Starting phenix.real_space_refine on Sat Aug 3 20:20:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsq_41598/08_2024/8tsq_41598.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsq_41598/08_2024/8tsq_41598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsq_41598/08_2024/8tsq_41598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsq_41598/08_2024/8tsq_41598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsq_41598/08_2024/8tsq_41598.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsq_41598/08_2024/8tsq_41598.cif" } resolution = 3.6 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= 0.052 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 54 5.16 5 C 5652 2.51 5 N 1552 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 54": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A ASP 524": "OD1" <-> "OD2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B ASP 512": "OD1" <-> "OD2" Residue "B GLU 525": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4459 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 13, 'TRANS': 561} Chain: "B" Number of atoms: 4459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4459 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 13, 'TRANS': 561} Time building chain proxies: 5.41, per 1000 atoms: 0.61 Number of scatterers: 8918 At special positions: 0 Unit cell: (75.615, 133.125, 135.255, 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 54 16.00 O 1660 8.00 N 1552 7.00 C 5652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.40 Conformation dependent library (CDL) restraints added in 1.6 seconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 69.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 23 through 47 removed outlier: 3.538A pdb=" N LEU A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 62 through 109 Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.817A pdb=" N PHE A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 164 removed outlier: 4.054A pdb=" N ASP A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 212 Proline residue: A 176 - end of helix removed outlier: 4.072A pdb=" N THR A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 removed outlier: 4.132A pdb=" N ILE A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 272 removed outlier: 3.953A pdb=" N GLU A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 3.583A pdb=" N PHE A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 4.108A pdb=" N ASP A 277 " --> pdb=" O PRO A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 294 removed outlier: 3.724A pdb=" N ILE A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 322 removed outlier: 3.696A pdb=" N LYS A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 459 through 465 removed outlier: 4.022A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.540A pdb=" N ASP A 471 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 497 Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.868A pdb=" N ILE A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'B' and resid 8 through 21 removed outlier: 3.799A pdb=" N THR B 12 " --> pdb=" O SER B 8 " (cutoff:3.500A) Proline residue: B 18 - end of helix Processing helix chain 'B' and resid 23 through 47 removed outlier: 3.513A pdb=" N LEU B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.541A pdb=" N LEU B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 54 " --> pdb=" O PRO B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 109 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.779A pdb=" N PHE B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 164 removed outlier: 3.597A pdb=" N LEU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 212 Proline residue: B 176 - end of helix removed outlier: 4.102A pdb=" N THR B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 removed outlier: 4.130A pdb=" N ILE B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 250 removed outlier: 3.970A pdb=" N GLU B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 272 removed outlier: 3.906A pdb=" N ILE B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 4.046A pdb=" N ASP B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 294 removed outlier: 3.760A pdb=" N ILE B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 322 removed outlier: 3.560A pdb=" N LYS B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASN B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 389 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.744A pdb=" N GLN B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 414 through 418' Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 465 removed outlier: 4.036A pdb=" N LYS B 465 " --> pdb=" O ASP B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 472 Processing helix chain 'B' and resid 482 through 497 Processing helix chain 'B' and resid 515 through 527 removed outlier: 3.853A pdb=" N ILE B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 570 through 578 Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 366 removed outlier: 5.628A pdb=" N PHE A 344 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU A 401 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASN A 346 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU A 399 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422 removed outlier: 6.449A pdb=" N LEU A 502 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE A 535 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU A 504 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 372 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR A 371 " --> pdb=" O GLU A 547 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 359 through 366 removed outlier: 6.474A pdb=" N ARG B 360 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR B 348 " --> pdb=" O ARG B 360 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE B 362 " --> pdb=" O ASN B 346 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N PHE B 344 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU B 401 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASN B 346 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU B 399 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 422 removed outlier: 6.218A pdb=" N ALA B 420 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ASP B 505 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 422 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU B 502 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE B 535 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B 504 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL B 372 " --> pdb=" O VAL B 534 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1668 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: 2.57 Time building geometry restraints manager: 4.72 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: 2801 1.34 - 1.46: 1173 1.46 - 1.58: 4972 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 9050 Sorted by residual: bond pdb=" N VAL B 113 " pdb=" CA VAL B 113 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.24e-02 6.50e+03 6.93e+00 bond pdb=" N VAL A 113 " pdb=" CA VAL A 113 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.26e-02 6.30e+03 6.89e+00 bond pdb=" N MET A 109 " pdb=" CA MET A 109 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.22e-02 6.72e+03 5.43e+00 bond pdb=" N MET A 111 " pdb=" CA MET A 111 " ideal model delta sigma weight residual 1.452 1.488 -0.035 1.54e-02 4.22e+03 5.29e+00 bond pdb=" N MET B 111 " pdb=" CA MET B 111 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.69e-02 3.50e+03 4.89e+00 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.06: 122 105.06 - 112.31: 4722 112.31 - 119.55: 3040 119.55 - 126.80: 4271 126.80 - 134.05: 75 Bond angle restraints: 12230 Sorted by residual: angle pdb=" N GLY B 110 " pdb=" CA GLY B 110 " pdb=" C GLY B 110 " ideal model delta sigma weight residual 115.32 109.41 5.91 1.48e+00 4.57e-01 1.60e+01 angle pdb=" N GLY A 110 " pdb=" CA GLY A 110 " pdb=" C GLY A 110 " ideal model delta sigma weight residual 115.32 110.13 5.19 1.48e+00 4.57e-01 1.23e+01 angle pdb=" CA MET A 109 " pdb=" C MET A 109 " pdb=" O MET A 109 " ideal model delta sigma weight residual 121.16 117.74 3.42 1.12e+00 7.97e-01 9.30e+00 angle pdb=" CB MET B 200 " pdb=" CG MET B 200 " pdb=" SD MET B 200 " ideal model delta sigma weight residual 112.70 121.38 -8.68 3.00e+00 1.11e-01 8.37e+00 angle pdb=" CA LEU A 294 " pdb=" CB LEU A 294 " pdb=" CG LEU A 294 " ideal model delta sigma weight residual 116.30 126.33 -10.03 3.50e+00 8.16e-02 8.22e+00 ... (remaining 12225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4777 17.95 - 35.90: 545 35.90 - 53.84: 133 53.84 - 71.79: 41 71.79 - 89.74: 8 Dihedral angle restraints: 5504 sinusoidal: 2182 harmonic: 3322 Sorted by residual: dihedral pdb=" CA ARG A 391 " pdb=" C ARG A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ARG B 391 " pdb=" C ARG B 391 " pdb=" N PHE B 392 " pdb=" CA PHE B 392 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASP B 467 " pdb=" CB ASP B 467 " pdb=" CG ASP B 467 " pdb=" OD1 ASP B 467 " ideal model delta sinusoidal sigma weight residual -30.00 -89.42 59.42 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 5501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1037 0.040 - 0.080: 319 0.080 - 0.120: 90 0.120 - 0.160: 5 0.160 - 0.200: 3 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CA MET A 109 " pdb=" N MET A 109 " pdb=" C MET A 109 " pdb=" CB MET A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CB ILE B 258 " pdb=" CA ILE B 258 " pdb=" CG1 ILE B 258 " pdb=" CG2 ILE B 258 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA MET B 111 " pdb=" N MET B 111 " pdb=" C MET B 111 " pdb=" CB MET B 111 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.04e-01 ... (remaining 1451 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 410 " -0.017 2.00e-02 2.50e+03 1.15e-02 2.63e+00 pdb=" CG TYR B 410 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 410 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 410 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 410 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 410 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 410 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 410 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 109 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C MET B 109 " 0.028 2.00e-02 2.50e+03 pdb=" O MET B 109 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY B 110 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 462 " 0.008 2.00e-02 2.50e+03 1.07e-02 2.00e+00 pdb=" CG PHE A 462 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 462 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 462 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 462 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 462 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 462 " -0.000 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1544 2.77 - 3.30: 9259 3.30 - 3.83: 14858 3.83 - 4.37: 16240 4.37 - 4.90: 28196 Nonbonded interactions: 70097 Sorted by model distance: nonbonded pdb=" O PRO B 357 " pdb=" NH2 ARG B 360 " model vdw 2.234 3.120 nonbonded pdb=" OD1 ASN A 430 " pdb=" NE2 GLN B 209 " model vdw 2.239 3.120 nonbonded pdb=" NE2 GLN A 209 " pdb=" OD1 ASN B 430 " model vdw 2.239 3.120 nonbonded pdb=" OG1 THR A 561 " pdb=" OD1 ASN A 563 " model vdw 2.268 3.040 nonbonded pdb=" OG SER B 446 " pdb=" OE1 GLN B 449 " model vdw 2.311 3.040 ... (remaining 70092 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.550 Find NCS groups from input model: 0.230 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9050 Z= 0.238 Angle : 0.655 10.034 12230 Z= 0.361 Chirality : 0.041 0.200 1454 Planarity : 0.004 0.045 1548 Dihedral : 16.891 89.739 3356 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.51 % Allowed : 22.90 % Favored : 76.58 % 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: 1.04 (0.25), residues: 1146 helix: 1.68 (0.19), residues: 720 sheet: 0.31 (0.55), residues: 86 loop : -1.40 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 17 HIS 0.005 0.001 HIS A 107 PHE 0.024 0.001 PHE A 462 TYR 0.026 0.002 TYR B 410 ARG 0.014 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7367 (ttm) cc_final: 0.7138 (ttm) outliers start: 5 outliers final: 1 residues processed: 119 average time/residue: 0.1948 time to fit residues: 33.4289 Evaluate side-chains 111 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 0.0980 chunk 103 optimal weight: 5.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN B 405 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9050 Z= 0.173 Angle : 0.531 8.432 12230 Z= 0.279 Chirality : 0.040 0.135 1454 Planarity : 0.004 0.035 1548 Dihedral : 4.317 42.281 1252 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.37 % Allowed : 19.94 % Favored : 76.69 % 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: 1.16 (0.25), residues: 1146 helix: 1.79 (0.19), residues: 738 sheet: 0.24 (0.56), residues: 86 loop : -1.53 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 17 HIS 0.003 0.001 HIS A 107 PHE 0.018 0.001 PHE B 189 TYR 0.016 0.001 TYR B 410 ARG 0.008 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 0.977 Fit side-chains REVERT: A 312 MET cc_start: 0.7873 (mmp) cc_final: 0.7533 (mmp) REVERT: B 312 MET cc_start: 0.7813 (mmp) cc_final: 0.7419 (mmp) REVERT: B 416 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8177 (mtt-85) outliers start: 33 outliers final: 17 residues processed: 148 average time/residue: 0.1743 time to fit residues: 38.1867 Evaluate side-chains 134 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 470 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 9050 Z= 0.486 Angle : 0.729 8.616 12230 Z= 0.387 Chirality : 0.047 0.194 1454 Planarity : 0.005 0.041 1548 Dihedral : 4.935 51.787 1252 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.91 % Allowed : 19.94 % Favored : 75.15 % 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: 0.28 (0.25), residues: 1146 helix: 1.05 (0.19), residues: 748 sheet: -0.09 (0.57), residues: 88 loop : -1.83 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 17 HIS 0.007 0.001 HIS A 214 PHE 0.024 0.003 PHE B 189 TYR 0.024 0.003 TYR B 393 ARG 0.009 0.001 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 116 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8080 (ttm) cc_final: 0.7721 (ttm) REVERT: A 382 LYS cc_start: 0.6400 (OUTLIER) cc_final: 0.5712 (pptt) REVERT: B 416 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8498 (mtt-85) outliers start: 48 outliers final: 25 residues processed: 150 average time/residue: 0.2001 time to fit residues: 42.0478 Evaluate side-chains 136 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9050 Z= 0.263 Angle : 0.583 8.493 12230 Z= 0.307 Chirality : 0.042 0.145 1454 Planarity : 0.004 0.039 1548 Dihedral : 4.699 56.571 1252 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.21 % Allowed : 20.25 % Favored : 74.54 % 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: 0.68 (0.25), residues: 1146 helix: 1.42 (0.19), residues: 748 sheet: -0.19 (0.56), residues: 88 loop : -1.75 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 17 HIS 0.006 0.001 HIS B 537 PHE 0.017 0.002 PHE B 189 TYR 0.015 0.002 TYR B 393 ARG 0.009 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 120 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8048 (ttm) cc_final: 0.7638 (ttm) REVERT: A 111 MET cc_start: 0.6762 (ttt) cc_final: 0.6434 (ttp) REVERT: A 382 LYS cc_start: 0.6345 (OUTLIER) cc_final: 0.5663 (pptt) REVERT: B 416 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8343 (mtt-85) outliers start: 51 outliers final: 27 residues processed: 158 average time/residue: 0.1781 time to fit residues: 41.2144 Evaluate side-chains 147 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN B 240 GLN B 405 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9050 Z= 0.205 Angle : 0.568 10.703 12230 Z= 0.293 Chirality : 0.041 0.160 1454 Planarity : 0.004 0.039 1548 Dihedral : 4.597 58.533 1252 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.89 % Allowed : 21.88 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1146 helix: 1.64 (0.19), residues: 750 sheet: -0.20 (0.56), residues: 88 loop : -1.77 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 91 HIS 0.003 0.001 HIS B 405 PHE 0.017 0.001 PHE B 189 TYR 0.017 0.001 TYR B 410 ARG 0.010 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 117 time to evaluate : 1.012 Fit side-chains REVERT: A 98 MET cc_start: 0.7527 (ttm) cc_final: 0.7287 (ttm) REVERT: A 312 MET cc_start: 0.8034 (mmp) cc_final: 0.7739 (mmp) REVERT: A 382 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5390 (pptt) REVERT: B 310 ARG cc_start: 0.7062 (tmm-80) cc_final: 0.6454 (tmm-80) outliers start: 38 outliers final: 29 residues processed: 143 average time/residue: 0.1891 time to fit residues: 38.7851 Evaluate side-chains 148 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.0770 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 HIS ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9050 Z= 0.192 Angle : 0.554 9.822 12230 Z= 0.286 Chirality : 0.040 0.130 1454 Planarity : 0.004 0.037 1548 Dihedral : 4.487 53.728 1252 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.68 % Allowed : 22.80 % Favored : 73.52 % 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: 1.07 (0.25), residues: 1146 helix: 1.77 (0.19), residues: 750 sheet: -0.21 (0.56), residues: 88 loop : -1.72 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.003 0.001 HIS A 405 PHE 0.021 0.001 PHE B 56 TYR 0.018 0.001 TYR B 410 ARG 0.011 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 122 time to evaluate : 0.939 Fit side-chains REVERT: A 310 ARG cc_start: 0.7055 (tmm-80) cc_final: 0.6789 (tmm-80) REVERT: A 312 MET cc_start: 0.7871 (mmp) cc_final: 0.7593 (mmp) REVERT: A 382 LYS cc_start: 0.6148 (OUTLIER) cc_final: 0.5414 (pptt) REVERT: B 75 MET cc_start: 0.6489 (mtp) cc_final: 0.6279 (mtp) outliers start: 36 outliers final: 28 residues processed: 146 average time/residue: 0.1801 time to fit residues: 37.7716 Evaluate side-chains 143 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN B 405 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9050 Z= 0.213 Angle : 0.578 10.067 12230 Z= 0.296 Chirality : 0.041 0.131 1454 Planarity : 0.004 0.041 1548 Dihedral : 4.438 49.557 1252 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.99 % Allowed : 22.39 % Favored : 73.62 % 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 (0.25), residues: 1146 helix: 1.76 (0.19), residues: 750 sheet: -0.26 (0.56), residues: 88 loop : -1.70 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 91 HIS 0.003 0.001 HIS B 405 PHE 0.026 0.002 PHE B 462 TYR 0.024 0.001 TYR B 410 ARG 0.012 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 114 time to evaluate : 1.007 Fit side-chains REVERT: A 310 ARG cc_start: 0.7096 (tmm-80) cc_final: 0.6442 (tmm-80) REVERT: A 312 MET cc_start: 0.7932 (mmp) cc_final: 0.7623 (mmp) REVERT: A 382 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5450 (pptt) REVERT: B 310 ARG cc_start: 0.7081 (tmm-80) cc_final: 0.6464 (tmm-80) REVERT: B 393 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7711 (p90) outliers start: 39 outliers final: 32 residues processed: 140 average time/residue: 0.1893 time to fit residues: 37.8034 Evaluate side-chains 148 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS B 405 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9050 Z= 0.219 Angle : 0.596 11.502 12230 Z= 0.301 Chirality : 0.041 0.144 1454 Planarity : 0.004 0.046 1548 Dihedral : 4.415 44.655 1252 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.11 % Allowed : 21.27 % Favored : 73.62 % 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: 1.08 (0.26), residues: 1146 helix: 1.76 (0.19), residues: 750 sheet: -0.25 (0.56), residues: 88 loop : -1.65 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 91 HIS 0.005 0.001 HIS B 537 PHE 0.017 0.002 PHE B 189 TYR 0.022 0.001 TYR B 410 ARG 0.013 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 115 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 312 MET cc_start: 0.7937 (mmp) cc_final: 0.7640 (mmp) REVERT: A 382 LYS cc_start: 0.6162 (OUTLIER) cc_final: 0.5487 (pptt) REVERT: B 310 ARG cc_start: 0.7069 (tmm-80) cc_final: 0.6505 (tmm-80) REVERT: B 393 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7699 (p90) outliers start: 50 outliers final: 39 residues processed: 151 average time/residue: 0.1952 time to fit residues: 41.8370 Evaluate side-chains 156 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 115 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 523 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 405 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9050 Z= 0.223 Angle : 0.617 11.639 12230 Z= 0.310 Chirality : 0.041 0.159 1454 Planarity : 0.004 0.046 1548 Dihedral : 4.409 42.051 1252 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.99 % Allowed : 22.29 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1146 helix: 1.77 (0.19), residues: 750 sheet: -0.40 (0.55), residues: 88 loop : -1.71 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 91 HIS 0.005 0.001 HIS B 537 PHE 0.017 0.002 PHE B 189 TYR 0.028 0.001 TYR B 410 ARG 0.014 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 119 time to evaluate : 1.059 Fit side-chains REVERT: A 310 ARG cc_start: 0.7111 (tmm-80) cc_final: 0.6762 (tmm-80) REVERT: A 312 MET cc_start: 0.7977 (mmp) cc_final: 0.7687 (mmp) REVERT: A 382 LYS cc_start: 0.6186 (OUTLIER) cc_final: 0.5505 (pptt) REVERT: B 310 ARG cc_start: 0.7076 (tmm-80) cc_final: 0.6513 (tmm-80) REVERT: B 393 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7729 (p90) outliers start: 39 outliers final: 35 residues processed: 147 average time/residue: 0.1971 time to fit residues: 41.3256 Evaluate side-chains 152 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 115 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 523 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 HIS B 405 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9050 Z= 0.185 Angle : 0.583 10.959 12230 Z= 0.295 Chirality : 0.041 0.132 1454 Planarity : 0.004 0.051 1548 Dihedral : 4.300 38.892 1252 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.37 % Allowed : 22.70 % Favored : 73.93 % 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: 1.19 (0.26), residues: 1146 helix: 1.91 (0.19), residues: 750 sheet: -0.44 (0.55), residues: 88 loop : -1.71 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.005 0.001 HIS B 537 PHE 0.016 0.001 PHE B 189 TYR 0.031 0.001 TYR B 410 ARG 0.014 0.000 ARG B 559 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 125 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 312 MET cc_start: 0.7862 (mmp) cc_final: 0.7657 (mmp) REVERT: A 382 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.5408 (pptt) REVERT: A 466 MET cc_start: 0.4629 (mmt) cc_final: 0.4132 (mmt) REVERT: B 310 ARG cc_start: 0.7075 (tmm-80) cc_final: 0.6488 (tmm-80) REVERT: B 393 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7899 (p90) outliers start: 33 outliers final: 25 residues processed: 148 average time/residue: 0.2046 time to fit residues: 42.2468 Evaluate side-chains 147 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 523 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 0.0050 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 65 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 197 GLN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 HIS B 405 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.259034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.224710 restraints weight = 9769.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.210267 restraints weight = 14195.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.209054 restraints weight = 9185.576| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9050 Z= 0.214 Angle : 0.634 12.819 12230 Z= 0.316 Chirality : 0.041 0.140 1454 Planarity : 0.004 0.056 1548 Dihedral : 4.398 38.139 1252 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.48 % Allowed : 22.90 % Favored : 73.62 % 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: 1.07 (0.25), residues: 1146 helix: 1.82 (0.19), residues: 750 sheet: -0.59 (0.54), residues: 88 loop : -1.73 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 91 HIS 0.006 0.001 HIS A 405 PHE 0.016 0.001 PHE B 189 TYR 0.033 0.002 TYR B 410 ARG 0.015 0.000 ARG B 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1821.53 seconds wall clock time: 33 minutes 6.32 seconds (1986.32 seconds total)