 90 " " NAG D 701 " - " ASN D 322 " " NAG D 702 " - " ASN D 432 " " NAG D 703 " - " ASN D 53 " " NAG E 1 " - " ASN D 103 " Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 53.2% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.566A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.560A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.851A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 92 through 104 removed outlier: 3.666A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.652A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.837A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 233 removed outlier: 3.933A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.534A pdb=" N TYR D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.831A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.617A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.733A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.236A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.574A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.328A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 482 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.218A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.677A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.944A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.671A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.726A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.698A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.796A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 350 284 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2091 1.34 - 1.46: 1769 1.46 - 1.58: 2895 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6813 Sorted by residual: bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" CA LEU D 351 " pdb=" C LEU D 351 " ideal model delta sigma weight residual 1.523 1.500 0.022 1.41e-02 5.03e+03 2.47e+00 bond pdb=" C1 MAN E 4 " pdb=" C2 MAN E 4 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C1 NAG D 703 " pdb=" O5 NAG D 703 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 6808 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.52: 226 106.52 - 113.38: 3612 113.38 - 120.25: 2504 120.25 - 127.11: 2816 127.11 - 133.98: 104 Bond angle restraints: 9262 Sorted by residual: angle pdb=" C HIS D 34 " pdb=" N GLU D 35 " pdb=" CA GLU D 35 " ideal model delta sigma weight residual 120.31 114.89 5.42 1.52e+00 4.33e-01 1.27e+01 angle pdb=" C GLU D 182 " pdb=" N TYR D 183 " pdb=" CA TYR D 183 " ideal model delta sigma weight residual 120.44 124.57 -4.13 1.30e+00 5.92e-01 1.01e+01 angle pdb=" C PRO D 135 " pdb=" N ASP D 136 " pdb=" CA ASP D 136 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.91e+00 2.74e-01 8.17e+00 angle pdb=" C ALA A 344 " pdb=" N THR A 345 " pdb=" CA THR A 345 " ideal model delta sigma weight residual 121.54 126.77 -5.23 1.91e+00 2.74e-01 7.51e+00 angle pdb=" C ASN D 432 " pdb=" CA ASN D 432 " pdb=" CB ASN D 432 " ideal model delta sigma weight residual 110.84 106.66 4.18 1.66e+00 3.63e-01 6.35e+00 ... (remaining 9257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 3930 21.77 - 43.54: 234 43.54 - 65.31: 16 65.31 - 87.08: 18 87.08 - 108.85: 8 Dihedral angle restraints: 4206 sinusoidal: 1870 harmonic: 2336 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 36.06 56.94 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -141.77 55.77 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 46.67 46.33 1 1.00e+01 1.00e-02 2.97e+01 ... (remaining 4203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 998 0.125 - 0.250: 7 0.250 - 0.375: 5 0.375 - 0.500: 0 0.500 - 0.625: 1 Chirality restraints: 1011 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.76e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN D 546 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 1008 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 163 " 0.016 2.00e-02 2.50e+03 1.16e-02 3.34e+00 pdb=" CG TRP D 163 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP D 163 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP D 163 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 163 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 163 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 163 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 163 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 163 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 163 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 103 " 0.016 2.00e-02 2.50e+03 1.57e-02 3.08e+00 pdb=" CG ASN D 103 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN D 103 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN D 103 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 373 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.021 5.00e-02 4.00e+02 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1896 2.81 - 3.33: 6469 3.33 - 3.86: 10683 3.86 - 4.38: 11942 4.38 - 4.90: 20760 Nonbonded interactions: 51750 Sorted by model distance: nonbonded pdb=" O ASP D 499 " pdb=" OG SER D 502 " model vdw 2.291 2.440 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR D 41 " model vdw 2.294 2.440 nonbonded pdb=" OG SER D 611 " pdb=" O ALA D 614 " model vdw 2.296 2.440 nonbonded pdb=" O GLY D 268 " pdb=" ND2 ASN D 277 " model vdw 2.315 2.520 nonbonded pdb=" OD1 ASP D 494 " pdb=" OG1 THR D 496 " model vdw 2.322 2.440 ... (remaining 51745 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.930 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.490 Find NCS groups from input model: 0.060 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: 35.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 0.035 6813 Z= 0.213 Angle : 0.622 7.805 9262 Z= 0.312 Chirality : 0.051 0.625 1011 Planarity : 0.003 0.038 1179 Dihedral : 14.643 108.849 2685 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.31), residues: 791 helix: 1.06 (0.27), residues: 394 sheet: 1.22 (0.77), residues: 44 loop : -0.77 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 163 HIS 0.003 0.001 HIS D 34 PHE 0.016 0.001 PHE D 32 TYR 0.011 0.001 TYR A 453 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 493 GLN cc_start: 0.8999 (tp40) cc_final: 0.8665 (tp-100) REVERT: D 270 MET cc_start: 0.8223 (tpt) cc_final: 0.7974 (tpp) REVERT: D 474 MET cc_start: 0.8654 (mmp) cc_final: 0.8451 (mmp) REVERT: D 531 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8653 (tm-30) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1476 time to fit residues: 11.0793 Evaluate side-chains 38 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 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 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6813 Z= 0.205 Angle : 0.547 7.340 9262 Z= 0.270 Chirality : 0.044 0.287 1011 Planarity : 0.003 0.036 1179 Dihedral : 9.947 73.976 1148 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.86 % Allowed : 5.01 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.31), residues: 791 helix: 1.72 (0.27), residues: 391 sheet: 0.93 (0.78), residues: 44 loop : -0.84 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 163 HIS 0.003 0.001 HIS D 373 PHE 0.008 0.001 PHE D 512 TYR 0.012 0.001 TYR A 453 ARG 0.002 0.000 ARG D 518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 493 GLN cc_start: 0.9008 (tp40) cc_final: 0.8718 (tp-100) REVERT: D 108 LEU cc_start: 0.9090 (mm) cc_final: 0.8831 (tp) REVERT: D 270 MET cc_start: 0.8258 (tpt) cc_final: 0.8056 (tpp) REVERT: D 531 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8682 (tm-30) outliers start: 6 outliers final: 2 residues processed: 39 average time/residue: 0.1424 time to fit residues: 8.8239 Evaluate side-chains 39 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6813 Z= 0.210 Angle : 0.532 8.110 9262 Z= 0.259 Chirality : 0.044 0.291 1011 Planarity : 0.003 0.036 1179 Dihedral : 8.046 63.887 1148 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.86 % Allowed : 7.74 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.31), residues: 791 helix: 1.82 (0.27), residues: 394 sheet: 0.63 (0.79), residues: 44 loop : -0.79 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 163 HIS 0.002 0.001 HIS D 373 PHE 0.012 0.001 PHE D 315 TYR 0.013 0.001 TYR A 453 ARG 0.001 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 493 GLN cc_start: 0.8999 (tp40) cc_final: 0.8713 (tp-100) REVERT: D 108 LEU cc_start: 0.9131 (mm) cc_final: 0.8858 (tp) REVERT: D 531 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8756 (tm-30) outliers start: 6 outliers final: 3 residues processed: 41 average time/residue: 0.1420 time to fit residues: 9.0826 Evaluate side-chains 36 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 427 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 75 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6813 Z= 0.143 Angle : 0.520 8.262 9262 Z= 0.248 Chirality : 0.044 0.292 1011 Planarity : 0.003 0.036 1179 Dihedral : 7.145 57.722 1148 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.15 % Allowed : 8.02 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.31), residues: 791 helix: 1.85 (0.27), residues: 396 sheet: 0.79 (0.82), residues: 42 loop : -0.73 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 163 HIS 0.002 0.001 HIS D 373 PHE 0.009 0.001 PHE D 315 TYR 0.009 0.001 TYR D 50 ARG 0.001 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 493 GLN cc_start: 0.8995 (tp40) cc_final: 0.8683 (tp-100) REVERT: D 75 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8724 (mt-10) REVERT: D 108 LEU cc_start: 0.9107 (mm) cc_final: 0.8835 (tp) REVERT: D 531 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8720 (tm-30) outliers start: 8 outliers final: 2 residues processed: 42 average time/residue: 0.1467 time to fit residues: 9.9880 Evaluate side-chains 38 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain D residue 75 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6813 Z= 0.261 Angle : 0.564 9.232 9262 Z= 0.272 Chirality : 0.045 0.298 1011 Planarity : 0.003 0.034 1179 Dihedral : 6.758 53.046 1148 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.58 % Allowed : 9.31 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.31), residues: 791 helix: 1.89 (0.27), residues: 394 sheet: 0.56 (0.79), residues: 43 loop : -0.77 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 477 HIS 0.003 0.001 HIS D 195 PHE 0.011 0.001 PHE D 315 TYR 0.013 0.001 TYR A 453 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.9009 (tp40) cc_final: 0.8682 (tp-100) REVERT: D 75 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8693 (mt-10) REVERT: D 303 ASP cc_start: 0.6538 (OUTLIER) cc_final: 0.6239 (p0) REVERT: D 531 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8789 (tm-30) outliers start: 11 outliers final: 6 residues processed: 43 average time/residue: 0.1385 time to fit residues: 9.3264 Evaluate side-chains 42 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.0060 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 42 optimal weight: 8.9990 overall best weight: 0.5354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6813 Z= 0.142 Angle : 0.535 9.532 9262 Z= 0.252 Chirality : 0.044 0.303 1011 Planarity : 0.003 0.036 1179 Dihedral : 6.220 53.835 1148 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.72 % Allowed : 9.60 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.31), residues: 791 helix: 1.94 (0.27), residues: 393 sheet: 0.72 (0.83), residues: 42 loop : -0.73 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 271 HIS 0.002 0.001 HIS D 373 PHE 0.008 0.001 PHE D 315 TYR 0.009 0.001 TYR D 50 ARG 0.001 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.8995 (tp40) cc_final: 0.8673 (tp-100) REVERT: D 133 CYS cc_start: 0.6276 (OUTLIER) cc_final: 0.4871 (p) REVERT: D 303 ASP cc_start: 0.6384 (OUTLIER) cc_final: 0.6081 (p0) REVERT: D 531 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8768 (tm-30) outliers start: 12 outliers final: 4 residues processed: 45 average time/residue: 0.1403 time to fit residues: 9.8364 Evaluate side-chains 40 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6813 Z= 0.324 Angle : 0.602 10.753 9262 Z= 0.290 Chirality : 0.045 0.303 1011 Planarity : 0.003 0.040 1179 Dihedral : 6.158 52.418 1148 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.44 % Allowed : 9.89 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.31), residues: 791 helix: 1.89 (0.27), residues: 392 sheet: 0.40 (0.78), residues: 43 loop : -0.82 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 610 HIS 0.004 0.001 HIS D 195 PHE 0.010 0.001 PHE D 315 TYR 0.014 0.001 TYR A 453 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 34 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8627 (p0) REVERT: A 493 GLN cc_start: 0.9016 (tp40) cc_final: 0.8618 (tp-100) REVERT: D 133 CYS cc_start: 0.6223 (OUTLIER) cc_final: 0.4803 (p) REVERT: D 152 MET cc_start: 0.9360 (mtm) cc_final: 0.8803 (ptp) REVERT: D 303 ASP cc_start: 0.6548 (OUTLIER) cc_final: 0.6241 (p0) REVERT: D 531 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8822 (tm-30) outliers start: 17 outliers final: 8 residues processed: 49 average time/residue: 0.1349 time to fit residues: 10.1856 Evaluate side-chains 45 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 34 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 468 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6813 Z= 0.170 Angle : 0.544 10.573 9262 Z= 0.256 Chirality : 0.044 0.313 1011 Planarity : 0.003 0.046 1179 Dihedral : 5.706 53.581 1148 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.72 % Allowed : 10.60 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.31), residues: 791 helix: 1.91 (0.27), residues: 394 sheet: 0.52 (0.80), residues: 43 loop : -0.77 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS D 373 PHE 0.008 0.001 PHE D 315 TYR 0.010 0.001 TYR A 453 ARG 0.001 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 34 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.9016 (tp40) cc_final: 0.8664 (tp-100) REVERT: D 133 CYS cc_start: 0.6350 (OUTLIER) cc_final: 0.5055 (p) REVERT: D 152 MET cc_start: 0.9354 (mtm) cc_final: 0.8868 (ptp) REVERT: D 303 ASP cc_start: 0.6396 (OUTLIER) cc_final: 0.6096 (p0) REVERT: D 531 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8801 (tm-30) outliers start: 12 outliers final: 7 residues processed: 44 average time/residue: 0.1370 time to fit residues: 9.4161 Evaluate side-chains 43 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 468 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6813 Z= 0.197 Angle : 0.564 10.237 9262 Z= 0.266 Chirality : 0.044 0.304 1011 Planarity : 0.003 0.045 1179 Dihedral : 5.581 53.357 1148 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.72 % Allowed : 10.89 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.31), residues: 791 helix: 1.90 (0.27), residues: 394 sheet: 0.49 (0.80), residues: 43 loop : -0.78 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 477 HIS 0.002 0.001 HIS D 195 PHE 0.009 0.001 PHE D 452 TYR 0.009 0.001 TYR A 453 ARG 0.001 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 35 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.9024 (tp40) cc_final: 0.8651 (tp-100) REVERT: D 133 CYS cc_start: 0.6217 (OUTLIER) cc_final: 0.4889 (p) REVERT: D 152 MET cc_start: 0.9362 (mtm) cc_final: 0.8971 (ptp) REVERT: D 303 ASP cc_start: 0.6426 (OUTLIER) cc_final: 0.6126 (p0) REVERT: D 531 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8811 (tm-30) outliers start: 12 outliers final: 8 residues processed: 45 average time/residue: 0.1355 time to fit residues: 9.5679 Evaluate side-chains 44 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 34 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6813 Z= 0.200 Angle : 0.563 10.562 9262 Z= 0.265 Chirality : 0.043 0.315 1011 Planarity : 0.003 0.045 1179 Dihedral : 5.510 53.062 1148 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.86 % Allowed : 10.89 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.31), residues: 791 helix: 1.91 (0.27), residues: 394 sheet: 0.47 (0.80), residues: 43 loop : -0.79 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS D 195 PHE 0.009 0.001 PHE D 315 TYR 0.010 0.001 TYR A 453 ARG 0.001 0.000 ARG D 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 35 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.9014 (tp40) cc_final: 0.8591 (tp-100) REVERT: D 133 CYS cc_start: 0.6093 (OUTLIER) cc_final: 0.4751 (p) REVERT: D 152 MET cc_start: 0.9324 (mtm) cc_final: 0.8990 (ptp) REVERT: D 303 ASP cc_start: 0.6427 (OUTLIER) cc_final: 0.6127 (p0) REVERT: D 531 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8797 (tm-30) outliers start: 13 outliers final: 8 residues processed: 46 average time/residue: 0.1346 time to fit residues: 9.8282 Evaluate side-chains 45 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.0000 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.070574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.049163 restraints weight = 25890.724| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 4.55 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6813 Z= 0.178 Angle : 0.549 10.482 9262 Z= 0.260 Chirality : 0.043 0.314 1011 Planarity : 0.003 0.045 1179 Dihedral : 5.441 53.686 1148 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.86 % Allowed : 10.89 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.31), residues: 791 helix: 1.94 (0.27), residues: 394 sheet: 0.58 (0.82), residues: 42 loop : -0.78 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS D 373 PHE 0.008 0.001 PHE D 315 TYR 0.009 0.001 TYR D 50 ARG 0.001 0.000 ARG D 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1569.84 seconds wall clock time: 28 minutes 59.46 seconds (1739.46 seconds total)