Starting phenix.real_space_refine on Fri Feb 14 01:55:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k17_36787/02_2025/8k17_36787.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k17_36787/02_2025/8k17_36787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k17_36787/02_2025/8k17_36787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k17_36787/02_2025/8k17_36787.map" model { file = "/net/cci-nas-00/data/ceres_data/8k17_36787/02_2025/8k17_36787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k17_36787/02_2025/8k17_36787.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 51 5.16 5 C 6207 2.51 5 N 1658 2.21 5 O 1831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9748 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5193 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 33, 'TRANS': 612} Chain breaks: 2 Chain: "B" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2994 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "C" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1438 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 66 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 4, 'TRANS': 5} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' FE': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.74, per 1000 atoms: 0.59 Number of scatterers: 9748 At special positions: 0 Unit cell: (93.5, 115.5, 124.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 51 16.00 O 1831 8.00 N 1658 7.00 C 6207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 123 " distance=2.06 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 600 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 540 " " NAG A 802 " - " ASN A 316 " " NAG B 501 " - " ASN B 87 " " NAG B 502 " - " ASN B 363 " Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.0 seconds 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 57.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.798A pdb=" N LEU A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 83 removed outlier: 3.558A pdb=" N PHE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 125 removed outlier: 3.534A pdb=" N ALA A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 143 through 156 removed outlier: 3.792A pdb=" N ASN A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.514A pdb=" N GLN A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 218 Processing helix chain 'A' and resid 220 through 223 Processing helix chain 'A' and resid 224 through 244 removed outlier: 3.510A pdb=" N ALA A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 286 removed outlier: 3.654A pdb=" N THR A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.796A pdb=" N PHE A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 334 through 348 removed outlier: 3.633A pdb=" N ASN A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 359 through 384 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.655A pdb=" N VAL A 398 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 428 Processing helix chain 'A' and resid 441 through 447 removed outlier: 3.672A pdb=" N ARG A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 479 through 493 removed outlier: 3.661A pdb=" N CYS A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 528 Processing helix chain 'A' and resid 531 through 553 removed outlier: 3.741A pdb=" N ALA A 535 " --> pdb=" O PRO A 531 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 699 removed outlier: 4.295A pdb=" N GLN A 689 " --> pdb=" O ARG A 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.533A pdb=" N GLU B 40 " --> pdb=" O PRO B 37 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 41 " --> pdb=" O ARG B 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 37 through 41' Processing helix chain 'B' and resid 43 through 57 Processing helix chain 'B' and resid 59 through 89 removed outlier: 3.558A pdb=" N SER B 63 " --> pdb=" O HIS B 59 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 88 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 89 " --> pdb=" O HIS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.625A pdb=" N GLN B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.520A pdb=" N ARG B 130 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN B 131 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'B' and resid 146 through 158 removed outlier: 4.204A pdb=" N PHE B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.932A pdb=" N LYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.933A pdb=" N LYS B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.641A pdb=" N SER B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 246 Proline residue: B 234 - end of helix Processing helix chain 'B' and resid 258 through 276 removed outlier: 3.806A pdb=" N ASP B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 308 Processing helix chain 'B' and resid 310 through 325 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.551A pdb=" N HIS B 341 " --> pdb=" O TYR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 removed outlier: 4.184A pdb=" N GLN B 353 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 379 removed outlier: 4.025A pdb=" N GLU B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 378 " --> pdb=" O PHE B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 50 Processing helix chain 'C' and resid 143 through 152 removed outlier: 3.508A pdb=" N VAL C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 458 through 461 removed outlier: 5.798A pdb=" N LEU A 459 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP A 475 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE A 676 " --> pdb=" O ASP A 611 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER A 613 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A 674 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 615 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 672 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TYR A 617 " --> pdb=" O CYS A 670 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N CYS A 670 " --> pdb=" O TYR A 617 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR A 677 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N PHE A 561 " --> pdb=" O THR A 677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 592 through 594 removed outlier: 3.673A pdb=" N VAL A 601 " --> pdb=" O ILE A 592 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 623 through 624 removed outlier: 3.826A pdb=" N ARG A 666 " --> pdb=" O ASP A 623 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 637 through 641 removed outlier: 6.608A pdb=" N PHE A 629 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU A 640 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE A 627 " --> pdb=" O GLU A 640 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AA6, first strand: chain 'B' and resid 384 through 386 removed outlier: 3.688A pdb=" N VAL C 12 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY C 26 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE C 20 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP C 24 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL C 106 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP C 105 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C 63 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 384 through 386 removed outlier: 8.062A pdb=" N GLY C 7 " --> pdb=" O PHE C 179 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N PHE C 179 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N LYS C 9 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 10.571A pdb=" N LYS C 177 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR C 11 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL C 175 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP C 169 " --> pdb=" O ASP C 17 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG C 19 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE C 167 " --> pdb=" O ARG C 19 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1527 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: 2.70 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: 1.21 - 1.33: 2783 1.33 - 1.45: 1797 1.45 - 1.57: 5330 1.57 - 1.69: 0 1.69 - 1.82: 77 Bond restraints: 9987 Sorted by residual: bond pdb=" CB CYS A 123 " pdb=" SG CYS A 123 " ideal model delta sigma weight residual 1.808 1.715 0.093 3.30e-02 9.18e+02 7.95e+00 bond pdb=" CB CYS A 75 " pdb=" SG CYS A 75 " ideal model delta sigma weight residual 1.808 1.736 0.072 3.30e-02 9.18e+02 4.72e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" C GLY A 254 " pdb=" O GLY A 254 " ideal model delta sigma weight residual 1.235 1.212 0.022 1.35e-02 5.49e+03 2.71e+00 bond pdb=" C TYR C 87 " pdb=" N GLY C 88 " ideal model delta sigma weight residual 1.331 1.307 0.023 1.46e-02 4.69e+03 2.54e+00 ... (remaining 9982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 13461 3.97 - 7.93: 39 7.93 - 11.90: 3 11.90 - 15.86: 0 15.86 - 19.83: 1 Bond angle restraints: 13504 Sorted by residual: angle pdb=" CA CYS A 123 " pdb=" CB CYS A 123 " pdb=" SG CYS A 123 " ideal model delta sigma weight residual 114.40 134.23 -19.83 2.30e+00 1.89e-01 7.43e+01 angle pdb=" C CYS A 123 " pdb=" CA CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sigma weight residual 110.42 99.27 11.15 1.99e+00 2.53e-01 3.14e+01 angle pdb=" C ARG A 122 " pdb=" N CYS A 123 " pdb=" CA CYS A 123 " ideal model delta sigma weight residual 121.54 111.78 9.76 1.91e+00 2.74e-01 2.61e+01 angle pdb=" N CYS A 123 " pdb=" CA CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sigma weight residual 110.49 118.35 -7.86 1.69e+00 3.50e-01 2.16e+01 angle pdb=" C CYS A 75 " pdb=" N ARG A 76 " pdb=" CA ARG A 76 " ideal model delta sigma weight residual 120.28 114.96 5.32 1.34e+00 5.57e-01 1.58e+01 ... (remaining 13499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 5134 17.28 - 34.55: 670 34.55 - 51.83: 196 51.83 - 69.10: 40 69.10 - 86.38: 13 Dihedral angle restraints: 6053 sinusoidal: 2530 harmonic: 3523 Sorted by residual: dihedral pdb=" CA CYS A 123 " pdb=" C CYS A 123 " pdb=" N LEU A 124 " pdb=" CA LEU A 124 " ideal model delta harmonic sigma weight residual 180.00 -139.93 -40.07 0 5.00e+00 4.00e-02 6.42e+01 dihedral pdb=" CA ARG A 122 " pdb=" C ARG A 122 " pdb=" N CYS A 123 " pdb=" CA CYS A 123 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LYS A 158 " pdb=" C LYS A 158 " pdb=" N LEU A 159 " pdb=" CA LEU A 159 " ideal model delta harmonic sigma weight residual 180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 6050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1202 0.067 - 0.133: 211 0.133 - 0.200: 10 0.200 - 0.267: 0 0.267 - 0.333: 1 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA CYS A 75 " pdb=" N CYS A 75 " pdb=" C CYS A 75 " pdb=" CB CYS A 75 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA PRO A 451 " pdb=" N PRO A 451 " pdb=" C PRO A 451 " pdb=" CB PRO A 451 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 363 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 1421 not shown) Planarity restraints: 1775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 603 " -0.041 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO A 604 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 604 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 604 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 621 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C ASP A 621 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP A 621 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE A 622 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 604 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO A 605 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " 0.029 5.00e-02 4.00e+02 ... (remaining 1772 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 43 2.56 - 3.15: 7435 3.15 - 3.73: 13829 3.73 - 4.32: 19123 4.32 - 4.90: 33240 Nonbonded interactions: 73670 Sorted by model distance: nonbonded pdb=" OD1 ASP A 589 " pdb="FE FE A 803 " model vdw 1.978 2.260 nonbonded pdb=" OG1 THR A 630 " pdb=" O THR A 636 " model vdw 2.085 3.040 nonbonded pdb=" N GLN B 27 " pdb=" NE2 GLN B 27 " model vdw 2.109 3.200 nonbonded pdb=" CE1 HIS A 659 " pdb="FE FE A 803 " model vdw 2.119 2.480 nonbonded pdb=" O ASP A 253 " pdb=" ND2 ASN A 256 " model vdw 2.135 3.120 ... (remaining 73665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.360 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.380 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 : 0.008 0.093 9987 Z= 0.531 Angle : 0.737 19.831 13504 Z= 0.394 Chirality : 0.049 0.333 1424 Planarity : 0.005 0.063 1771 Dihedral : 16.981 86.376 3787 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.29 % Allowed : 17.72 % Favored : 81.99 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.57 (0.24), residues: 1191 helix: 1.72 (0.20), residues: 633 sheet: 0.12 (0.48), residues: 105 loop : -1.57 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 91 HIS 0.016 0.003 HIS B 266 PHE 0.022 0.002 PHE B 324 TYR 0.021 0.002 TYR A 539 ARG 0.005 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8671 (mmt) cc_final: 0.8114 (mmt) REVERT: B 341 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.7051 (m-70) outliers start: 3 outliers final: 0 residues processed: 115 average time/residue: 0.2072 time to fit residues: 34.4905 Evaluate side-chains 110 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.0570 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 0.0010 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 0.0870 chunk 56 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 27 GLN B 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.155067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.118178 restraints weight = 11644.969| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.32 r_work: 0.2975 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9987 Z= 0.148 Angle : 0.477 6.732 13504 Z= 0.257 Chirality : 0.039 0.184 1424 Planarity : 0.004 0.049 1771 Dihedral : 4.356 39.529 1422 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.17 % Allowed : 17.72 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.24), residues: 1191 helix: 2.20 (0.21), residues: 636 sheet: 0.82 (0.50), residues: 94 loop : -1.30 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 105 HIS 0.004 0.000 HIS A 303 PHE 0.014 0.001 PHE B 156 TYR 0.012 0.001 TYR A 539 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7780 (m-30) cc_final: 0.7572 (m-30) REVERT: A 137 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7631 (mm-30) REVERT: A 337 MET cc_start: 0.8979 (tpp) cc_final: 0.8630 (tpt) REVERT: A 482 GLU cc_start: 0.7674 (mp0) cc_final: 0.7414 (mp0) REVERT: B 78 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.7885 (mmt180) REVERT: C 154 LYS cc_start: 0.6828 (mtpt) cc_final: 0.6487 (ptmt) outliers start: 12 outliers final: 5 residues processed: 127 average time/residue: 0.2404 time to fit residues: 42.5834 Evaluate side-chains 113 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain C residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 116 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 113 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.152025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.114681 restraints weight = 11743.158| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.43 r_work: 0.2921 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9987 Z= 0.201 Angle : 0.484 10.666 13504 Z= 0.257 Chirality : 0.039 0.155 1424 Planarity : 0.004 0.049 1771 Dihedral : 3.981 30.856 1420 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.85 % Allowed : 17.53 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.39 (0.24), residues: 1191 helix: 2.37 (0.21), residues: 637 sheet: 0.94 (0.51), residues: 94 loop : -1.25 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 105 HIS 0.005 0.001 HIS B 266 PHE 0.013 0.001 PHE C 91 TYR 0.015 0.001 TYR A 539 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7661 (mm-30) REVERT: A 337 MET cc_start: 0.8902 (tpp) cc_final: 0.8540 (tpt) REVERT: A 482 GLU cc_start: 0.7926 (mp0) cc_final: 0.7645 (mp0) REVERT: C 154 LYS cc_start: 0.6814 (mtpt) cc_final: 0.6503 (ptmt) outliers start: 19 outliers final: 7 residues processed: 126 average time/residue: 0.2210 time to fit residues: 39.4062 Evaluate side-chains 116 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 110 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 52 optimal weight: 0.0010 chunk 83 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 351 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.157418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.122323 restraints weight = 11566.691| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.36 r_work: 0.2977 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9987 Z= 0.223 Angle : 0.479 6.802 13504 Z= 0.258 Chirality : 0.040 0.159 1424 Planarity : 0.004 0.050 1771 Dihedral : 3.858 26.743 1420 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.24 % Allowed : 17.92 % Favored : 79.84 % 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: 1191 helix: 2.39 (0.20), residues: 637 sheet: 0.89 (0.50), residues: 94 loop : -1.23 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 105 HIS 0.006 0.001 HIS B 266 PHE 0.014 0.001 PHE C 91 TYR 0.017 0.001 TYR B 306 ARG 0.003 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: A 134 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.6071 (mm-30) REVERT: A 337 MET cc_start: 0.8852 (tpp) cc_final: 0.8447 (tpt) REVERT: A 482 GLU cc_start: 0.7913 (mp0) cc_final: 0.7604 (mp0) REVERT: C 154 LYS cc_start: 0.6762 (mtpt) cc_final: 0.6462 (ptmt) outliers start: 23 outliers final: 9 residues processed: 131 average time/residue: 0.2330 time to fit residues: 42.9524 Evaluate side-chains 125 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 2 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 0.0970 chunk 9 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 341 HIS B 351 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.155429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118490 restraints weight = 11643.432| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.43 r_work: 0.2962 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9987 Z= 0.140 Angle : 0.445 10.710 13504 Z= 0.235 Chirality : 0.038 0.161 1424 Planarity : 0.004 0.048 1771 Dihedral : 3.499 19.654 1420 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.04 % Allowed : 18.01 % Favored : 79.94 % 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: 1.59 (0.24), residues: 1191 helix: 2.54 (0.20), residues: 637 sheet: 0.96 (0.51), residues: 93 loop : -1.15 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 105 HIS 0.003 0.000 HIS B 351 PHE 0.008 0.001 PHE C 121 TYR 0.012 0.001 TYR A 539 ARG 0.004 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 78 GLN cc_start: 0.7865 (tt0) cc_final: 0.7582 (tt0) REVERT: A 134 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.6048 (mm-30) REVERT: A 208 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8024 (mt-10) REVERT: A 337 MET cc_start: 0.8838 (tpp) cc_final: 0.8375 (tpt) REVERT: A 448 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7630 (mm-30) REVERT: A 475 ASP cc_start: 0.8046 (m-30) cc_final: 0.7752 (m-30) REVERT: A 482 GLU cc_start: 0.7962 (mp0) cc_final: 0.7668 (mp0) REVERT: C 154 LYS cc_start: 0.6889 (mtpt) cc_final: 0.6591 (ptmt) outliers start: 21 outliers final: 9 residues processed: 133 average time/residue: 0.2130 time to fit residues: 40.1037 Evaluate side-chains 124 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 16 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 341 HIS B 351 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.153810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117636 restraints weight = 11621.718| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.31 r_work: 0.3077 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9987 Z= 0.178 Angle : 0.479 8.602 13504 Z= 0.252 Chirality : 0.040 0.220 1424 Planarity : 0.004 0.048 1771 Dihedral : 3.461 21.888 1420 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.56 % Allowed : 18.70 % Favored : 79.75 % 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: 1.63 (0.25), residues: 1191 helix: 2.49 (0.20), residues: 647 sheet: 1.04 (0.50), residues: 92 loop : -1.09 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 105 HIS 0.004 0.001 HIS B 266 PHE 0.012 0.001 PHE C 91 TYR 0.014 0.001 TYR A 539 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.018 Fit side-chains REVERT: A 208 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7810 (mt-10) REVERT: A 337 MET cc_start: 0.8958 (tpp) cc_final: 0.8409 (tpt) REVERT: A 482 GLU cc_start: 0.7751 (mp0) cc_final: 0.7536 (mp0) REVERT: C 154 LYS cc_start: 0.6998 (mtpt) cc_final: 0.6791 (ptmt) outliers start: 16 outliers final: 8 residues processed: 127 average time/residue: 0.2200 time to fit residues: 39.5349 Evaluate side-chains 125 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 113 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 117 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN B 27 GLN B 351 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.151722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.112692 restraints weight = 11804.855| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.78 r_work: 0.2917 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9987 Z= 0.136 Angle : 0.441 7.711 13504 Z= 0.232 Chirality : 0.038 0.177 1424 Planarity : 0.004 0.047 1771 Dihedral : 3.345 20.778 1420 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.46 % Allowed : 18.70 % Favored : 79.84 % 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: 1.69 (0.25), residues: 1191 helix: 2.58 (0.20), residues: 644 sheet: 0.99 (0.52), residues: 92 loop : -1.08 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 105 HIS 0.003 0.000 HIS B 351 PHE 0.009 0.001 PHE C 121 TYR 0.012 0.001 TYR A 539 ARG 0.002 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.024 Fit side-chains REVERT: A 208 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7864 (mt-10) REVERT: A 337 MET cc_start: 0.8866 (tpp) cc_final: 0.8372 (tpt) REVERT: A 448 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7623 (mm-30) REVERT: A 475 ASP cc_start: 0.7928 (m-30) cc_final: 0.7692 (m-30) REVERT: A 482 GLU cc_start: 0.7845 (mp0) cc_final: 0.7595 (mp0) REVERT: C 154 LYS cc_start: 0.6964 (mtpt) cc_final: 0.6697 (ptmt) outliers start: 15 outliers final: 9 residues processed: 128 average time/residue: 0.2196 time to fit residues: 39.9264 Evaluate side-chains 124 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 105 optimal weight: 0.0470 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 0.0570 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 351 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.153248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.114460 restraints weight = 11759.289| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.70 r_work: 0.2945 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9987 Z= 0.131 Angle : 0.441 7.064 13504 Z= 0.229 Chirality : 0.038 0.160 1424 Planarity : 0.004 0.046 1771 Dihedral : 3.208 18.828 1420 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.46 % Allowed : 18.79 % Favored : 79.75 % 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: 1.77 (0.25), residues: 1191 helix: 2.64 (0.20), residues: 645 sheet: 1.00 (0.52), residues: 92 loop : -1.04 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 105 HIS 0.003 0.000 HIS B 351 PHE 0.008 0.001 PHE C 121 TYR 0.010 0.001 TYR A 539 ARG 0.002 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.089 Fit side-chains REVERT: A 208 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7935 (mt-10) REVERT: A 337 MET cc_start: 0.8848 (tpp) cc_final: 0.8428 (mmm) REVERT: A 448 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7640 (mm-30) REVERT: A 475 ASP cc_start: 0.7883 (m-30) cc_final: 0.7624 (m-30) REVERT: A 482 GLU cc_start: 0.7951 (mp0) cc_final: 0.7719 (mp0) REVERT: B 282 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8941 (t) REVERT: C 154 LYS cc_start: 0.7025 (mtpt) cc_final: 0.6754 (ptmt) outliers start: 15 outliers final: 9 residues processed: 137 average time/residue: 0.2412 time to fit residues: 45.9136 Evaluate side-chains 128 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 92 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 104 optimal weight: 0.3980 chunk 89 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 351 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.155203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.119151 restraints weight = 11632.157| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.32 r_work: 0.2992 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9987 Z= 0.154 Angle : 0.460 7.746 13504 Z= 0.241 Chirality : 0.039 0.183 1424 Planarity : 0.004 0.046 1771 Dihedral : 3.225 19.084 1420 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.27 % Allowed : 19.18 % Favored : 79.55 % 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: 1.79 (0.25), residues: 1191 helix: 2.63 (0.20), residues: 646 sheet: 1.07 (0.52), residues: 92 loop : -1.02 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 105 HIS 0.003 0.000 HIS B 351 PHE 0.010 0.001 PHE C 121 TYR 0.019 0.001 TYR A 185 ARG 0.004 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.199 Fit side-chains REVERT: A 208 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8115 (mt-10) REVERT: A 337 MET cc_start: 0.8843 (tpp) cc_final: 0.8439 (mmm) REVERT: A 448 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7647 (mm-30) REVERT: A 482 GLU cc_start: 0.8023 (mp0) cc_final: 0.7728 (mp0) REVERT: B 183 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.7214 (ttp-110) REVERT: B 282 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.9020 (t) REVERT: C 154 LYS cc_start: 0.7052 (mtpt) cc_final: 0.6776 (ptmt) outliers start: 13 outliers final: 10 residues processed: 127 average time/residue: 0.2356 time to fit residues: 42.0311 Evaluate side-chains 127 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 115 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 351 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.155638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.119128 restraints weight = 11690.987| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.48 r_work: 0.3109 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9987 Z= 0.144 Angle : 0.456 7.154 13504 Z= 0.237 Chirality : 0.039 0.173 1424 Planarity : 0.004 0.046 1771 Dihedral : 3.203 19.227 1420 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.27 % Allowed : 19.28 % Favored : 79.45 % 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: 1.82 (0.25), residues: 1191 helix: 2.66 (0.20), residues: 645 sheet: 1.09 (0.52), residues: 92 loop : -1.01 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 105 HIS 0.003 0.000 HIS B 351 PHE 0.009 0.001 PHE C 121 TYR 0.019 0.001 TYR A 185 ARG 0.003 0.000 ARG A 488 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.891 Fit side-chains REVERT: A 208 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7881 (mt-10) REVERT: A 337 MET cc_start: 0.8908 (tpp) cc_final: 0.8468 (mmm) REVERT: A 448 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7650 (mm-30) REVERT: B 183 ARG cc_start: 0.7406 (ttp-110) cc_final: 0.7188 (ttp-110) REVERT: B 282 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.9058 (t) REVERT: C 154 LYS cc_start: 0.7088 (mtpt) cc_final: 0.6855 (ptmt) outliers start: 13 outliers final: 11 residues processed: 125 average time/residue: 0.2182 time to fit residues: 38.5623 Evaluate side-chains 128 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 0.0020 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 81 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 351 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.156057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.119618 restraints weight = 11611.841| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.39 r_work: 0.2968 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9987 Z= 0.142 Angle : 0.448 7.012 13504 Z= 0.235 Chirality : 0.038 0.172 1424 Planarity : 0.004 0.046 1771 Dihedral : 3.187 19.500 1420 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.36 % Allowed : 18.99 % Favored : 79.65 % 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: 1.85 (0.25), residues: 1191 helix: 2.68 (0.20), residues: 645 sheet: 1.12 (0.52), residues: 92 loop : -1.00 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 105 HIS 0.003 0.000 HIS B 351 PHE 0.010 0.001 PHE C 121 TYR 0.018 0.001 TYR A 185 ARG 0.003 0.000 ARG A 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5148.80 seconds wall clock time: 91 minutes 49.69 seconds (5509.69 seconds total)