Starting phenix.real_space_refine on Mon May 12 20:12:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcx_37451/05_2025/8wcx_37451.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcx_37451/05_2025/8wcx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wcx_37451/05_2025/8wcx_37451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcx_37451/05_2025/8wcx_37451.map" model { file = "/net/cci-nas-00/data/ceres_data/8wcx_37451/05_2025/8wcx_37451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcx_37451/05_2025/8wcx_37451.cif" } resolution = 3.09 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.55, per 1000 atoms: 0.60 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.94 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: 2.85 Time building geometry restraints manager: 2.75 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: 2.410 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.480 Find NCS groups from input model: 0.140 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 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 (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: -0.07 (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 TRP 0.013 0.001 TRP A 408 HIS 0.006 0.001 HIS B 616 PHE 0.008 0.001 PHE A 472 TYR 0.016 0.001 TYR A 343 ARG 0.014 0.000 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.15529 ( 583) hydrogen bonds : angle 5.54825 ( 1701) covalent geometry : bond 0.00498 ( 9357) covalent geometry : angle 0.73651 (12753) *********************** 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 : 0.943 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: 0.6400 (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: 0.2671 time to fit residues: 65.1283 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 : 1.043 ------------------------------------------------------------------------------- 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 100 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3412 r_free = 0.3412 target = 0.124484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.106400 restraints weight = 11759.929| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.46 r_work: 0.3067 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9357 Z= 0.145 Angle : 0.582 8.620 12753 Z= 0.294 Chirality : 0.041 0.145 1532 Planarity : 0.004 0.050 1628 Dihedral : 9.312 74.968 1381 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 4.05 % Allowed : 17.57 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1195 helix: 1.12 (0.19), residues: 781 sheet: -1.51 (0.66), residues: 55 loop : -1.77 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 620 HIS 0.004 0.001 HIS A 88 PHE 0.010 0.001 PHE A 453 TYR 0.015 0.001 TYR B 339 ARG 0.005 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 583) hydrogen bonds : angle 4.21787 ( 1701) covalent geometry : bond 0.00335 ( 9357) covalent geometry : angle 0.58152 (12753) *********************** 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 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.894 Fit side-chains REVERT: A 170 LEU cc_start: 0.8820 (tt) cc_final: 0.8402 (mp) REVERT: A 222 GLU cc_start: 0.8002 (pp20) cc_final: 0.7632 (pt0) REVERT: A 417 ARG cc_start: 0.7661 (mmm-85) cc_final: 0.7459 (mtm110) REVERT: B 327 GLN cc_start: 0.8769 (mm110) cc_final: 0.8502 (mt0) REVERT: B 624 ARG cc_start: 0.7902 (mmp-170) cc_final: 0.7664 (ttp80) outliers start: 39 outliers final: 18 residues processed: 150 average time/residue: 0.2188 time to fit residues: 45.2760 Evaluate side-chains 124 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 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 458 VAL Chi-restraints excluded: chain B residue 594 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN B 186 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 = 0.3356 r_free = 0.3356 target = 0.120447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.102005 restraints weight = 11982.113| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.44 r_work: 0.3006 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9357 Z= 0.197 Angle : 0.599 8.593 12753 Z= 0.303 Chirality : 0.043 0.154 1532 Planarity : 0.004 0.051 1628 Dihedral : 7.445 73.559 1377 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.64 % Rotamer: Outliers : 3.85 % Allowed : 19.13 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1195 helix: 1.09 (0.19), residues: 782 sheet: -1.54 (0.67), residues: 55 loop : -1.81 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 408 HIS 0.005 0.001 HIS A 88 PHE 0.014 0.002 PHE A 210 TYR 0.015 0.002 TYR B 487 ARG 0.005 0.000 ARG A 484 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 583) hydrogen bonds : angle 4.22408 ( 1701) covalent geometry : bond 0.00477 ( 9357) covalent geometry : angle 0.59921 (12753) *********************** 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 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 1.359 Fit side-chains REVERT: A 170 LEU cc_start: 0.8858 (tt) cc_final: 0.8382 (mp) REVERT: A 222 GLU cc_start: 0.8036 (pp20) cc_final: 0.7693 (pt0) REVERT: A 233 GLU cc_start: 0.8326 (tp30) cc_final: 0.7705 (tt0) REVERT: A 417 ARG cc_start: 0.7802 (mmm-85) cc_final: 0.7546 (mtm110) REVERT: A 438 ASP cc_start: 0.7290 (m-30) cc_final: 0.6906 (t0) REVERT: B 241 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8182 (mm) REVERT: B 327 GLN cc_start: 0.8787 (mm110) cc_final: 0.8457 (mt0) REVERT: B 624 ARG cc_start: 0.7904 (mmp-170) cc_final: 0.7589 (ttp80) outliers start: 37 outliers final: 23 residues processed: 136 average time/residue: 0.2635 time to fit residues: 49.0439 Evaluate side-chains 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 73 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 PHE 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 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 445 LEU Chi-restraints excluded: chain A residue 517 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 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 7 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 428 ASN B 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.103558 restraints weight = 11760.106| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.45 r_work: 0.3030 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2209 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= 0.136 Angle : 0.544 9.475 12753 Z= 0.272 Chirality : 0.040 0.134 1532 Planarity : 0.004 0.048 1628 Dihedral : 6.570 70.815 1377 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 3.33 % Allowed : 20.48 % 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 (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: 0.42 (0.25), residues: 1195 helix: 1.31 (0.19), residues: 784 sheet: -1.48 (0.68), residues: 55 loop : -1.76 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 408 HIS 0.004 0.001 HIS A 88 PHE 0.012 0.001 PHE A 453 TYR 0.013 0.001 TYR A 343 ARG 0.004 0.000 ARG B 618 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 583) hydrogen bonds : angle 4.05214 ( 1701) covalent geometry : bond 0.00320 ( 9357) covalent geometry : angle 0.54393 (12753) *********************** 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 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.936 Fit side-chains REVERT: A 170 LEU cc_start: 0.8822 (tt) cc_final: 0.8353 (mp) REVERT: A 222 GLU cc_start: 0.8023 (pp20) cc_final: 0.7690 (pt0) REVERT: A 233 GLU cc_start: 0.8302 (tp30) cc_final: 0.7716 (tt0) REVERT: A 401 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7613 (p0) REVERT: A 417 ARG cc_start: 0.7840 (mmm-85) cc_final: 0.7607 (mtm110) REVERT: A 438 ASP cc_start: 0.7267 (m-30) cc_final: 0.6873 (t0) REVERT: B 208 MET cc_start: 0.8561 (tpp) cc_final: 0.8250 (tpp) REVERT: B 241 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8145 (mm) REVERT: B 624 ARG cc_start: 0.7898 (mmp-170) cc_final: 0.7536 (ttp80) outliers start: 32 outliers final: 23 residues processed: 136 average time/residue: 0.2253 time to fit residues: 41.9583 Evaluate side-chains 129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 297 ILE 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 401 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 517 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 54 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 66 optimal weight: 0.0670 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.104336 restraints weight = 11819.959| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.45 r_work: 0.3038 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9357 Z= 0.123 Angle : 0.529 9.378 12753 Z= 0.265 Chirality : 0.039 0.151 1532 Planarity : 0.003 0.048 1628 Dihedral : 6.322 68.881 1377 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.39 % Rotamer: Outliers : 3.22 % Allowed : 21.00 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1195 helix: 1.44 (0.19), residues: 784 sheet: -1.49 (0.68), residues: 55 loop : -1.73 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 408 HIS 0.005 0.001 HIS A 88 PHE 0.013 0.001 PHE A 453 TYR 0.013 0.001 TYR B 354 ARG 0.003 0.000 ARG B 618 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 583) hydrogen bonds : angle 3.93696 ( 1701) covalent geometry : bond 0.00285 ( 9357) covalent geometry : angle 0.52932 (12753) *********************** 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 146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 1.075 Fit side-chains REVERT: A 170 LEU cc_start: 0.8828 (tt) cc_final: 0.8374 (mp) REVERT: A 222 GLU cc_start: 0.8021 (pp20) cc_final: 0.7712 (pt0) REVERT: A 233 GLU cc_start: 0.8261 (tp30) cc_final: 0.7693 (tt0) REVERT: A 438 ASP cc_start: 0.7234 (m-30) cc_final: 0.6849 (t0) REVERT: B 13 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6894 (mmp-170) REVERT: B 208 MET cc_start: 0.8564 (tpp) cc_final: 0.8266 (tpp) REVERT: B 241 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8080 (mm) REVERT: B 624 ARG cc_start: 0.7905 (mmp-170) cc_final: 0.7559 (ttp80) outliers start: 31 outliers final: 21 residues processed: 140 average time/residue: 0.2311 time to fit residues: 44.4235 Evaluate side-chains 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 336 VAL 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 445 LEU Chi-restraints excluded: chain A residue 517 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 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 458 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 1 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.0050 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.105544 restraints weight = 11746.505| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.45 r_work: 0.3054 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2388 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= 0.113 Angle : 0.519 9.247 12753 Z= 0.260 Chirality : 0.039 0.132 1532 Planarity : 0.003 0.047 1628 Dihedral : 6.132 67.785 1377 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 3.53 % Allowed : 21.10 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1195 helix: 1.59 (0.19), residues: 784 sheet: -1.56 (0.67), residues: 55 loop : -1.75 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 408 HIS 0.005 0.001 HIS A 88 PHE 0.013 0.001 PHE A 453 TYR 0.016 0.001 TYR B 354 ARG 0.008 0.000 ARG B 590 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 583) hydrogen bonds : angle 3.86349 ( 1701) covalent geometry : bond 0.00256 ( 9357) covalent geometry : angle 0.51879 (12753) *********************** 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 148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.966 Fit side-chains REVERT: A 29 MET cc_start: 0.8558 (mmp) cc_final: 0.8137 (mmp) REVERT: A 170 LEU cc_start: 0.8812 (tt) cc_final: 0.8374 (mp) REVERT: A 222 GLU cc_start: 0.8000 (pp20) cc_final: 0.7697 (pt0) REVERT: A 233 GLU cc_start: 0.8275 (tp30) cc_final: 0.7693 (tt0) REVERT: A 401 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7603 (p0) REVERT: A 438 ASP cc_start: 0.7206 (m-30) cc_final: 0.6859 (t0) REVERT: B 13 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6905 (mmp-170) REVERT: B 208 MET cc_start: 0.8481 (tpp) cc_final: 0.8223 (tpp) REVERT: B 241 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8013 (mm) REVERT: B 365 GLU cc_start: 0.8274 (tp30) cc_final: 0.7929 (tt0) REVERT: B 386 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8249 (p) REVERT: B 522 ASP cc_start: 0.8193 (p0) cc_final: 0.7972 (p0) REVERT: B 624 ARG cc_start: 0.7913 (mmp-170) cc_final: 0.7535 (ttp80) outliers start: 34 outliers final: 22 residues processed: 143 average time/residue: 0.2331 time to fit residues: 46.0935 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 : 0.943 ------------------------------------------------------------------------------- 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 340 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 517 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 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 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 71 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.104159 restraints weight = 11874.528| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.44 r_work: 0.3039 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2486 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= 0.132 Angle : 0.556 13.471 12753 Z= 0.271 Chirality : 0.040 0.156 1532 Planarity : 0.003 0.050 1628 Dihedral : 6.051 68.583 1377 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.44 % Favored : 94.48 % Rotamer: Outliers : 3.53 % Allowed : 20.89 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1195 helix: 1.64 (0.19), residues: 782 sheet: -1.62 (0.66), residues: 55 loop : -1.75 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 408 HIS 0.005 0.001 HIS A 88 PHE 0.012 0.001 PHE A 453 TYR 0.010 0.001 TYR B 487 ARG 0.004 0.000 ARG B 590 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 583) hydrogen bonds : angle 3.86731 ( 1701) covalent geometry : bond 0.00310 ( 9357) covalent geometry : angle 0.55609 (12753) *********************** 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 141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 1.133 Fit side-chains REVERT: A 29 MET cc_start: 0.8577 (mmp) cc_final: 0.8246 (mmp) REVERT: A 170 LEU cc_start: 0.8821 (tt) cc_final: 0.8380 (mp) REVERT: A 222 GLU cc_start: 0.8025 (pp20) cc_final: 0.7723 (pt0) REVERT: A 401 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7676 (p0) REVERT: A 438 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6857 (t0) REVERT: B 13 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7057 (mmp-170) REVERT: B 208 MET cc_start: 0.8503 (tpp) cc_final: 0.8249 (tpp) REVERT: B 241 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8073 (mm) REVERT: B 365 GLU cc_start: 0.8264 (tp30) cc_final: 0.7910 (tt0) REVERT: B 386 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8288 (p) REVERT: B 522 ASP cc_start: 0.8191 (p0) cc_final: 0.7932 (p0) REVERT: B 624 ARG cc_start: 0.7892 (mmp-170) cc_final: 0.7539 (ttp80) outliers start: 34 outliers final: 25 residues processed: 135 average time/residue: 0.2241 time to fit residues: 41.7185 Evaluate side-chains 135 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 340 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 438 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 75 optimal weight: 0.0570 chunk 108 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.123487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.105404 restraints weight = 11951.584| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.45 r_work: 0.3054 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2545 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= 0.113 Angle : 0.523 9.902 12753 Z= 0.260 Chirality : 0.039 0.130 1532 Planarity : 0.003 0.049 1628 Dihedral : 5.931 68.210 1377 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 3.64 % Allowed : 20.69 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1195 helix: 1.75 (0.19), residues: 782 sheet: -1.62 (0.66), residues: 55 loop : -1.77 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 408 HIS 0.005 0.001 HIS A 88 PHE 0.012 0.001 PHE A 453 TYR 0.011 0.001 TYR A 343 ARG 0.002 0.000 ARG B 590 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 583) hydrogen bonds : angle 3.81197 ( 1701) covalent geometry : bond 0.00259 ( 9357) covalent geometry : angle 0.52322 (12753) *********************** 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 140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.987 Fit side-chains REVERT: A 29 MET cc_start: 0.8576 (mmp) cc_final: 0.8153 (mmp) REVERT: A 170 LEU cc_start: 0.8791 (tt) cc_final: 0.8358 (mp) REVERT: A 222 GLU cc_start: 0.8008 (pp20) cc_final: 0.7706 (pt0) REVERT: A 233 GLU cc_start: 0.8149 (tp30) cc_final: 0.7615 (tt0) REVERT: A 401 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7629 (p0) REVERT: A 438 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6915 (t0) REVERT: B 12 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6973 (mt-10) REVERT: B 13 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7190 (mmp-170) REVERT: B 208 MET cc_start: 0.8480 (tpp) cc_final: 0.8257 (tpp) REVERT: B 241 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8037 (mm) REVERT: B 365 GLU cc_start: 0.8236 (tp30) cc_final: 0.7888 (tt0) REVERT: B 386 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8271 (p) REVERT: B 522 ASP cc_start: 0.8245 (p0) cc_final: 0.8034 (p0) REVERT: B 624 ARG cc_start: 0.7890 (mmp-170) cc_final: 0.7540 (ttp80) outliers start: 35 outliers final: 26 residues processed: 133 average time/residue: 0.2265 time to fit residues: 41.5161 Evaluate side-chains 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 340 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 438 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 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 329 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.121530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103492 restraints weight = 11790.365| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.41 r_work: 0.3039 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9357 Z= 0.143 Angle : 0.552 10.619 12753 Z= 0.273 Chirality : 0.040 0.128 1532 Planarity : 0.003 0.051 1628 Dihedral : 5.956 70.501 1377 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 3.53 % Allowed : 21.21 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1195 helix: 1.70 (0.19), residues: 783 sheet: -1.58 (0.67), residues: 55 loop : -1.73 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 408 HIS 0.005 0.001 HIS A 88 PHE 0.011 0.001 PHE A 453 TYR 0.011 0.001 TYR B 487 ARG 0.002 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 583) hydrogen bonds : angle 3.86723 ( 1701) covalent geometry : bond 0.00343 ( 9357) covalent geometry : angle 0.55216 (12753) *********************** 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: 34 poor density : 102 time to evaluate : 0.891 Fit side-chains REVERT: A 29 MET cc_start: 0.8589 (mmp) cc_final: 0.8249 (mmp) REVERT: A 105 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: A 170 LEU cc_start: 0.8810 (tt) cc_final: 0.8352 (mp) REVERT: A 222 GLU cc_start: 0.8014 (pp20) cc_final: 0.7716 (pt0) REVERT: A 233 GLU cc_start: 0.8226 (tp30) cc_final: 0.7698 (tt0) REVERT: A 401 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7717 (p0) REVERT: A 438 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6889 (t0) REVERT: B 12 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6957 (mt-10) REVERT: B 13 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7362 (mmp-170) REVERT: B 208 MET cc_start: 0.8467 (tpp) cc_final: 0.8231 (tpp) REVERT: B 241 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8111 (mm) REVERT: B 365 GLU cc_start: 0.8284 (tp30) cc_final: 0.7888 (tt0) REVERT: B 386 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8312 (p) REVERT: B 522 ASP cc_start: 0.8260 (p0) cc_final: 0.8048 (p0) REVERT: B 624 ARG cc_start: 0.7836 (mmp-170) cc_final: 0.7520 (ttp80) outliers start: 34 outliers final: 26 residues processed: 130 average time/residue: 0.2186 time to fit residues: 39.6304 Evaluate side-chains 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 105 GLU 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 340 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 438 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 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 329 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103235 restraints weight = 11966.796| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.44 r_work: 0.3029 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9357 Z= 0.143 Angle : 0.548 9.379 12753 Z= 0.274 Chirality : 0.040 0.127 1532 Planarity : 0.003 0.050 1628 Dihedral : 5.970 72.339 1377 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.44 % Favored : 94.48 % Rotamer: Outliers : 3.53 % Allowed : 21.21 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1195 helix: 1.71 (0.19), residues: 783 sheet: -1.63 (0.66), residues: 55 loop : -1.73 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 408 HIS 0.005 0.001 HIS A 88 PHE 0.011 0.001 PHE A 453 TYR 0.011 0.001 TYR B 487 ARG 0.002 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 583) hydrogen bonds : angle 3.88143 ( 1701) covalent geometry : bond 0.00344 ( 9357) covalent geometry : angle 0.54813 (12753) ********************** 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 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.926 Fit side-chains REVERT: A 29 MET cc_start: 0.8595 (mmp) cc_final: 0.8160 (mmp) REVERT: A 105 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: A 170 LEU cc_start: 0.8826 (tt) cc_final: 0.8360 (mp) REVERT: A 222 GLU cc_start: 0.8045 (pp20) cc_final: 0.7729 (pt0) REVERT: A 233 GLU cc_start: 0.8234 (tp30) cc_final: 0.7690 (tt0) REVERT: A 401 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7774 (p0) REVERT: A 438 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6899 (t0) REVERT: B 12 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7030 (mt-10) REVERT: B 208 MET cc_start: 0.8490 (tpp) cc_final: 0.8263 (tpp) REVERT: B 241 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8145 (mm) REVERT: B 365 GLU cc_start: 0.8295 (tp30) cc_final: 0.7887 (tt0) REVERT: B 386 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8324 (p) REVERT: B 522 ASP cc_start: 0.8270 (p0) cc_final: 0.8056 (p0) REVERT: B 624 ARG cc_start: 0.7858 (mmp-170) cc_final: 0.7518 (ttp80) outliers start: 34 outliers final: 27 residues processed: 125 average time/residue: 0.2195 time to fit residues: 37.8788 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 105 GLU 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 340 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 547 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 329 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 100 optimal weight: 0.0170 chunk 99 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.102976 restraints weight = 11798.269| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.42 r_work: 0.3026 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2675 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= 0.146 Angle : 0.552 9.262 12753 Z= 0.276 Chirality : 0.040 0.128 1532 Planarity : 0.003 0.050 1628 Dihedral : 5.969 72.635 1377 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.44 % Favored : 94.48 % Rotamer: Outliers : 3.43 % Allowed : 21.41 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1195 helix: 1.72 (0.19), residues: 784 sheet: -1.65 (0.66), residues: 55 loop : -1.72 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 408 HIS 0.005 0.001 HIS A 88 PHE 0.011 0.001 PHE A 453 TYR 0.011 0.001 TYR B 487 ARG 0.003 0.000 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 583) hydrogen bonds : angle 3.89134 ( 1701) covalent geometry : bond 0.00352 ( 9357) covalent geometry : angle 0.55216 (12753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4528.01 seconds wall clock time: 79 minutes 7.53 seconds (4747.53 seconds total)