Starting phenix.real_space_refine on Wed Aug 5 09:40:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcx_37451/08_2026/8wcx_37451.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcx_37451/08_2026/8wcx_37451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wcx_37451/08_2026/8wcx_37451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcx_37451/08_2026/8wcx_37451.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wcx_37451/08_2026/8wcx_37451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcx_37451/08_2026/8wcx_37451.map" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.072 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 P 6 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 5820 2.51 5 N 1625 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9199 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4348 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 19, 'TRANS': 554} Chain: "B" Number of atoms: 4787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4787 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 20, 'TRANS': 604} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.01, per 1000 atoms: 0.22 Number of scatterers: 9199 At special positions: 0 Unit cell: (69.056, 94.848, 150.592, 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) S 33 16.00 P 6 15.00 Mg 2 11.99 O 1713 8.00 N 1625 7.00 C 5820 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: 0.87 Conformation dependent library (CDL) restraints added in 382.3 milliseconds 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 7 sheets defined 68.1% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 0 through 10 Processing helix chain 'A' and resid 16 through 45 removed outlier: 3.501A pdb=" N VAL A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 51 through 100 removed outlier: 3.743A pdb=" N VAL A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 75 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.647A pdb=" N PHE A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.562A pdb=" N LEU A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 134 removed outlier: 3.731A pdb=" N ILE A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 154 removed outlier: 3.552A pdb=" N ILE A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 203 Proline residue: A 166 - end of helix removed outlier: 3.583A pdb=" N ILE A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS A 178 " --> pdb=" O TRP A 174 " (cutoff:3.500A) Proline residue: A 181 - end of helix removed outlier: 3.653A pdb=" N GLY A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 212 through 239 removed outlier: 3.547A pdb=" N VAL A 218 " --> pdb=" O PRO A 214 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 267 removed outlier: 3.627A pdb=" N ARG A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 295 removed outlier: 4.075A pdb=" N ALA A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.580A pdb=" N CYS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.746A pdb=" N ALA A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 437 through 448 removed outlier: 3.613A pdb=" N GLU A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.715A pdb=" N PHE A 453 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.518A pdb=" N ILE A 482 " --> pdb=" O GLN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.595A pdb=" N ARG A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'B' and resid 16 through 28 removed outlier: 3.747A pdb=" N LEU B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 71 Proline residue: B 53 - end of helix removed outlier: 4.075A pdb=" N GLU B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.604A pdb=" N GLU B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.764A pdb=" N GLY B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 160 removed outlier: 3.712A pdb=" N LEU B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TRP B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 171 through 178 removed outlier: 3.501A pdb=" N VAL B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 191 removed outlier: 3.700A pdb=" N ILE B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 213 Processing helix chain 'B' and resid 213 through 222 removed outlier: 3.580A pdb=" N PHE B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 262 removed outlier: 3.767A pdb=" N ALA B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Proline residue: B 240 - end of helix removed outlier: 3.579A pdb=" N VAL B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 271 through 299 removed outlier: 3.848A pdb=" N SER B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 326 Processing helix chain 'B' and resid 329 through 349 removed outlier: 3.790A pdb=" N GLN B 345 " --> pdb=" O ARG B 341 " (cutoff:3.500A) Proline residue: B 346 - end of helix removed outlier: 4.108A pdb=" N GLN B 349 " --> pdb=" O GLN B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 372 removed outlier: 4.527A pdb=" N GLY B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 438 Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 481 through 487 Processing helix chain 'B' and resid 496 through 504 Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 529 through 544 removed outlier: 3.567A pdb=" N LEU B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 570 removed outlier: 3.746A pdb=" N LEU B 565 " --> pdb=" O ARG B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 590 removed outlier: 4.021A pdb=" N ILE B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 590' Processing helix chain 'B' and resid 608 through 615 Processing helix chain 'B' and resid 618 through 627 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.994A pdb=" N VAL A 354 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 414 removed outlier: 6.466A pdb=" N THR A 363 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL A 540 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA A 365 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE A 542 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL A 367 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A 539 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A 541 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AA4, first strand: chain 'B' and resid 413 through 414 Processing sheet with id=AA5, first strand: chain 'B' and resid 396 through 398 removed outlier: 5.694A pdb=" N VAL B 396 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 469 through 470 removed outlier: 6.433A pdb=" N VAL B 470 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU B 549 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE B 582 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 551 " --> pdb=" O ILE B 582 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL B 597 " --> pdb=" O ILE B 604 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 479 through 480 583 hydrogen bonds defined for protein. 1701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1584 1.32 - 1.45: 2389 1.45 - 1.57: 5311 1.57 - 1.70: 12 1.70 - 1.82: 61 Bond restraints: 9357 Sorted by residual: bond pdb=" O3A ANP A 601 " pdb=" PB ANP A 601 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" O3A ANP B 701 " pdb=" PB ANP B 701 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" N3B ANP B 701 " pdb=" PG ANP B 701 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" N3B ANP A 601 " pdb=" PG ANP A 601 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O5' ANP A 601 " pdb=" PA ANP A 601 " ideal model delta sigma weight residual 1.655 1.579 0.076 2.00e-02 2.50e+03 1.44e+01 ... (remaining 9352 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 12669 3.50 - 7.00: 67 7.00 - 10.50: 12 10.50 - 14.00: 3 14.00 - 17.50: 2 Bond angle restraints: 12753 Sorted by residual: angle pdb=" PB ANP B 701 " pdb=" N3B ANP B 701 " pdb=" PG ANP B 701 " ideal model delta sigma weight residual 126.95 109.45 17.50 3.00e+00 1.11e-01 3.40e+01 angle pdb=" PB ANP A 601 " pdb=" N3B ANP A 601 " pdb=" PG ANP A 601 " ideal model delta sigma weight residual 126.95 110.47 16.48 3.00e+00 1.11e-01 3.02e+01 angle pdb=" N LEU A 445 " pdb=" CA LEU A 445 " pdb=" C LEU A 445 " ideal model delta sigma weight residual 111.14 105.25 5.89 1.08e+00 8.57e-01 2.98e+01 angle pdb=" C VAL A 447 " pdb=" CA VAL A 447 " pdb=" CB VAL A 447 " ideal model delta sigma weight residual 111.81 105.75 6.06 1.25e+00 6.40e-01 2.35e+01 angle pdb=" C SER A 569 " pdb=" N GLN A 570 " pdb=" CA GLN A 570 " ideal model delta sigma weight residual 122.86 116.45 6.41 1.53e+00 4.27e-01 1.75e+01 ... (remaining 12748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4899 17.99 - 35.98: 520 35.98 - 53.97: 117 53.97 - 71.96: 37 71.96 - 89.95: 21 Dihedral angle restraints: 5594 sinusoidal: 2167 harmonic: 3427 Sorted by residual: dihedral pdb=" CA ASP A 452 " pdb=" C ASP A 452 " pdb=" N PHE A 453 " pdb=" CA PHE A 453 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ILE A 297 " pdb=" C ILE A 297 " pdb=" N PHE A 298 " pdb=" CA PHE A 298 " ideal model delta harmonic sigma weight residual 180.00 155.65 24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PRO A 344 " pdb=" C PRO A 344 " pdb=" N GLY A 345 " pdb=" CA GLY A 345 " ideal model delta harmonic sigma weight residual -180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 5591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1259 0.055 - 0.109: 247 0.109 - 0.164: 21 0.164 - 0.218: 0 0.218 - 0.272: 5 Chirality restraints: 1532 Sorted by residual: chirality pdb=" C3' ANP B 701 " pdb=" C2' ANP B 701 " pdb=" C4' ANP B 701 " pdb=" O3' ANP B 701 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3' ANP A 601 " pdb=" C2' ANP A 601 " pdb=" C4' ANP A 601 " pdb=" O3' ANP A 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA LEU B 29 " pdb=" N LEU B 29 " pdb=" C LEU B 29 " pdb=" CB LEU B 29 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1529 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 541 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C VAL A 541 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL A 541 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE A 542 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 444 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C ALA A 444 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA A 444 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU A 445 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 28 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" C LEU B 28 " 0.034 2.00e-02 2.50e+03 pdb=" O LEU B 28 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU B 29 " -0.011 2.00e-02 2.50e+03 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 84 2.54 - 3.13: 7218 3.13 - 3.72: 14889 3.72 - 4.31: 19722 4.31 - 4.90: 33828 Nonbonded interactions: 75741 Sorted by model distance: nonbonded pdb=" O2B ANP A 601 " pdb="MG MG A 602 " model vdw 1.945 2.170 nonbonded pdb=" O2G ANP B 701 " pdb="MG MG B 702 " model vdw 1.972 2.170 nonbonded pdb=" OG1 THR B 431 " pdb="MG MG B 702 " model vdw 1.993 2.170 nonbonded pdb=" OG SER A 375 " pdb="MG MG A 602 " model vdw 2.015 2.170 nonbonded pdb=" O1B ANP B 701 " pdb="MG MG B 702 " model vdw 2.016 2.170 ... (remaining 75736 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: 2.500 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.540 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 0.145 9357 Z= 0.278 Angle : 0.737 17.498 12753 Z= 0.375 Chirality : 0.043 0.272 1532 Planarity : 0.004 0.047 1628 Dihedral : 17.056 89.949 3388 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.69 % Favored : 95.15 % Rotamer: Outliers : 0.42 % Allowed : 18.40 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.25), residues: 1195 helix: 0.87 (0.20), residues: 782 sheet: -1.57 (0.66), residues: 55 loop : -1.79 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 170 TYR 0.016 0.001 TYR A 343 PHE 0.008 0.001 PHE A 472 TRP 0.013 0.001 TRP A 408 HIS 0.006 0.001 HIS B 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.28 ( 9357) covalent geometry : angle 0.73651 / 0.38 (12753) hydrogen bonds : bond 0.15529 / 10.31 ( 583) hydrogen bonds : angle 5.54825 / 4.00 ( 1701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7479 (tpp) cc_final: 0.7143 (tpt) REVERT: A 142 MET cc_start: 0.6823 (mmt) cc_final: 0.6499 (mmt) REVERT: A 158 SER cc_start: 0.6889 (p) cc_final: 0.6678 (p) REVERT: A 170 LEU cc_start: 0.7324 (tt) cc_final: 0.6886 (mp) REVERT: A 222 GLU cc_start: 0.6683 (pp20) cc_final: 0.6220 (pt0) REVERT: A 233 GLU cc_start: 0.6756 (tp30) cc_final: 0.6375 (tp30) REVERT: A 290 MET cc_start: 0.6252 (tpp) cc_final: 0.5683 (mmm) REVERT: A 417 ARG cc_start: 0.7450 (mmm-85) cc_final: 0.6636 (mtm110) REVERT: A 568 GLU cc_start: 0.7906 (tt0) cc_final: 0.7658 (pt0) REVERT: B 155 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6342 (mm-30) REVERT: B 175 SER cc_start: 0.6894 (m) cc_final: 0.6680 (t) REVERT: B 186 ASN cc_start: 0.5882 (m-40) cc_final: 0.5634 (m110) REVERT: B 236 ARG cc_start: 0.6585 (ttm-80) cc_final: 0.6351 (mtm110) REVERT: B 281 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6192 (pt0) REVERT: B 327 GLN cc_start: 0.7816 (mm110) cc_final: 0.7211 (mp10) REVERT: B 355 ASN cc_start: 0.7223 (t0) cc_final: 0.6743 (t0) REVERT: B 365 GLU cc_start: 0.6608 (tt0) cc_final: 0.6399 (tp30) REVERT: B 408 GLU cc_start: 0.7641 (mm-30) cc_final: 0.6633 (mt-10) REVERT: B 461 GLU cc_start: 0.7278 (tt0) cc_final: 0.7043 (mt-10) REVERT: B 590 ARG cc_start: 0.7598 (tpt90) cc_final: 0.6690 (ppt170) REVERT: B 618 ARG cc_start: 0.6098 (OUTLIER) cc_final: 0.5491 (tpp80) REVERT: B 624 ARG cc_start: 0.6666 (mmp-170) cc_final: 0.6230 (ttp80) outliers start: 4 outliers final: 0 residues processed: 185 average time/residue: 0.1145 time to fit residues: 28.2290 Evaluate side-chains 130 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 618 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 HIS A 428 ASN B 139 ASN B 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.103977 restraints weight = 11856.310| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.47 r_work: 0.3039 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9357 Z= 0.179 Angle : 0.610 8.403 12753 Z= 0.309 Chirality : 0.043 0.158 1532 Planarity : 0.004 0.051 1628 Dihedral : 9.280 72.796 1381 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 4.05 % Allowed : 17.78 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.25), residues: 1195 helix: 0.98 (0.19), residues: 780 sheet: -1.58 (0.65), residues: 55 loop : -1.83 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 117 TYR 0.015 0.002 TYR B 339 PHE 0.011 0.002 PHE A 453 TRP 0.011 0.001 TRP B 620 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 9357) covalent geometry : angle 0.61036 / 0.31 (12753) hydrogen bonds : bond 0.04596 / 3.03 ( 583) hydrogen bonds : angle 4.28768 / 3.03 ( 1701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.354 Fit side-chains REVERT: A 170 LEU cc_start: 0.8862 (tt) cc_final: 0.8408 (mp) REVERT: A 222 GLU cc_start: 0.8034 (pp20) cc_final: 0.7668 (pt0) REVERT: A 417 ARG cc_start: 0.7727 (mmm-85) cc_final: 0.7447 (mtm110) REVERT: B 15 ARG cc_start: 0.7223 (mtm-85) cc_final: 0.6960 (mtm-85) REVERT: B 241 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8072 (mm) REVERT: B 327 GLN cc_start: 0.8798 (mm110) cc_final: 0.8484 (mt0) REVERT: B 386 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8217 (p) REVERT: B 618 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7615 (tpp80) REVERT: B 624 ARG cc_start: 0.7850 (mmp-170) cc_final: 0.7547 (ttp80) outliers start: 39 outliers final: 20 residues processed: 151 average time/residue: 0.1012 time to fit residues: 21.2829 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 618 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 72 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 108 optimal weight: 0.0770 chunk 115 optimal weight: 0.0770 chunk 87 optimal weight: 0.5980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 ASN B 139 ASN B 294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.108102 restraints weight = 11841.018| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.43 r_work: 0.3088 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9357 Z= 0.108 Angle : 0.513 7.737 12753 Z= 0.260 Chirality : 0.039 0.139 1532 Planarity : 0.004 0.047 1628 Dihedral : 7.149 74.580 1381 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 3.53 % Allowed : 19.33 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1195 helix: 1.34 (0.19), residues: 782 sheet: -1.32 (0.68), residues: 55 loop : -1.83 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.014 0.001 TYR A 343 PHE 0.012 0.001 PHE A 453 TRP 0.012 0.001 TRP A 408 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 9357) covalent geometry : angle 0.51335 / 0.26 (12753) hydrogen bonds : bond 0.03712 / 2.45 ( 583) hydrogen bonds : angle 4.00396 / 2.82 ( 1701) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.357 Fit side-chains REVERT: A 170 LEU cc_start: 0.8790 (tt) cc_final: 0.8396 (mp) REVERT: A 222 GLU cc_start: 0.7993 (pp20) cc_final: 0.7673 (pt0) REVERT: A 233 GLU cc_start: 0.8204 (tp30) cc_final: 0.7682 (tt0) REVERT: A 438 ASP cc_start: 0.7165 (m-30) cc_final: 0.6844 (t0) REVERT: B 327 GLN cc_start: 0.8779 (mm110) cc_final: 0.8540 (mt0) REVERT: B 386 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8184 (p) REVERT: B 624 ARG cc_start: 0.7908 (mmp-170) cc_final: 0.7645 (ttp80) outliers start: 34 outliers final: 16 residues processed: 145 average time/residue: 0.1004 time to fit residues: 20.3714 Evaluate side-chains 126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 15 optimal weight: 0.0270 chunk 110 optimal weight: 0.2980 chunk 86 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.107371 restraints weight = 11959.068| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.47 r_work: 0.3081 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9357 Z= 0.109 Angle : 0.507 8.439 12753 Z= 0.255 Chirality : 0.039 0.132 1532 Planarity : 0.003 0.048 1628 Dihedral : 6.248 73.274 1377 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 3.22 % Allowed : 19.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.25), residues: 1195 helix: 1.47 (0.19), residues: 787 sheet: -1.22 (0.69), residues: 55 loop : -1.81 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 236 TYR 0.015 0.001 TYR B 354 PHE 0.011 0.001 PHE A 453 TRP 0.009 0.001 TRP A 408 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9357) covalent geometry : angle 0.50658 / 0.25 (12753) hydrogen bonds : bond 0.03566 / 2.34 ( 583) hydrogen bonds : angle 3.88343 / 2.74 ( 1701) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.346 Fit side-chains REVERT: A 170 LEU cc_start: 0.8795 (tt) cc_final: 0.8390 (mp) REVERT: A 222 GLU cc_start: 0.7986 (pp20) cc_final: 0.7665 (pt0) REVERT: A 233 GLU cc_start: 0.8254 (tp30) cc_final: 0.7681 (tt0) REVERT: A 401 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7230 (p0) REVERT: A 438 ASP cc_start: 0.7143 (m-30) cc_final: 0.6817 (t0) REVERT: B 327 GLN cc_start: 0.8779 (mm110) cc_final: 0.8546 (mt0) REVERT: B 386 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8158 (p) REVERT: B 624 ARG cc_start: 0.7897 (mmp-170) cc_final: 0.7562 (ttp80) outliers start: 31 outliers final: 22 residues processed: 137 average time/residue: 0.0956 time to fit residues: 18.0728 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 113 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 96 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.107312 restraints weight = 11843.022| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.45 r_work: 0.3081 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9357 Z= 0.109 Angle : 0.504 7.615 12753 Z= 0.253 Chirality : 0.039 0.130 1532 Planarity : 0.003 0.048 1628 Dihedral : 6.076 71.027 1377 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.69 % Favored : 95.23 % Rotamer: Outliers : 3.64 % Allowed : 19.65 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.25), residues: 1195 helix: 1.60 (0.19), residues: 787 sheet: -1.41 (0.67), residues: 55 loop : -1.78 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 618 TYR 0.011 0.001 TYR A 343 PHE 0.011 0.001 PHE A 453 TRP 0.009 0.001 TRP A 408 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9357) covalent geometry : angle 0.50357 / 0.25 (12753) hydrogen bonds : bond 0.03491 / 2.29 ( 583) hydrogen bonds : angle 3.82758 / 2.69 ( 1701) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.242 Fit side-chains REVERT: A 170 LEU cc_start: 0.8780 (tt) cc_final: 0.8397 (mp) REVERT: A 222 GLU cc_start: 0.7990 (pp20) cc_final: 0.7672 (pt0) REVERT: A 233 GLU cc_start: 0.8230 (tp30) cc_final: 0.7699 (tt0) REVERT: A 401 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7283 (p0) REVERT: A 438 ASP cc_start: 0.7150 (m-30) cc_final: 0.6828 (t0) REVERT: B 386 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8204 (p) REVERT: B 522 ASP cc_start: 0.8206 (p0) cc_final: 0.7984 (p0) REVERT: B 624 ARG cc_start: 0.7933 (mmp-170) cc_final: 0.7584 (ttp80) outliers start: 35 outliers final: 24 residues processed: 138 average time/residue: 0.0847 time to fit residues: 16.5429 Evaluate side-chains 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.123600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.105391 restraints weight = 11844.516| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.46 r_work: 0.3051 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9357 Z= 0.128 Angle : 0.518 8.699 12753 Z= 0.261 Chirality : 0.039 0.127 1532 Planarity : 0.003 0.049 1628 Dihedral : 6.011 68.943 1377 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.94 % Favored : 94.98 % Rotamer: Outliers : 3.33 % Allowed : 20.27 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.25), residues: 1195 helix: 1.65 (0.19), residues: 784 sheet: -1.47 (0.68), residues: 55 loop : -1.74 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 590 TYR 0.014 0.001 TYR B 487 PHE 0.011 0.001 PHE A 453 TRP 0.008 0.001 TRP A 408 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9357) covalent geometry : angle 0.51756 / 0.26 (12753) hydrogen bonds : bond 0.03676 / 2.41 ( 583) hydrogen bonds : angle 3.85129 / 2.70 ( 1701) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.368 Fit side-chains REVERT: A 7 ARG cc_start: 0.8267 (ptm160) cc_final: 0.7999 (ttp80) REVERT: A 170 LEU cc_start: 0.8797 (tt) cc_final: 0.8365 (mp) REVERT: A 222 GLU cc_start: 0.7993 (pp20) cc_final: 0.7671 (pt0) REVERT: A 438 ASP cc_start: 0.7182 (m-30) cc_final: 0.6854 (t0) REVERT: B 241 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8034 (mm) REVERT: B 386 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8229 (p) REVERT: B 522 ASP cc_start: 0.8214 (p0) cc_final: 0.8000 (p0) REVERT: B 624 ARG cc_start: 0.7933 (mmp-170) cc_final: 0.7542 (ttp80) outliers start: 32 outliers final: 27 residues processed: 135 average time/residue: 0.0974 time to fit residues: 18.2565 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.0010 chunk 85 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.106484 restraints weight = 11868.795| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.45 r_work: 0.3077 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9357 Z= 0.114 Angle : 0.510 8.712 12753 Z= 0.257 Chirality : 0.039 0.142 1532 Planarity : 0.003 0.048 1628 Dihedral : 5.913 66.935 1377 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 3.33 % Allowed : 20.58 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.25), residues: 1195 helix: 1.74 (0.19), residues: 787 sheet: -1.54 (0.67), residues: 55 loop : -1.75 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 590 TYR 0.012 0.001 TYR A 343 PHE 0.011 0.001 PHE A 453 TRP 0.010 0.001 TRP A 408 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 9357) covalent geometry : angle 0.50987 / 0.26 (12753) hydrogen bonds : bond 0.03473 / 2.28 ( 583) hydrogen bonds : angle 3.77985 / 2.66 ( 1701) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.291 Fit side-chains REVERT: A 7 ARG cc_start: 0.8257 (ptm160) cc_final: 0.7962 (ttp80) REVERT: A 170 LEU cc_start: 0.8780 (tt) cc_final: 0.8350 (mp) REVERT: A 222 GLU cc_start: 0.7989 (pp20) cc_final: 0.7656 (pt0) REVERT: A 233 GLU cc_start: 0.8210 (tp30) cc_final: 0.7705 (tt0) REVERT: A 438 ASP cc_start: 0.7192 (m-30) cc_final: 0.6883 (t0) REVERT: B 241 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7969 (mm) REVERT: B 386 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8201 (p) REVERT: B 522 ASP cc_start: 0.8172 (p0) cc_final: 0.7911 (p0) REVERT: B 624 ARG cc_start: 0.7926 (mmp-170) cc_final: 0.7521 (ttp80) outliers start: 32 outliers final: 24 residues processed: 133 average time/residue: 0.1048 time to fit residues: 19.3857 Evaluate side-chains 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.124088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.106019 restraints weight = 11747.075| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.45 r_work: 0.3064 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9357 Z= 0.123 Angle : 0.525 11.134 12753 Z= 0.261 Chirality : 0.039 0.134 1532 Planarity : 0.003 0.049 1628 Dihedral : 5.876 65.702 1377 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 3.33 % Allowed : 20.17 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.25), residues: 1195 helix: 1.78 (0.19), residues: 785 sheet: -1.52 (0.68), residues: 55 loop : -1.72 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 618 TYR 0.012 0.001 TYR B 354 PHE 0.011 0.001 PHE A 453 TRP 0.008 0.001 TRP A 408 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 9357) covalent geometry : angle 0.52472 / 0.26 (12753) hydrogen bonds : bond 0.03545 / 2.33 ( 583) hydrogen bonds : angle 3.77781 / 2.66 ( 1701) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.385 Fit side-chains REVERT: A 7 ARG cc_start: 0.8253 (ptm160) cc_final: 0.8003 (ttp80) REVERT: A 170 LEU cc_start: 0.8793 (tt) cc_final: 0.8376 (mp) REVERT: A 222 GLU cc_start: 0.7988 (pp20) cc_final: 0.7672 (pt0) REVERT: A 233 GLU cc_start: 0.8217 (tp30) cc_final: 0.7704 (tt0) REVERT: A 438 ASP cc_start: 0.7200 (m-30) cc_final: 0.6912 (t0) REVERT: B 241 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8016 (mm) REVERT: B 386 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8241 (p) REVERT: B 522 ASP cc_start: 0.8261 (p0) cc_final: 0.7999 (p0) REVERT: B 624 ARG cc_start: 0.7960 (mmp-170) cc_final: 0.7590 (ttp80) outliers start: 32 outliers final: 26 residues processed: 137 average time/residue: 0.0999 time to fit residues: 19.0519 Evaluate side-chains 135 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 23 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.9565 > 50:) chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 76 optimal weight: 0.0670 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.123623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.105570 restraints weight = 11791.108| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.43 r_work: 0.3059 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9357 Z= 0.127 Angle : 0.530 10.685 12753 Z= 0.264 Chirality : 0.039 0.133 1532 Planarity : 0.003 0.050 1628 Dihedral : 5.842 64.737 1377 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 3.12 % Allowed : 20.69 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.25), residues: 1195 helix: 1.80 (0.19), residues: 786 sheet: -1.54 (0.67), residues: 55 loop : -1.65 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 618 TYR 0.011 0.001 TYR A 343 PHE 0.011 0.001 PHE A 453 TRP 0.008 0.001 TRP A 408 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9357) covalent geometry : angle 0.52964 / 0.26 (12753) hydrogen bonds : bond 0.03607 / 2.36 ( 583) hydrogen bonds : angle 3.78532 / 2.67 ( 1701) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.238 Fit side-chains REVERT: A 7 ARG cc_start: 0.8243 (ptm160) cc_final: 0.7966 (ttp80) REVERT: A 170 LEU cc_start: 0.8791 (tt) cc_final: 0.8343 (mp) REVERT: A 222 GLU cc_start: 0.7989 (pp20) cc_final: 0.7656 (pt0) REVERT: A 233 GLU cc_start: 0.8210 (tp30) cc_final: 0.7709 (tt0) REVERT: B 13 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6676 (mmm160) REVERT: B 208 MET cc_start: 0.8471 (tpp) cc_final: 0.8154 (tpp) REVERT: B 241 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8010 (mm) REVERT: B 386 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8245 (p) REVERT: B 522 ASP cc_start: 0.8223 (p0) cc_final: 0.7949 (p0) REVERT: B 624 ARG cc_start: 0.7912 (mmp-170) cc_final: 0.7520 (ttp80) outliers start: 30 outliers final: 25 residues processed: 132 average time/residue: 0.0987 time to fit residues: 18.1398 Evaluate side-chains 129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 67 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 73 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.105752 restraints weight = 11884.040| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.43 r_work: 0.3065 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9357 Z= 0.124 Angle : 0.534 10.580 12753 Z= 0.267 Chirality : 0.039 0.132 1532 Planarity : 0.003 0.050 1628 Dihedral : 5.797 65.606 1377 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 2.81 % Allowed : 21.10 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.25), residues: 1195 helix: 1.82 (0.19), residues: 788 sheet: -1.51 (0.68), residues: 55 loop : -1.62 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 618 TYR 0.015 0.001 TYR B 354 PHE 0.011 0.001 PHE A 453 TRP 0.009 0.001 TRP A 408 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 9357) covalent geometry : angle 0.53370 / 0.27 (12753) hydrogen bonds : bond 0.03557 / 2.33 ( 583) hydrogen bonds : angle 3.76612 / 2.65 ( 1701) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.374 Fit side-chains REVERT: A 7 ARG cc_start: 0.8272 (ptm160) cc_final: 0.7988 (ttp80) REVERT: A 170 LEU cc_start: 0.8782 (tt) cc_final: 0.8337 (mp) REVERT: A 222 GLU cc_start: 0.8005 (pp20) cc_final: 0.7672 (pt0) REVERT: A 233 GLU cc_start: 0.8217 (tp30) cc_final: 0.7713 (tt0) REVERT: B 13 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6522 (mmm160) REVERT: B 208 MET cc_start: 0.8472 (tpp) cc_final: 0.8151 (tpp) REVERT: B 241 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8009 (mm) REVERT: B 386 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8253 (p) REVERT: B 522 ASP cc_start: 0.8221 (p0) cc_final: 0.8009 (p0) REVERT: B 624 ARG cc_start: 0.7903 (mmp-170) cc_final: 0.7523 (ttp80) outliers start: 27 outliers final: 22 residues processed: 126 average time/residue: 0.1057 time to fit residues: 18.1754 Evaluate side-chains 126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 59 optimal weight: 0.2980 chunk 89 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 91 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.124026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.106482 restraints weight = 11652.365| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.38 r_work: 0.3075 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9357 Z= 0.120 Angle : 0.535 10.375 12753 Z= 0.266 Chirality : 0.039 0.131 1532 Planarity : 0.003 0.050 1628 Dihedral : 5.749 66.331 1377 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 2.91 % Allowed : 20.89 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.25), residues: 1195 helix: 1.86 (0.19), residues: 788 sheet: -1.55 (0.67), residues: 55 loop : -1.62 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 170 TYR 0.017 0.001 TYR B 354 PHE 0.011 0.001 PHE A 453 TRP 0.009 0.001 TRP A 408 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 9357) covalent geometry : angle 0.53533 / 0.27 (12753) hydrogen bonds : bond 0.03518 / 2.31 ( 583) hydrogen bonds : angle 3.74923 / 2.64 ( 1701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.61 seconds wall clock time: 37 minutes 28.66 seconds (2248.66 seconds total)