Starting phenix.real_space_refine on Thu Mar 13 22:52:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ctc_26985/03_2025/8ctc_26985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ctc_26985/03_2025/8ctc_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/cci-nas-00/data/ceres_data/8ctc_26985/03_2025/8ctc_26985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ctc_26985/03_2025/8ctc_26985.map" model { file = "/net/cci-nas-00/data/ceres_data/8ctc_26985/03_2025/8ctc_26985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ctc_26985/03_2025/8ctc_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-5624/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: 5.81, per 1000 atoms: 0.62 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 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: 1.19 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: 3.07 Time building geometry restraints manager: 2.76 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.620 Find NCS groups from input model: 0.180 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:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- 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 : 0.889 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: 1.2335 time to fit residues: 242.3899 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 : 1.005 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118731 restraints weight = 3629.313| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.27 r_work: 0.3140 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 1.130 Fit side-chains REVERT: A 256 TRP cc_start: 0.8186 (m-10) cc_final: 0.7537 (m100) REVERT: B 48 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7446 (mt-10) REVERT: B 208 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: B 304 ILE cc_start: 0.7608 (tt) cc_final: 0.7146 (mt) REVERT: B 342 ARG cc_start: 0.6931 (ttm110) cc_final: 0.6689 (ttp-110) REVERT: C 275 ASP cc_start: 0.7402 (p0) cc_final: 0.7067 (p0) REVERT: C 600 GLU cc_start: 0.8489 (mp0) cc_final: 0.8047 (mp0) outliers start: 36 outliers final: 12 residues processed: 182 average time/residue: 1.1385 time to fit residues: 223.0525 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 : 0.966 ------------------------------------------------------------------------------- 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 37 optimal weight: 0.0970 chunk 45 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.175612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.119260 restraints weight = 4083.072| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.31 r_work: 0.3189 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1855 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= 0.162 Angle : 0.479 8.557 12786 Z= 0.249 Chirality : 0.037 0.124 1626 Planarity : 0.004 0.031 1557 Dihedral : 3.893 33.278 1281 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.06 % Allowed : 16.57 % Favored : 80.37 % 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 (0.24), residues: 1200 helix: 1.40 (0.17), residues: 957 sheet: -0.75 (0.60), residues: 54 loop : -1.87 (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 0.021 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 185 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.015 Fit side-chains REVERT: A 256 TRP cc_start: 0.8148 (m-10) cc_final: 0.7467 (m100) REVERT: A 277 GLU cc_start: 0.6864 (mp0) cc_final: 0.6658 (mp0) REVERT: B 274 GLU cc_start: 0.7491 (mp0) cc_final: 0.7244 (mp0) REVERT: B 304 ILE cc_start: 0.7636 (tt) cc_final: 0.7194 (mt) REVERT: B 342 ARG cc_start: 0.6837 (ttm110) cc_final: 0.6601 (ttp-110) REVERT: C 113 VAL cc_start: 0.6956 (p) cc_final: 0.6734 (p) REVERT: C 255 MET cc_start: 0.8359 (mmm) cc_final: 0.7947 (mmp) REVERT: C 277 GLU cc_start: 0.6686 (mp0) cc_final: 0.6408 (mp0) REVERT: C 318 MET cc_start: 0.7897 (tpt) cc_final: 0.7674 (mmm) REVERT: B 600 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: C 600 GLU cc_start: 0.8526 (mp0) cc_final: 0.7943 (mp0) outliers start: 31 outliers final: 12 residues processed: 169 average time/residue: 1.0669 time to fit residues: 194.3314 Evaluate side-chains 158 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 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 419 MET 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 B residue 600 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 118 optimal weight: 0.9990 chunk 34 optimal weight: 0.0770 chunk 93 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.173688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116933 restraints weight = 3759.404| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.26 r_work: 0.3104 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2024 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= 0.206 Angle : 0.490 7.554 12786 Z= 0.257 Chirality : 0.038 0.160 1626 Planarity : 0.004 0.031 1557 Dihedral : 3.944 35.356 1281 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.75 % Allowed : 17.26 % Favored : 78.99 % 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: 1.11 (0.24), residues: 1200 helix: 1.37 (0.17), residues: 957 sheet: -0.88 (0.60), residues: 54 loop : -1.89 (0.37), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 19 HIS 0.003 0.001 HIS C 41 PHE 0.013 0.002 PHE B 240 TYR 0.007 0.001 TYR A 97 ARG 0.002 0.000 ARG A 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 190 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.999 Fit side-chains REVERT: A 275 ASP cc_start: 0.7474 (p0) cc_final: 0.6786 (p0) REVERT: A 277 GLU cc_start: 0.6859 (mp0) cc_final: 0.6311 (mp0) REVERT: A 318 MET cc_start: 0.7932 (tpt) cc_final: 0.7586 (mmm) REVERT: B 304 ILE cc_start: 0.7686 (tt) cc_final: 0.7214 (mt) REVERT: B 342 ARG cc_start: 0.6817 (ttm110) cc_final: 0.6572 (ttp-110) REVERT: B 400 THR cc_start: 0.8177 (m) cc_final: 0.7625 (p) REVERT: C 48 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7182 (mp0) REVERT: C 318 MET cc_start: 0.7884 (tpt) cc_final: 0.7663 (mmm) REVERT: C 419 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7463 (ttt) REVERT: A 600 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: B 600 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7833 (mp0) outliers start: 38 outliers final: 20 residues processed: 174 average time/residue: 1.0488 time to fit residues: 197.0717 Evaluate side-chains 167 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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 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 269 CYS 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 A residue 600 GLU 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 94 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.174740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118454 restraints weight = 3726.294| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.25 r_work: 0.3206 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9420 Z= 0.174 Angle : 0.474 7.167 12786 Z= 0.249 Chirality : 0.037 0.125 1626 Planarity : 0.004 0.032 1557 Dihedral : 3.882 34.681 1281 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.85 % Allowed : 17.26 % Favored : 78.90 % 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: 1.21 (0.24), residues: 1200 helix: 1.45 (0.17), residues: 951 sheet: -0.80 (0.60), residues: 54 loop : -1.83 (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 C 41 PHE 0.021 0.001 PHE A 306 TYR 0.007 0.001 TYR A 97 ARG 0.002 0.000 ARG C 342 *********************** 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 187 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.008 Fit side-chains REVERT: A 277 GLU cc_start: 0.6864 (mp0) cc_final: 0.6276 (mp0) REVERT: A 318 MET cc_start: 0.7957 (tpt) cc_final: 0.7596 (mmm) REVERT: B 200 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.7131 (m-10) REVERT: B 304 ILE cc_start: 0.7719 (tt) cc_final: 0.7238 (mt) REVERT: B 342 ARG cc_start: 0.6880 (ttm110) cc_final: 0.6621 (ttp-110) REVERT: B 400 THR cc_start: 0.8168 (m) cc_final: 0.7701 (p) REVERT: C 200 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.7108 (m-10) REVERT: C 255 MET cc_start: 0.8396 (mmm) cc_final: 0.7951 (mmp) REVERT: C 277 GLU cc_start: 0.6762 (mp0) cc_final: 0.6487 (mp0) REVERT: C 318 MET cc_start: 0.7901 (tpt) cc_final: 0.7683 (mmm) REVERT: C 355 THR cc_start: 0.7548 (OUTLIER) cc_final: 0.7347 (m) REVERT: C 419 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7367 (ttt) REVERT: A 600 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: B 600 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: C 600 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7897 (mp0) outliers start: 39 outliers final: 19 residues processed: 169 average time/residue: 1.0981 time to fit residues: 199.8184 Evaluate side-chains 165 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 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 200 TYR 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 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 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 A residue 600 GLU 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 22 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.174395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117754 restraints weight = 3644.625| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.24 r_work: 0.3199 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9420 Z= 0.188 Angle : 0.478 6.885 12786 Z= 0.252 Chirality : 0.037 0.126 1626 Planarity : 0.004 0.032 1557 Dihedral : 3.873 35.261 1281 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.85 % Allowed : 17.46 % 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: 1.24 (0.24), residues: 1200 helix: 1.52 (0.17), residues: 942 sheet: -0.82 (0.59), residues: 54 loop : -1.98 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 19 HIS 0.003 0.001 HIS C 41 PHE 0.014 0.001 PHE B 306 TYR 0.008 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 182 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 1.132 Fit side-chains REVERT: A 277 GLU cc_start: 0.6862 (mp0) cc_final: 0.6291 (mp0) REVERT: A 318 MET cc_start: 0.7949 (tpt) cc_final: 0.7595 (mmm) REVERT: B 276 TRP cc_start: 0.5960 (m100) cc_final: 0.5470 (m-10) REVERT: B 304 ILE cc_start: 0.7723 (tt) cc_final: 0.7242 (mt) REVERT: B 342 ARG cc_start: 0.6881 (ttm110) cc_final: 0.6610 (ttp-110) REVERT: C 277 GLU cc_start: 0.6874 (mp0) cc_final: 0.6672 (mp0) REVERT: C 279 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.7167 (t80) REVERT: C 318 MET cc_start: 0.7907 (tpt) cc_final: 0.7683 (mmm) REVERT: C 355 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.7336 (m) REVERT: C 419 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7458 (ttt) REVERT: A 600 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: B 600 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: C 600 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8024 (mp0) outliers start: 39 outliers final: 23 residues processed: 164 average time/residue: 1.2011 time to fit residues: 212.5147 Evaluate side-chains 167 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 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 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 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 419 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain A residue 600 GLU 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 105 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.175029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.118457 restraints weight = 3681.688| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.25 r_work: 0.3205 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9420 Z= 0.177 Angle : 0.482 6.666 12786 Z= 0.253 Chirality : 0.037 0.123 1626 Planarity : 0.004 0.032 1557 Dihedral : 3.859 34.932 1281 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.65 % Allowed : 18.64 % Favored : 77.71 % 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: 1.32 (0.24), residues: 1200 helix: 1.58 (0.17), residues: 942 sheet: -0.80 (0.60), residues: 54 loop : -1.92 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 19 HIS 0.003 0.001 HIS C 41 PHE 0.022 0.002 PHE A 306 TYR 0.007 0.001 TYR A 97 ARG 0.002 0.000 ARG A 310 *********************** 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 180 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.072 Fit side-chains REVERT: A 318 MET cc_start: 0.7914 (tpt) cc_final: 0.7575 (mmm) REVERT: B 304 ILE cc_start: 0.7699 (tt) cc_final: 0.7223 (mt) REVERT: B 342 ARG cc_start: 0.6887 (ttm110) cc_final: 0.6610 (ttp-110) REVERT: C 255 MET cc_start: 0.8369 (mmm) cc_final: 0.7912 (mmp) REVERT: C 277 GLU cc_start: 0.6862 (mp0) cc_final: 0.6253 (mp0) REVERT: C 279 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7215 (t80) REVERT: C 318 MET cc_start: 0.7905 (tpt) cc_final: 0.7685 (mmm) REVERT: C 346 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6233 (mm-30) REVERT: C 355 THR cc_start: 0.7571 (OUTLIER) cc_final: 0.7348 (m) REVERT: C 419 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7434 (ttt) REVERT: A 600 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8151 (mp0) REVERT: B 600 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: C 600 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8020 (mp0) outliers start: 37 outliers final: 22 residues processed: 166 average time/residue: 1.2876 time to fit residues: 230.3923 Evaluate side-chains 165 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 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 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 A residue 600 GLU 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 37 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.174700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117771 restraints weight = 3695.653| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.25 r_work: 0.3190 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2392 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= 0.190 Angle : 0.490 6.547 12786 Z= 0.258 Chirality : 0.037 0.127 1626 Planarity : 0.004 0.032 1557 Dihedral : 3.866 35.429 1281 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.65 % Allowed : 19.03 % Favored : 77.32 % 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: 1.35 (0.24), residues: 1200 helix: 1.59 (0.17), residues: 942 sheet: -0.80 (0.59), residues: 54 loop : -1.88 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 19 HIS 0.004 0.001 HIS C 41 PHE 0.018 0.002 PHE B 306 TYR 0.008 0.001 TYR A 97 ARG 0.002 0.000 ARG B 61 *********************** 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 180 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.308 Fit side-chains REVERT: A 318 MET cc_start: 0.7828 (tpt) cc_final: 0.7478 (mmm) REVERT: A 346 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6413 (pt0) REVERT: B 304 ILE cc_start: 0.7737 (tt) cc_final: 0.7260 (mt) REVERT: B 342 ARG cc_start: 0.6894 (ttm110) cc_final: 0.6611 (ttp-110) REVERT: B 465 LEU cc_start: 0.7693 (mt) cc_final: 0.7451 (mt) REVERT: C 142 MET cc_start: 0.8319 (tpp) cc_final: 0.8074 (mmm) REVERT: C 279 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7216 (t80) REVERT: C 318 MET cc_start: 0.7908 (tpt) cc_final: 0.7687 (mmm) REVERT: C 346 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6297 (mm-30) REVERT: C 355 THR cc_start: 0.7528 (OUTLIER) cc_final: 0.7302 (m) REVERT: C 419 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7391 (ttt) REVERT: A 600 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: B 600 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: C 600 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8026 (mp0) outliers start: 37 outliers final: 25 residues processed: 163 average time/residue: 1.9362 time to fit residues: 338.0844 Evaluate side-chains 170 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 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 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 22 LEU 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 A residue 600 GLU 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 11 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.175611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118893 restraints weight = 3655.757| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.25 r_work: 0.3179 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2458 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= 0.179 Angle : 0.493 6.515 12786 Z= 0.258 Chirality : 0.037 0.126 1626 Planarity : 0.004 0.033 1557 Dihedral : 3.841 35.083 1281 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.35 % Allowed : 19.63 % Favored : 77.02 % 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: 1.43 (0.24), residues: 1200 helix: 1.64 (0.17), residues: 942 sheet: -0.76 (0.60), residues: 54 loop : -1.79 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 19 HIS 0.003 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 A 310 *********************** 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 174 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 1.426 Fit side-chains REVERT: A 318 MET cc_start: 0.7820 (tpt) cc_final: 0.7487 (mmm) REVERT: A 346 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6404 (pt0) REVERT: B 304 ILE cc_start: 0.7700 (tt) cc_final: 0.7213 (mt) REVERT: B 342 ARG cc_start: 0.6886 (ttm110) cc_final: 0.6606 (ttp-110) REVERT: B 465 LEU cc_start: 0.7674 (mt) cc_final: 0.7416 (mt) REVERT: C 142 MET cc_start: 0.8290 (tpp) cc_final: 0.8073 (mmm) REVERT: C 279 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.7242 (t80) REVERT: C 318 MET cc_start: 0.7861 (tpt) cc_final: 0.7643 (mmm) REVERT: C 346 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6296 (mm-30) REVERT: C 355 THR cc_start: 0.7571 (OUTLIER) cc_final: 0.7350 (m) REVERT: C 419 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7405 (ttt) REVERT: A 600 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: B 600 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: C 600 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7887 (mp0) outliers start: 34 outliers final: 22 residues processed: 159 average time/residue: 1.1004 time to fit residues: 188.7386 Evaluate side-chains 166 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 258 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU 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 22 LEU 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 A residue 600 GLU 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 29 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 33 optimal weight: 0.0060 chunk 113 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.176570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.120132 restraints weight = 3706.289| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.25 r_work: 0.3192 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9420 Z= 0.169 Angle : 0.497 7.039 12786 Z= 0.260 Chirality : 0.037 0.131 1626 Planarity : 0.004 0.033 1557 Dihedral : 3.802 34.293 1281 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.96 % Allowed : 20.12 % 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: 1.54 (0.24), residues: 1200 helix: 1.71 (0.17), residues: 942 sheet: -0.70 (0.60), residues: 54 loop : -1.71 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 19 HIS 0.003 0.001 HIS C 41 PHE 0.011 0.001 PHE B 316 TYR 0.007 0.001 TYR A 97 ARG 0.001 0.000 ARG C 342 ********************** 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 171 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.935 Fit side-chains REVERT: A 318 MET cc_start: 0.7713 (tpt) cc_final: 0.7360 (mmm) REVERT: B 304 ILE cc_start: 0.7685 (tt) cc_final: 0.7196 (mt) REVERT: B 342 ARG cc_start: 0.6883 (ttm110) cc_final: 0.6606 (ttp-110) REVERT: B 465 LEU cc_start: 0.7571 (mt) cc_final: 0.7326 (mt) REVERT: C 142 MET cc_start: 0.8267 (tpp) cc_final: 0.8049 (mmm) REVERT: C 279 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.7202 (t80) REVERT: C 318 MET cc_start: 0.7847 (tpt) cc_final: 0.7631 (mmm) REVERT: C 346 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6278 (mm-30) REVERT: C 355 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.7334 (m) REVERT: A 600 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: B 600 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: C 600 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7916 (mp0) outliers start: 30 outliers final: 15 residues processed: 158 average time/residue: 1.1471 time to fit residues: 194.9308 Evaluate side-chains 155 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 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 424 SER Chi-restraints excluded: chain A residue 600 GLU 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 12 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.174509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117350 restraints weight = 3645.266| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.25 r_work: 0.3168 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9420 Z= 0.211 Angle : 0.522 8.235 12786 Z= 0.273 Chirality : 0.038 0.157 1626 Planarity : 0.004 0.032 1557 Dihedral : 3.885 35.861 1281 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.66 % Allowed : 21.10 % Favored : 76.23 % 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: 1.41 (0.24), residues: 1200 helix: 1.62 (0.17), residues: 939 sheet: -0.78 (0.60), residues: 54 loop : -1.69 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 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 A 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7253.13 seconds wall clock time: 126 minutes 27.26 seconds (7587.26 seconds total)