Starting phenix.real_space_refine on Sun Jun 8 06:12:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcx_37451/06_2025/8wcx_37451.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcx_37451/06_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_37451/06_2025/8wcx_37451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcx_37451/06_2025/8wcx_37451.map" model { file = "/net/cci-nas-00/data/ceres_data/8wcx_37451/06_2025/8wcx_37451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcx_37451/06_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-5710/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: 6.40, per 1000 atoms: 0.70 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: 2.52 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: 1.01 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: 3.02 Time building geometry restraints manager: 2.98 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: 2.950 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.800 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.510 ------------------------------------------------------------------------------- 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 : 1.064 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: 0.2724 time to fit residues: 66.6291 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 : 0.925 ------------------------------------------------------------------------------- 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 = 41)----------------| | 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: 0.3069 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 : 0.982 Fit side-chains REVERT: A 170 LEU cc_start: 0.8818 (tt) cc_final: 0.8403 (mp) REVERT: A 222 GLU cc_start: 0.7982 (pp20) cc_final: 0.7618 (pt0) REVERT: B 327 GLN cc_start: 0.8775 (mm110) cc_final: 0.8507 (mt0) REVERT: B 624 ARG cc_start: 0.7897 (mmp-170) cc_final: 0.7677 (ttp80) outliers start: 39 outliers final: 18 residues processed: 150 average time/residue: 0.2141 time to fit residues: 44.5565 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 : 0.903 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.117942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.099439 restraints weight = 12025.923| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.44 r_work: 0.2968 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9357 Z= 0.257 Angle : 0.653 8.172 12753 Z= 0.330 Chirality : 0.045 0.161 1532 Planarity : 0.005 0.053 1628 Dihedral : 7.701 76.048 1377 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.39 % Rotamer: Outliers : 4.05 % Allowed : 19.54 % 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 (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: -0.08 (0.24), residues: 1195 helix: 0.86 (0.18), residues: 787 sheet: -1.67 (0.66), residues: 55 loop : -1.83 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 3 HIS 0.005 0.001 HIS A 88 PHE 0.017 0.002 PHE A 210 TYR 0.017 0.002 TYR B 487 ARG 0.006 0.000 ARG A 484 Details of bonding type rmsd hydrogen bonds : bond 0.05057 ( 583) hydrogen bonds : angle 4.37302 ( 1701) covalent geometry : bond 0.00628 ( 9357) covalent geometry : angle 0.65281 (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 141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 1.090 Fit side-chains REVERT: A 170 LEU cc_start: 0.8882 (tt) cc_final: 0.8325 (mp) REVERT: A 222 GLU cc_start: 0.8068 (pp20) cc_final: 0.7713 (pt0) REVERT: A 233 GLU cc_start: 0.8368 (tp30) cc_final: 0.7739 (tt0) REVERT: A 438 ASP cc_start: 0.7365 (m-30) cc_final: 0.6958 (t0) REVERT: B 208 MET cc_start: 0.8627 (tpp) cc_final: 0.8284 (tpp) REVERT: B 241 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8260 (mm) REVERT: B 624 ARG cc_start: 0.7953 (mmp-170) cc_final: 0.7583 (ttp80) outliers start: 39 outliers final: 25 residues processed: 136 average time/residue: 0.2360 time to fit residues: 44.0640 Evaluate side-chains 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 7 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.101529 restraints weight = 11776.863| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.42 r_work: 0.2999 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9357 Z= 0.156 Angle : 0.574 9.337 12753 Z= 0.288 Chirality : 0.041 0.156 1532 Planarity : 0.004 0.049 1628 Dihedral : 6.995 77.888 1377 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 3.74 % Allowed : 20.58 % 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: 0.17 (0.25), residues: 1195 helix: 1.14 (0.19), residues: 782 sheet: -1.68 (0.67), residues: 55 loop : -1.89 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 487 ARG 0.002 0.000 ARG B 618 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 583) hydrogen bonds : angle 4.17904 ( 1701) covalent geometry : bond 0.00375 ( 9357) covalent geometry : angle 0.57417 (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: 36 poor density : 106 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8855 (tt) cc_final: 0.8334 (mp) REVERT: A 222 GLU cc_start: 0.8053 (pp20) cc_final: 0.7717 (pt0) REVERT: A 233 GLU cc_start: 0.8338 (tp30) cc_final: 0.7734 (tt0) REVERT: A 438 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6946 (t0) REVERT: B 208 MET cc_start: 0.8609 (tpp) cc_final: 0.8345 (tpp) REVERT: B 241 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8189 (mm) REVERT: B 594 LEU cc_start: 0.8615 (tp) cc_final: 0.8410 (tp) REVERT: B 624 ARG cc_start: 0.7929 (mmp-170) cc_final: 0.7570 (ttp80) outliers start: 36 outliers final: 26 residues processed: 135 average time/residue: 0.2289 time to fit residues: 42.9020 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 293 PHE 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 397 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 512 ASP 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 404 THR 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: 0.0050 chunk 91 optimal weight: 0.2980 chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 0.0010 chunk 66 optimal weight: 0.0470 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.2098 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.124741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.106692 restraints weight = 11744.634| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.44 r_work: 0.3073 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9357 Z= 0.104 Angle : 0.509 9.432 12753 Z= 0.257 Chirality : 0.038 0.137 1532 Planarity : 0.003 0.046 1628 Dihedral : 6.227 70.824 1377 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 2.91 % Allowed : 21.41 % 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: 0.53 (0.25), residues: 1195 helix: 1.45 (0.19), residues: 785 sheet: -1.61 (0.67), residues: 55 loop : -1.84 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 408 HIS 0.004 0.001 HIS A 88 PHE 0.014 0.001 PHE A 453 TYR 0.014 0.001 TYR A 343 ARG 0.002 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 583) hydrogen bonds : angle 3.89874 ( 1701) covalent geometry : bond 0.00221 ( 9357) covalent geometry : angle 0.50918 (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 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.089 Fit side-chains REVERT: A 170 LEU cc_start: 0.8799 (tt) cc_final: 0.8370 (mp) REVERT: A 222 GLU cc_start: 0.7977 (pp20) cc_final: 0.7678 (pt0) REVERT: A 233 GLU cc_start: 0.8253 (tp30) cc_final: 0.7666 (tt0) REVERT: A 401 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7540 (p0) REVERT: B 208 MET cc_start: 0.8545 (tpp) cc_final: 0.8309 (tpp) REVERT: B 522 ASP cc_start: 0.8195 (p0) cc_final: 0.7984 (p0) REVERT: B 624 ARG cc_start: 0.7888 (mmp-170) cc_final: 0.7513 (ttp80) outliers start: 28 outliers final: 16 residues processed: 135 average time/residue: 0.2232 time to fit residues: 41.6713 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 : 0.940 ------------------------------------------------------------------------------- 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 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 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 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 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 = 0.123694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105583 restraints weight = 11734.135| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.44 r_work: 0.3055 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2440 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= 0.116 Angle : 0.523 9.499 12753 Z= 0.262 Chirality : 0.039 0.130 1532 Planarity : 0.003 0.049 1628 Dihedral : 6.095 69.379 1377 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 2.81 % Allowed : 22.04 % 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: 0.67 (0.25), residues: 1195 helix: 1.58 (0.19), residues: 784 sheet: -1.57 (0.68), residues: 55 loop : -1.82 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 408 HIS 0.005 0.001 HIS A 88 PHE 0.013 0.001 PHE A 453 TYR 0.011 0.001 TYR A 343 ARG 0.003 0.000 ARG B 618 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 583) hydrogen bonds : angle 3.85244 ( 1701) covalent geometry : bond 0.00268 ( 9357) covalent geometry : angle 0.52346 (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 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.921 Fit side-chains REVERT: A 7 ARG cc_start: 0.8203 (ptm160) cc_final: 0.7927 (ttp80) REVERT: A 29 MET cc_start: 0.8547 (mmp) cc_final: 0.8135 (mmp) REVERT: A 170 LEU cc_start: 0.8802 (tt) cc_final: 0.8375 (mp) REVERT: A 222 GLU cc_start: 0.8000 (pp20) cc_final: 0.7700 (pt0) REVERT: A 233 GLU cc_start: 0.8279 (tp30) cc_final: 0.7698 (tt0) REVERT: A 401 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7611 (p0) REVERT: A 438 ASP cc_start: 0.7225 (m-30) cc_final: 0.6881 (t0) REVERT: B 208 MET cc_start: 0.8560 (tpp) cc_final: 0.8313 (tpp) REVERT: B 241 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8021 (mm) REVERT: B 365 GLU cc_start: 0.8309 (tp30) cc_final: 0.7919 (tt0) REVERT: B 624 ARG cc_start: 0.7908 (mmp-170) cc_final: 0.7547 (ttp80) outliers start: 27 outliers final: 21 residues processed: 136 average time/residue: 0.2468 time to fit residues: 45.8410 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 458 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 586 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 71 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 0.0370 chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.123350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.105135 restraints weight = 11854.551| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.45 r_work: 0.3058 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9357 Z= 0.119 Angle : 0.527 10.351 12753 Z= 0.261 Chirality : 0.039 0.130 1532 Planarity : 0.003 0.050 1628 Dihedral : 5.996 69.708 1377 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.94 % Favored : 94.98 % 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: 0.79 (0.25), residues: 1195 helix: 1.68 (0.19), residues: 783 sheet: -1.62 (0.67), residues: 55 loop : -1.79 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.003 0.000 ARG B 618 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 583) hydrogen bonds : angle 3.83327 ( 1701) covalent geometry : bond 0.00275 ( 9357) covalent geometry : angle 0.52674 (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 144 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.999 Fit side-chains REVERT: A 7 ARG cc_start: 0.8180 (ptm160) cc_final: 0.7914 (ttp80) REVERT: A 29 MET cc_start: 0.8557 (mmp) cc_final: 0.8131 (mmp) REVERT: A 105 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: A 170 LEU cc_start: 0.8803 (tt) cc_final: 0.8369 (mp) REVERT: A 222 GLU cc_start: 0.8001 (pp20) cc_final: 0.7706 (pt0) REVERT: A 233 GLU cc_start: 0.8298 (tp30) cc_final: 0.7705 (tt0) REVERT: A 401 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7646 (p0) REVERT: A 438 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6850 (t0) REVERT: B 208 MET cc_start: 0.8555 (tpp) cc_final: 0.8328 (tpp) REVERT: B 241 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8014 (mm) REVERT: B 365 GLU cc_start: 0.8279 (tp30) cc_final: 0.7929 (tt0) REVERT: B 386 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8282 (p) REVERT: B 522 ASP cc_start: 0.8159 (p0) cc_final: 0.7948 (p0) REVERT: B 624 ARG cc_start: 0.7892 (mmp-170) cc_final: 0.7522 (ttp80) outliers start: 35 outliers final: 20 residues processed: 138 average time/residue: 0.2335 time to fit residues: 44.2085 Evaluate side-chains 130 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 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 B residue 13 ARG Chi-restraints excluded: chain B residue 103 VAL 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 329 THR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.104147 restraints weight = 11963.465| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.45 r_work: 0.3037 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2574 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= 0.129 Angle : 0.537 9.970 12753 Z= 0.265 Chirality : 0.040 0.128 1532 Planarity : 0.003 0.051 1628 Dihedral : 5.942 70.785 1377 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 3.43 % Allowed : 21.00 % 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: 0.84 (0.25), residues: 1195 helix: 1.71 (0.19), residues: 782 sheet: -1.58 (0.67), residues: 55 loop : -1.74 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.003 0.000 ARG B 590 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 583) hydrogen bonds : angle 3.83378 ( 1701) covalent geometry : bond 0.00304 ( 9357) covalent geometry : angle 0.53714 (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 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 1.010 Fit side-chains REVERT: A 7 ARG cc_start: 0.8204 (ptm160) cc_final: 0.7949 (ttp80) REVERT: A 29 MET cc_start: 0.8571 (mmp) cc_final: 0.8232 (mmp) REVERT: A 170 LEU cc_start: 0.8818 (tt) cc_final: 0.8378 (mp) REVERT: A 222 GLU cc_start: 0.8020 (pp20) cc_final: 0.7721 (pt0) REVERT: A 401 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7698 (p0) REVERT: A 438 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6905 (t0) REVERT: B 13 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7163 (mmp-170) REVERT: B 208 MET cc_start: 0.8581 (tpp) cc_final: 0.8344 (tpp) REVERT: B 241 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8082 (mm) REVERT: B 365 GLU cc_start: 0.8308 (tp30) cc_final: 0.7950 (tt0) REVERT: B 386 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8312 (p) REVERT: B 624 ARG cc_start: 0.7908 (mmp-170) cc_final: 0.7528 (ttp80) outliers start: 33 outliers final: 23 residues processed: 134 average time/residue: 0.2394 time to fit residues: 44.5568 Evaluate side-chains 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 463 MET 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 101 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 chunk 117 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.103446 restraints weight = 11792.422| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.43 r_work: 0.3035 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9357 Z= 0.137 Angle : 0.546 10.414 12753 Z= 0.270 Chirality : 0.040 0.128 1532 Planarity : 0.003 0.051 1628 Dihedral : 5.925 71.772 1377 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 3.33 % Allowed : 21.00 % 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: 1.72 (0.19), residues: 783 sheet: -1.59 (0.67), residues: 55 loop : -1.75 (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 0.012 0.001 PHE A 453 TYR 0.010 0.001 TYR B 487 ARG 0.002 0.000 ARG B 618 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 583) hydrogen bonds : angle 3.84402 ( 1701) covalent geometry : bond 0.00328 ( 9357) covalent geometry : angle 0.54554 (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 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.904 Fit side-chains REVERT: A 29 MET cc_start: 0.8586 (mmp) cc_final: 0.8147 (mmp) REVERT: A 105 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: A 170 LEU cc_start: 0.8816 (tt) cc_final: 0.8358 (mp) REVERT: A 222 GLU cc_start: 0.8014 (pp20) cc_final: 0.7715 (pt0) REVERT: A 233 GLU cc_start: 0.8330 (tp30) cc_final: 0.7695 (tt0) REVERT: A 401 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7732 (p0) REVERT: B 12 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7046 (mt-10) REVERT: B 13 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7435 (mmp-170) REVERT: B 208 MET cc_start: 0.8570 (tpp) cc_final: 0.8340 (tpp) REVERT: B 241 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8091 (mm) REVERT: B 365 GLU cc_start: 0.8292 (tp30) cc_final: 0.7941 (tt0) REVERT: B 386 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8328 (p) REVERT: B 624 ARG cc_start: 0.7849 (mmp-170) cc_final: 0.7516 (ttp80) outliers start: 32 outliers final: 25 residues processed: 127 average time/residue: 0.2232 time to fit residues: 39.4113 Evaluate side-chains 129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 188 SER 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 463 MET 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.121651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.103443 restraints weight = 11942.358| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.44 r_work: 0.3034 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9357 Z= 0.136 Angle : 0.548 10.093 12753 Z= 0.271 Chirality : 0.040 0.127 1532 Planarity : 0.003 0.051 1628 Dihedral : 5.893 71.747 1377 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 3.33 % Allowed : 21.00 % 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: 0.88 (0.25), residues: 1195 helix: 1.74 (0.19), residues: 783 sheet: -1.61 (0.66), residues: 55 loop : -1.72 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.002 0.000 ARG B 590 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 583) hydrogen bonds : angle 3.84496 ( 1701) covalent geometry : bond 0.00327 ( 9357) covalent geometry : angle 0.54771 (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 130 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 1.045 Fit side-chains REVERT: A 29 MET cc_start: 0.8591 (mmp) cc_final: 0.8155 (mmp) REVERT: A 105 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: A 170 LEU cc_start: 0.8824 (tt) cc_final: 0.8362 (mp) REVERT: A 222 GLU cc_start: 0.8012 (pp20) cc_final: 0.7713 (pt0) REVERT: A 401 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7786 (p0) REVERT: A 438 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6925 (t0) REVERT: B 12 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6982 (mt-10) REVERT: B 208 MET cc_start: 0.8608 (tpp) cc_final: 0.8366 (tpp) REVERT: B 241 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8107 (mm) REVERT: B 365 GLU cc_start: 0.8309 (tp30) cc_final: 0.7935 (tt0) REVERT: B 386 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8353 (p) REVERT: B 624 ARG cc_start: 0.7855 (mmp-170) cc_final: 0.7517 (ttp80) outliers start: 32 outliers final: 26 residues processed: 125 average time/residue: 0.2234 time to fit residues: 38.7786 Evaluate side-chains 126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 188 SER 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 463 MET 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 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 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 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: 0.5980 chunk 47 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN B 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.104340 restraints weight = 11789.177| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.39 r_work: 0.3050 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9357 Z= 0.126 Angle : 0.533 9.929 12753 Z= 0.265 Chirality : 0.039 0.129 1532 Planarity : 0.003 0.050 1628 Dihedral : 5.841 71.493 1377 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 3.43 % Allowed : 21.31 % 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: 0.94 (0.25), residues: 1195 helix: 1.77 (0.19), residues: 785 sheet: -1.65 (0.65), residues: 55 loop : -1.67 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 170 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 583) hydrogen bonds : angle 3.81558 ( 1701) covalent geometry : bond 0.00300 ( 9357) covalent geometry : angle 0.53343 (12753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4632.32 seconds wall clock time: 80 minutes 33.54 seconds (4833.54 seconds total)