Starting phenix.real_space_refine on Fri Nov 15 17:20:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctc_26985/11_2024/8ctc_26985.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctc_26985/11_2024/8ctc_26985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctc_26985/11_2024/8ctc_26985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctc_26985/11_2024/8ctc_26985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctc_26985/11_2024/8ctc_26985.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctc_26985/11_2024/8ctc_26985.cif" } resolution = 2.8 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= 0.012 sd= 0.147 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: 6 Type Number sf(0) Gaussians Hg 3 10.96 5 S 60 5.16 5 Na 9 4.78 5 C 6090 2.51 5 N 1479 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9309 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3085 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' HG': 1, ' NA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1577 SG CYS A 269 83.711 62.418 25.018 1.00 74.49 S ATOM 2858 SG CYS A 441 81.025 63.145 27.129 1.00 85.07 S Restraints were copied for chains: C, B Time building chain proxies: 5.82, per 1000 atoms: 0.63 Number of scatterers: 9309 At special positions: 0 Unit cell: (108.3, 99.636, 73.644, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Hg 3 79.96 S 60 16.00 Na 9 11.00 O 1668 8.00 N 1479 7.00 C 6090 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 84.3% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 4.050A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 53 through 82 removed outlier: 3.570A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 4.100A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.601A pdb=" N TYR A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.839A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.539A pdb=" N ALA A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 233 through 268 removed outlier: 3.525A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 284 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.864A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 removed outlier: 4.029A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 4.521A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.524A pdb=" N ILE A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.970A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.520A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 437 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA A 438 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 465 removed outlier: 3.703A pdb=" N LEU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'B' and resid 18 through 42 removed outlier: 4.049A pdb=" N LEU B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 53 through 82 removed outlier: 3.571A pdb=" N ILE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix removed outlier: 4.100A pdb=" N LEU B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 117 removed outlier: 3.600A pdb=" N TYR B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.839A pdb=" N LEU B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.539A pdb=" N ALA B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 230 Processing helix chain 'B' and resid 233 through 268 removed outlier: 3.526A pdb=" N VAL B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TRP B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.864A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 351 through 366 removed outlier: 4.030A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix removed outlier: 4.521A pdb=" N THR B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 Processing helix chain 'B' and resid 390 through 408 removed outlier: 3.524A pdb=" N ILE B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 426 removed outlier: 3.970A pdb=" N VAL B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 438 removed outlier: 3.520A pdb=" N ASP B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL B 433 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 437 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA B 438 " --> pdb=" O LEU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 465 removed outlier: 3.703A pdb=" N LEU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'C' and resid 18 through 42 removed outlier: 4.050A pdb=" N LEU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 53 through 82 removed outlier: 3.571A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix removed outlier: 4.100A pdb=" N LEU C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 117 removed outlier: 3.601A pdb=" N TYR C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.839A pdb=" N LEU C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.539A pdb=" N ALA C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 230 Processing helix chain 'C' and resid 233 through 268 removed outlier: 3.525A pdb=" N VAL C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix Processing helix chain 'C' and resid 276 through 282 Processing helix chain 'C' and resid 284 through 299 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.863A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 351 through 366 removed outlier: 4.029A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix removed outlier: 4.520A pdb=" N THR C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 390 through 408 removed outlier: 3.524A pdb=" N ILE C 397 " --> pdb=" O GLN C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 426 removed outlier: 3.969A pdb=" N VAL C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 438 removed outlier: 3.520A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C 433 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 437 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ALA C 438 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 465 removed outlier: 3.702A pdb=" N LEU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 470 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167 699 hydrogen bonds defined for protein. 2043 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: 2.65 Time building geometry restraints manager: 2.88 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: 2837 1.34 - 1.46: 1120 1.46 - 1.57: 5352 1.57 - 1.69: 0 1.69 - 1.81: 111 Bond restraints: 9420 Sorted by residual: bond pdb=" N ASP B 275 " pdb=" CA ASP B 275 " ideal model delta sigma weight residual 1.458 1.494 -0.036 9.00e-03 1.23e+04 1.59e+01 bond pdb=" N ASP A 275 " pdb=" CA ASP A 275 " ideal model delta sigma weight residual 1.458 1.494 -0.036 9.00e-03 1.23e+04 1.59e+01 bond pdb=" N ASP C 275 " pdb=" CA ASP C 275 " ideal model delta sigma weight residual 1.458 1.493 -0.035 9.00e-03 1.23e+04 1.50e+01 bond pdb=" N TRP C 276 " pdb=" CA TRP C 276 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.45e+00 bond pdb=" N TRP B 276 " pdb=" CA TRP B 276 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 8.99e+00 ... (remaining 9415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 11892 1.33 - 2.65: 708 2.65 - 3.98: 156 3.98 - 5.30: 18 5.30 - 6.63: 12 Bond angle restraints: 12786 Sorted by residual: angle pdb=" CA GLU C 274 " pdb=" C GLU C 274 " pdb=" O GLU C 274 " ideal model delta sigma weight residual 120.70 116.80 3.90 1.03e+00 9.43e-01 1.44e+01 angle pdb=" CA GLU B 274 " pdb=" C GLU B 274 " pdb=" O GLU B 274 " ideal model delta sigma weight residual 120.70 116.80 3.90 1.03e+00 9.43e-01 1.43e+01 angle pdb=" CA GLU A 274 " pdb=" C GLU A 274 " pdb=" O GLU A 274 " ideal model delta sigma weight residual 120.70 116.84 3.86 1.03e+00 9.43e-01 1.41e+01 angle pdb=" N ARG B 315 " pdb=" CA ARG B 315 " pdb=" C ARG B 315 " ideal model delta sigma weight residual 111.36 107.48 3.88 1.09e+00 8.42e-01 1.26e+01 angle pdb=" N ARG A 315 " pdb=" CA ARG A 315 " pdb=" C ARG A 315 " ideal model delta sigma weight residual 111.36 107.52 3.84 1.09e+00 8.42e-01 1.24e+01 ... (remaining 12781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.44: 4906 14.44 - 28.89: 486 28.89 - 43.33: 176 43.33 - 57.77: 45 57.77 - 72.22: 12 Dihedral angle restraints: 5625 sinusoidal: 2130 harmonic: 3495 Sorted by residual: dihedral pdb=" CG ARG C 147 " pdb=" CD ARG C 147 " pdb=" NE ARG C 147 " pdb=" CZ ARG C 147 " ideal model delta sinusoidal sigma weight residual 180.00 136.17 43.83 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG A 147 " pdb=" CD ARG A 147 " pdb=" NE ARG A 147 " pdb=" CZ ARG A 147 " ideal model delta sinusoidal sigma weight residual 180.00 136.22 43.78 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG B 147 " pdb=" CD ARG B 147 " pdb=" NE ARG B 147 " pdb=" CZ ARG B 147 " ideal model delta sinusoidal sigma weight residual 180.00 136.22 43.78 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 5622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1099 0.040 - 0.079: 354 0.079 - 0.119: 124 0.119 - 0.159: 34 0.159 - 0.199: 15 Chirality restraints: 1626 Sorted by residual: chirality pdb=" CA VAL B 273 " pdb=" N VAL B 273 " pdb=" C VAL B 273 " pdb=" CB VAL B 273 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CA VAL A 273 " pdb=" N VAL A 273 " pdb=" C VAL A 273 " pdb=" CB VAL A 273 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CA VAL C 273 " pdb=" N VAL C 273 " pdb=" C VAL C 273 " pdb=" CB VAL C 273 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.67e-01 ... (remaining 1623 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 386 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C ASP B 386 " -0.046 2.00e-02 2.50e+03 pdb=" O ASP B 386 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU B 387 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 386 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C ASP A 386 " -0.046 2.00e-02 2.50e+03 pdb=" O ASP A 386 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 387 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 386 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C ASP C 386 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP C 386 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU C 387 " -0.016 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 46 2.51 - 3.11: 7202 3.11 - 3.71: 14387 3.71 - 4.30: 20421 4.30 - 4.90: 34361 Nonbonded interactions: 76417 Sorted by model distance: nonbonded pdb=" OG1 THR B 102 " pdb="NA NA B 603 " model vdw 1.917 2.470 nonbonded pdb=" OG1 THR A 102 " pdb="NA NA A 603 " model vdw 1.918 2.470 nonbonded pdb=" OG1 THR C 102 " pdb="NA NA C 603 " model vdw 1.918 2.470 nonbonded pdb=" SG CYS B 269 " pdb="HG HG B 604 " model vdw 2.067 2.880 nonbonded pdb=" SG CYS A 269 " pdb="HG HG A 604 " model vdw 2.067 2.880 ... (remaining 76412 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' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 23.790 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 : 0.005 0.042 9420 Z= 0.331 Angle : 0.736 6.630 12786 Z= 0.505 Chirality : 0.049 0.199 1626 Planarity : 0.003 0.030 1557 Dihedral : 14.007 72.218 3369 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 15.38 % Favored : 84.62 % 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: 0.39 (0.24), residues: 1200 helix: 0.77 (0.17), residues: 948 sheet: -0.59 (0.68), residues: 54 loop : -1.61 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 19 HIS 0.005 0.002 HIS A 41 PHE 0.011 0.001 PHE C 240 TYR 0.007 0.001 TYR C 257 ARG 0.001 0.000 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.989 Fit side-chains REVERT: A 353 ARG cc_start: 0.6985 (mtm180) cc_final: 0.6295 (mtp180) REVERT: A 367 MET cc_start: 0.9138 (mtt) cc_final: 0.8746 (mtm) REVERT: B 342 ARG cc_start: 0.7531 (ttm110) cc_final: 0.7173 (ttp-110) REVERT: B 346 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6229 (mm-30) REVERT: B 353 ARG cc_start: 0.7402 (mtm180) cc_final: 0.7067 (mtm180) REVERT: C 275 ASP cc_start: 0.7650 (p0) cc_final: 0.7392 (p0) REVERT: C 367 MET cc_start: 0.8994 (mtt) cc_final: 0.8791 (mtm) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 1.0316 time to fit residues: 202.9958 Evaluate side-chains 161 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 0.0670 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 347 ASN A 385 ASN B 348 ASN C 347 ASN C 385 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9420 Z= 0.191 Angle : 0.505 5.260 12786 Z= 0.268 Chirality : 0.038 0.134 1626 Planarity : 0.004 0.038 1557 Dihedral : 4.056 35.348 1281 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.55 % Allowed : 14.20 % Favored : 82.25 % 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: 0.89 (0.24), residues: 1200 helix: 1.21 (0.17), residues: 948 sheet: -0.73 (0.61), residues: 54 loop : -1.85 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 19 HIS 0.004 0.001 HIS B 41 PHE 0.013 0.002 PHE B 240 TYR 0.008 0.001 TYR B 97 ARG 0.007 0.000 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.966 Fit side-chains REVERT: A 256 TRP cc_start: 0.8196 (m-10) cc_final: 0.7818 (m100) REVERT: B 48 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7587 (mt-10) REVERT: B 208 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7979 (m-30) REVERT: B 304 ILE cc_start: 0.8290 (tt) cc_final: 0.7727 (mt) REVERT: B 342 ARG cc_start: 0.7645 (ttm110) cc_final: 0.7361 (ttp-110) REVERT: C 275 ASP cc_start: 0.7477 (p0) cc_final: 0.7196 (p0) REVERT: C 600 GLU cc_start: 0.8454 (mp0) cc_final: 0.8138 (mp0) outliers start: 36 outliers final: 12 residues processed: 182 average time/residue: 1.1139 time to fit residues: 218.2520 Evaluate side-chains 159 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 424 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 347 ASN A 385 ASN B 347 ASN C 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9420 Z= 0.182 Angle : 0.490 8.661 12786 Z= 0.254 Chirality : 0.037 0.123 1626 Planarity : 0.004 0.031 1557 Dihedral : 3.928 34.171 1281 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.65 % Allowed : 16.17 % Favored : 80.18 % 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 (0.24), residues: 1200 helix: 1.34 (0.17), residues: 957 sheet: -0.78 (0.60), residues: 54 loop : -1.90 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 19 HIS 0.003 0.001 HIS A 41 PHE 0.020 0.001 PHE A 306 TYR 0.007 0.001 TYR C 162 ARG 0.003 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 1.006 Fit side-chains REVERT: A 256 TRP cc_start: 0.8150 (m-10) cc_final: 0.7793 (m100) REVERT: B 208 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: B 304 ILE cc_start: 0.8346 (tt) cc_final: 0.7818 (mt) REVERT: B 342 ARG cc_start: 0.7607 (ttm110) cc_final: 0.7322 (ttp-110) REVERT: C 255 MET cc_start: 0.8311 (mmm) cc_final: 0.7975 (mmp) REVERT: C 318 MET cc_start: 0.7956 (tpt) cc_final: 0.7756 (mmm) REVERT: B 600 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8070 (mp0) outliers start: 37 outliers final: 16 residues processed: 172 average time/residue: 1.0519 time to fit residues: 195.6900 Evaluate side-chains 161 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain B residue 600 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9420 Z= 0.193 Angle : 0.484 7.409 12786 Z= 0.254 Chirality : 0.038 0.141 1626 Planarity : 0.004 0.031 1557 Dihedral : 3.934 35.027 1281 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.45 % Allowed : 17.26 % Favored : 79.29 % 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: 1.15 (0.24), residues: 1200 helix: 1.39 (0.17), residues: 957 sheet: -0.86 (0.60), residues: 54 loop : -1.85 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 19 HIS 0.003 0.001 HIS A 41 PHE 0.012 0.002 PHE B 240 TYR 0.007 0.001 TYR C 162 ARG 0.002 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 1.100 Fit side-chains REVERT: A 318 MET cc_start: 0.8019 (tpt) cc_final: 0.7705 (mmm) REVERT: A 354 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6573 (tp) REVERT: B 208 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8141 (m-30) REVERT: B 304 ILE cc_start: 0.8352 (tt) cc_final: 0.7810 (mt) REVERT: B 342 ARG cc_start: 0.7624 (ttm110) cc_final: 0.7350 (ttp-110) REVERT: B 400 THR cc_start: 0.8463 (m) cc_final: 0.7991 (p) REVERT: C 355 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7808 (m) REVERT: C 419 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7961 (ttt) REVERT: B 600 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8089 (mp0) outliers start: 35 outliers final: 16 residues processed: 173 average time/residue: 1.0545 time to fit residues: 197.5495 Evaluate side-chains 162 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain B residue 600 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9420 Z= 0.172 Angle : 0.474 7.096 12786 Z= 0.249 Chirality : 0.037 0.128 1626 Planarity : 0.004 0.031 1557 Dihedral : 3.861 34.455 1281 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.75 % Allowed : 17.46 % Favored : 78.80 % 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: 1.24 (0.24), residues: 1200 helix: 1.47 (0.17), residues: 951 sheet: -0.79 (0.60), residues: 54 loop : -1.79 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 19 HIS 0.003 0.001 HIS A 41 PHE 0.021 0.001 PHE A 306 TYR 0.007 0.001 TYR A 97 ARG 0.002 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 1.002 Fit side-chains REVERT: A 318 MET cc_start: 0.8039 (tpt) cc_final: 0.7725 (mmm) REVERT: B 304 ILE cc_start: 0.8346 (tt) cc_final: 0.7802 (mt) REVERT: B 342 ARG cc_start: 0.7628 (ttm110) cc_final: 0.7346 (ttp-110) REVERT: B 400 THR cc_start: 0.8433 (m) cc_final: 0.8027 (p) REVERT: C 200 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.7083 (m-10) REVERT: C 255 MET cc_start: 0.8367 (mmm) cc_final: 0.7999 (mmp) REVERT: C 277 GLU cc_start: 0.6693 (mp0) cc_final: 0.6267 (mp0) REVERT: C 279 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7479 (t80) REVERT: C 355 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7747 (m) REVERT: C 419 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7904 (ttt) REVERT: B 600 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: C 600 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8057 (mp0) outliers start: 38 outliers final: 14 residues processed: 165 average time/residue: 1.1416 time to fit residues: 202.5470 Evaluate side-chains 158 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 600 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7695 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9420 Z= 0.200 Angle : 0.488 6.830 12786 Z= 0.257 Chirality : 0.038 0.124 1626 Planarity : 0.004 0.032 1557 Dihedral : 3.872 35.567 1281 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.14 % Allowed : 17.16 % Favored : 78.70 % 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: 1.23 (0.24), residues: 1200 helix: 1.45 (0.17), residues: 951 sheet: -0.80 (0.59), residues: 54 loop : -1.76 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 19 HIS 0.004 0.001 HIS C 41 PHE 0.013 0.002 PHE A 240 TYR 0.007 0.001 TYR A 97 ARG 0.002 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 1.277 Fit side-chains REVERT: A 318 MET cc_start: 0.8046 (tpt) cc_final: 0.7739 (mmm) REVERT: A 354 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6548 (tp) REVERT: B 92 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6500 (mm) REVERT: B 276 TRP cc_start: 0.6291 (m100) cc_final: 0.5928 (m-10) REVERT: B 304 ILE cc_start: 0.8349 (tt) cc_final: 0.7819 (mt) REVERT: B 342 ARG cc_start: 0.7620 (ttm110) cc_final: 0.7324 (ttp-110) REVERT: C 279 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7513 (t80) REVERT: C 355 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7763 (m) REVERT: C 419 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7933 (ttt) REVERT: B 600 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: C 600 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8167 (mp0) outliers start: 42 outliers final: 24 residues processed: 165 average time/residue: 1.1353 time to fit residues: 201.8304 Evaluate side-chains 167 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 600 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 322 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9420 Z= 0.297 Angle : 0.547 6.858 12786 Z= 0.289 Chirality : 0.040 0.129 1626 Planarity : 0.004 0.032 1557 Dihedral : 4.077 38.663 1281 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.14 % Allowed : 18.74 % Favored : 77.12 % 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: 0.89 (0.24), residues: 1200 helix: 1.16 (0.17), residues: 960 sheet: -0.96 (0.58), residues: 54 loop : -1.69 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 19 HIS 0.005 0.002 HIS C 41 PHE 0.022 0.002 PHE A 306 TYR 0.007 0.001 TYR A 97 ARG 0.003 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.976 Fit side-chains REVERT: A 318 MET cc_start: 0.8049 (tpt) cc_final: 0.7740 (mmm) REVERT: A 354 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6580 (tp) REVERT: B 304 ILE cc_start: 0.8371 (tt) cc_final: 0.7854 (mt) REVERT: B 342 ARG cc_start: 0.7636 (ttm110) cc_final: 0.7321 (ttp-110) REVERT: C 277 GLU cc_start: 0.6896 (mp0) cc_final: 0.6635 (mp0) REVERT: C 279 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7627 (t80) REVERT: C 346 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6431 (mm-30) REVERT: C 355 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7785 (m) REVERT: B 600 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: C 600 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8193 (mp0) outliers start: 42 outliers final: 26 residues processed: 174 average time/residue: 1.1448 time to fit residues: 213.8315 Evaluate side-chains 177 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 600 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 322 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9420 Z= 0.178 Angle : 0.498 6.449 12786 Z= 0.263 Chirality : 0.037 0.127 1626 Planarity : 0.004 0.033 1557 Dihedral : 3.921 36.883 1281 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.65 % Allowed : 19.43 % Favored : 76.92 % 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: 1.23 (0.24), residues: 1200 helix: 1.44 (0.17), residues: 948 sheet: -0.82 (0.60), residues: 54 loop : -1.61 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 19 HIS 0.004 0.001 HIS C 41 PHE 0.010 0.001 PHE A 240 TYR 0.008 0.001 TYR B 162 ARG 0.001 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.984 Fit side-chains REVERT: A 318 MET cc_start: 0.7948 (tpt) cc_final: 0.7662 (mmm) REVERT: A 346 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6649 (pt0) REVERT: A 354 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6508 (tp) REVERT: B 92 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6465 (mm) REVERT: B 304 ILE cc_start: 0.8335 (tt) cc_final: 0.7800 (mt) REVERT: B 342 ARG cc_start: 0.7585 (ttm110) cc_final: 0.7274 (ttp-110) REVERT: C 277 GLU cc_start: 0.6811 (mp0) cc_final: 0.6359 (mp0) REVERT: C 279 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7506 (t80) REVERT: C 346 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6427 (mm-30) REVERT: C 355 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7762 (m) REVERT: B 600 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: C 600 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8155 (mp0) outliers start: 37 outliers final: 17 residues processed: 168 average time/residue: 1.1555 time to fit residues: 208.8753 Evaluate side-chains 166 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 600 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 322 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9420 Z= 0.202 Angle : 0.512 6.514 12786 Z= 0.270 Chirality : 0.038 0.126 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.904 36.799 1281 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.35 % Allowed : 19.72 % Favored : 76.92 % 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: 1.29 (0.24), residues: 1200 helix: 1.47 (0.17), residues: 948 sheet: -0.80 (0.60), residues: 54 loop : -1.55 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 19 HIS 0.004 0.001 HIS C 41 PHE 0.023 0.002 PHE A 306 TYR 0.007 0.001 TYR A 97 ARG 0.002 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.018 Fit side-chains REVERT: A 318 MET cc_start: 0.7929 (tpt) cc_final: 0.7603 (mmm) REVERT: A 354 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6554 (tp) REVERT: B 304 ILE cc_start: 0.8345 (tt) cc_final: 0.7805 (mt) REVERT: B 342 ARG cc_start: 0.7663 (ttm110) cc_final: 0.7362 (ttp-110) REVERT: B 465 LEU cc_start: 0.8111 (mt) cc_final: 0.7878 (mt) REVERT: C 277 GLU cc_start: 0.6847 (mp0) cc_final: 0.6382 (mp0) REVERT: C 279 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7538 (t80) REVERT: C 346 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6467 (mm-30) REVERT: C 355 THR cc_start: 0.7964 (OUTLIER) cc_final: 0.7700 (m) REVERT: B 600 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: C 600 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8162 (mp0) outliers start: 34 outliers final: 21 residues processed: 163 average time/residue: 1.1597 time to fit residues: 203.1043 Evaluate side-chains 168 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 600 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 322 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9420 Z= 0.208 Angle : 0.525 7.114 12786 Z= 0.275 Chirality : 0.038 0.145 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.909 36.770 1281 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.06 % Allowed : 20.32 % Favored : 76.63 % 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: 1.30 (0.24), residues: 1200 helix: 1.47 (0.17), residues: 948 sheet: -0.81 (0.61), residues: 54 loop : -1.51 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 19 HIS 0.004 0.001 HIS C 41 PHE 0.012 0.001 PHE A 240 TYR 0.008 0.001 TYR A 97 ARG 0.002 0.000 ARG A 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.981 Fit side-chains REVERT: A 276 TRP cc_start: 0.6392 (m100) cc_final: 0.6147 (m-10) REVERT: A 318 MET cc_start: 0.7935 (tpt) cc_final: 0.7609 (mmm) REVERT: A 354 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6553 (tp) REVERT: B 304 ILE cc_start: 0.8345 (tt) cc_final: 0.7795 (mt) REVERT: B 342 ARG cc_start: 0.7665 (ttm110) cc_final: 0.7362 (ttp-110) REVERT: B 465 LEU cc_start: 0.8112 (mt) cc_final: 0.7855 (mt) REVERT: C 277 GLU cc_start: 0.6853 (mp0) cc_final: 0.6389 (mp0) REVERT: C 279 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7541 (t80) REVERT: C 346 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6456 (mm-30) REVERT: C 355 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7701 (m) REVERT: B 600 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: C 600 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8179 (mp0) outliers start: 31 outliers final: 21 residues processed: 163 average time/residue: 1.1269 time to fit residues: 197.8557 Evaluate side-chains 170 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 600 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.173783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116989 restraints weight = 3556.428| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.22 r_work: 0.3184 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9420 Z= 0.212 Angle : 0.531 8.337 12786 Z= 0.277 Chirality : 0.038 0.164 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.913 36.816 1281 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.16 % Allowed : 20.32 % Favored : 76.53 % 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: 1.29 (0.24), residues: 1200 helix: 1.46 (0.17), residues: 948 sheet: -0.81 (0.61), residues: 54 loop : -1.50 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 19 HIS 0.004 0.001 HIS C 41 PHE 0.023 0.002 PHE A 306 TYR 0.008 0.001 TYR A 97 ARG 0.002 0.000 ARG B 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3664.19 seconds wall clock time: 67 minutes 37.67 seconds (4057.67 seconds total)