Starting phenix.real_space_refine on Sat Jan 18 18:35:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yo4_39435/01_2025/8yo4_39435.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yo4_39435/01_2025/8yo4_39435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yo4_39435/01_2025/8yo4_39435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yo4_39435/01_2025/8yo4_39435.map" model { file = "/net/cci-nas-00/data/ceres_data/8yo4_39435/01_2025/8yo4_39435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yo4_39435/01_2025/8yo4_39435.cif" } resolution = 3.2 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= 0.104 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 48 5.49 5 Mg 4 5.21 5 S 44 5.16 5 C 7953 2.51 5 N 2157 2.21 5 O 2492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12698 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3563 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 13, 'TRANS': 428} Chain: "C" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2292 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain: "B" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3563 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 13, 'TRANS': 428} Chain: "D" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2292 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain: "E" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 493 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "F" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 491 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.51, per 1000 atoms: 0.59 Number of scatterers: 12698 At special positions: 0 Unit cell: (142.48, 122.72, 118.56, 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 44 16.00 P 48 15.00 Mg 4 11.99 O 2492 8.00 N 2157 7.00 C 7953 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: 3.22 Conformation dependent library (CDL) restraints added in 1.5 seconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2716 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 19 sheets defined 42.6% alpha, 8.1% beta 17 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 37 through 54 removed outlier: 4.463A pdb=" N GLY A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.972A pdb=" N ALA A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 129 removed outlier: 3.648A pdb=" N TYR A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 156 through 161 removed outlier: 3.834A pdb=" N ASN A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 161' Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 247 through 254 removed outlier: 3.833A pdb=" N LEU A 251 " --> pdb=" O ILE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 323 through 365 removed outlier: 3.863A pdb=" N GLU A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 381 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 391 through 397 Processing helix chain 'A' and resid 404 through 427 removed outlier: 3.659A pdb=" N LYS A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 451 through 454 Processing helix chain 'C' and resid 455 through 466 removed outlier: 5.269A pdb=" N ILE C 461 " --> pdb=" O GLU C 457 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 513 Processing helix chain 'C' and resid 528 through 534 Processing helix chain 'C' and resid 559 through 565 Processing helix chain 'C' and resid 566 through 575 Processing helix chain 'C' and resid 579 through 583 removed outlier: 3.694A pdb=" N GLN C 583 " --> pdb=" O LEU C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 Processing helix chain 'C' and resid 613 through 618 removed outlier: 6.139A pdb=" N ASP C 616 " --> pdb=" O SER C 613 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 618 " --> pdb=" O LYS C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 643 Processing helix chain 'C' and resid 654 through 663 removed outlier: 3.505A pdb=" N LEU C 658 " --> pdb=" O ASN C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.551A pdb=" N LYS C 671 " --> pdb=" O ALA C 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 27 removed outlier: 4.213A pdb=" N ALA B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 51 Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 76 through 86 removed outlier: 3.809A pdb=" N ALA B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 removed outlier: 3.689A pdb=" N TYR B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.675A pdb=" N ASN B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 156 through 161' Processing helix chain 'B' and resid 177 through 191 removed outlier: 3.553A pdb=" N LYS B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.609A pdb=" N LEU B 251 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 319 through 364 removed outlier: 3.550A pdb=" N LEU B 323 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 removed outlier: 3.509A pdb=" N ILE B 385 " --> pdb=" O GLU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 392 Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.895A pdb=" N GLY B 397 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET B 398 " --> pdb=" O LYS B 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 393 through 398' Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.923A pdb=" N LYS B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 439 Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'D' and resid 455 through 466 removed outlier: 3.728A pdb=" N GLY D 466 " --> pdb=" O CYS D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 490 Processing helix chain 'D' and resid 509 through 513 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 559 through 565 Processing helix chain 'D' and resid 566 through 575 removed outlier: 4.542A pdb=" N GLY D 572 " --> pdb=" O PRO D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 583 removed outlier: 3.858A pdb=" N PHE D 581 " --> pdb=" O TRP D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 613 Processing helix chain 'D' and resid 628 through 632 removed outlier: 3.789A pdb=" N LEU D 632 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 643 Processing helix chain 'D' and resid 654 through 664 removed outlier: 3.654A pdb=" N MET D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU D 662 " --> pdb=" O LEU D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 675 removed outlier: 3.957A pdb=" N ARG D 670 " --> pdb=" O ASN D 666 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 6.745A pdb=" N ASN A 4 " --> pdb=" O VAL C 648 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LYS C 650 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A 6 " --> pdb=" O LYS C 650 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 131 removed outlier: 4.263A pdb=" N LEU A 151 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 166 Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 211 removed outlier: 3.553A pdb=" N ILE A 211 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 223 Processing sheet with id=AA7, first strand: chain 'A' and resid 306 through 308 Processing sheet with id=AA8, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AA9, first strand: chain 'C' and resid 499 through 501 Processing sheet with id=AB1, first strand: chain 'C' and resid 603 through 605 Processing sheet with id=AB2, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AB3, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AB4, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AB5, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AB6, first strand: chain 'B' and resid 228 through 230 Processing sheet with id=AB7, first strand: chain 'B' and resid 305 through 308 removed outlier: 4.390A pdb=" N ILE B 305 " --> pdb=" O TYR B 317 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 435 through 436 removed outlier: 8.123A pdb=" N TYR D 435 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE D 412 " --> pdb=" O TYR D 435 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU D 411 " --> pdb=" O ALA D 553 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 507 through 508 Processing sheet with id=AC1, first strand: chain 'D' and resid 594 through 598 402 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.23 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3350 1.33 - 1.45: 2492 1.45 - 1.57: 7034 1.57 - 1.69: 94 1.69 - 1.81: 82 Bond restraints: 13052 Sorted by residual: bond pdb=" CA VAL A 369 " pdb=" CB VAL A 369 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.31e-02 5.83e+03 1.71e+00 bond pdb=" CA ASN B 92 " pdb=" CB ASN B 92 " ideal model delta sigma weight residual 1.531 1.567 -0.036 3.12e-02 1.03e+03 1.33e+00 bond pdb=" CB ASP B 393 " pdb=" CG ASP B 393 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.32e+00 bond pdb=" CA PHE B 401 " pdb=" C PHE B 401 " ideal model delta sigma weight residual 1.522 1.540 -0.018 1.72e-02 3.38e+03 1.10e+00 bond pdb=" C ASP B 249 " pdb=" N PRO B 250 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.05e+00 ... (remaining 13047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 17366 1.59 - 3.18: 362 3.18 - 4.77: 46 4.77 - 6.36: 13 6.36 - 7.95: 3 Bond angle restraints: 17790 Sorted by residual: angle pdb=" N VAL D 593 " pdb=" CA VAL D 593 " pdb=" C VAL D 593 " ideal model delta sigma weight residual 113.42 108.40 5.02 1.17e+00 7.31e-01 1.84e+01 angle pdb=" CA ILE A 211 " pdb=" CB ILE A 211 " pdb=" CG1 ILE A 211 " ideal model delta sigma weight residual 110.40 115.21 -4.81 1.70e+00 3.46e-01 8.01e+00 angle pdb=" C ASP B 393 " pdb=" N LYS B 394 " pdb=" CA LYS B 394 " ideal model delta sigma weight residual 120.99 126.09 -5.10 1.86e+00 2.89e-01 7.53e+00 angle pdb=" CB LYS A 409 " pdb=" CG LYS A 409 " pdb=" CD LYS A 409 " ideal model delta sigma weight residual 111.30 117.50 -6.20 2.30e+00 1.89e-01 7.27e+00 angle pdb=" C TRP A 425 " pdb=" N LYS A 426 " pdb=" CA LYS A 426 " ideal model delta sigma weight residual 121.52 116.89 4.63 1.84e+00 2.95e-01 6.34e+00 ... (remaining 17785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.14: 7089 29.14 - 58.28: 624 58.28 - 87.42: 49 87.42 - 116.56: 2 116.56 - 145.70: 2 Dihedral angle restraints: 7766 sinusoidal: 3536 harmonic: 4230 Sorted by residual: dihedral pdb=" CA THR B 242 " pdb=" C THR B 242 " pdb=" N TYR B 243 " pdb=" CA TYR B 243 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LYS B 237 " pdb=" C LYS B 237 " pdb=" N TYR B 238 " pdb=" CA TYR B 238 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA VAL A 321 " pdb=" C VAL A 321 " pdb=" N ASP A 322 " pdb=" CA ASP A 322 " ideal model delta harmonic sigma weight residual 180.00 159.23 20.77 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 7763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1312 0.036 - 0.072: 484 0.072 - 0.108: 99 0.108 - 0.144: 32 0.144 - 0.180: 1 Chirality restraints: 1928 Sorted by residual: chirality pdb=" CG LEU A 395 " pdb=" CB LEU A 395 " pdb=" CD1 LEU A 395 " pdb=" CD2 LEU A 395 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA ILE A 217 " pdb=" N ILE A 217 " pdb=" C ILE A 217 " pdb=" CB ILE A 217 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE A 165 " pdb=" N ILE A 165 " pdb=" C ILE A 165 " pdb=" CB ILE A 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1925 not shown) Planarity restraints: 2110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 249 " 0.059 5.00e-02 4.00e+02 8.89e-02 1.27e+01 pdb=" N PRO A 250 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 250 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 250 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 37 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO A 38 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 37 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO B 38 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " -0.024 5.00e-02 4.00e+02 ... (remaining 2107 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 137 2.62 - 3.19: 10687 3.19 - 3.76: 19762 3.76 - 4.33: 27913 4.33 - 4.90: 45829 Nonbonded interactions: 104328 Sorted by model distance: nonbonded pdb=" OD2 ASP C 559 " pdb="MG MG C 702 " model vdw 2.047 2.170 nonbonded pdb=" O LEU C 431 " pdb=" ND1 HIS C 432 " model vdw 2.185 3.120 nonbonded pdb=" OD2 ASP D 557 " pdb="MG MG D 701 " model vdw 2.186 2.170 nonbonded pdb=" O TRP A 91 " pdb=" OH TYR A 236 " model vdw 2.193 3.040 nonbonded pdb=" O ALA D 419 " pdb=" OH TYR D 637 " model vdw 2.223 3.040 ... (remaining 104323 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 32.520 Find NCS groups from input model: 0.340 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.003 0.036 13052 Z= 0.173 Angle : 0.570 7.950 17790 Z= 0.322 Chirality : 0.039 0.180 1928 Planarity : 0.004 0.089 2110 Dihedral : 19.702 145.699 5050 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.24 % Allowed : 30.51 % Favored : 69.26 % 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: -2.05 (0.21), residues: 1444 helix: -0.52 (0.22), residues: 545 sheet: -2.34 (0.41), residues: 159 loop : -1.77 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 604 HIS 0.005 0.001 HIS C 432 PHE 0.017 0.001 PHE B 350 TYR 0.018 0.001 TYR C 567 ARG 0.006 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 347 GLU cc_start: 0.7491 (tt0) cc_final: 0.7149 (tm-30) REVERT: C 640 MET cc_start: 0.8373 (ptm) cc_final: 0.8017 (ptm) REVERT: B 361 LYS cc_start: 0.7889 (tttm) cc_final: 0.7407 (mtmt) outliers start: 3 outliers final: 3 residues processed: 155 average time/residue: 0.2892 time to fit residues: 63.0388 Evaluate side-chains 147 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.0870 chunk 134 optimal weight: 0.9980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 621 HIS C 642 GLN ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.168450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123377 restraints weight = 15264.121| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.51 r_work: 0.3286 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13052 Z= 0.220 Angle : 0.552 6.450 17790 Z= 0.303 Chirality : 0.040 0.153 1928 Planarity : 0.004 0.070 2110 Dihedral : 16.126 145.221 2130 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 2.69 % Allowed : 29.56 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.21), residues: 1444 helix: -0.26 (0.23), residues: 528 sheet: -2.38 (0.41), residues: 162 loop : -1.74 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 673 HIS 0.008 0.001 HIS C 621 PHE 0.017 0.001 PHE A 401 TYR 0.021 0.001 TYR C 532 ARG 0.004 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 1.328 Fit side-chains REVERT: A 387 MET cc_start: 0.7757 (tmm) cc_final: 0.7481 (ttt) REVERT: C 456 LYS cc_start: 0.7307 (tptp) cc_final: 0.7070 (ttmt) REVERT: B 11 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7429 (mt) REVERT: B 223 PHE cc_start: 0.8662 (m-10) cc_final: 0.8352 (m-10) REVERT: B 238 TYR cc_start: 0.8519 (m-80) cc_final: 0.8297 (m-10) REVERT: B 361 LYS cc_start: 0.7929 (tttm) cc_final: 0.7451 (mtmt) REVERT: B 433 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7141 (tm-30) REVERT: D 406 ASP cc_start: 0.7599 (p0) cc_final: 0.7335 (p0) REVERT: D 430 GLU cc_start: 0.7988 (pm20) cc_final: 0.7597 (mm-30) outliers start: 34 outliers final: 18 residues processed: 190 average time/residue: 0.2780 time to fit residues: 74.9902 Evaluate side-chains 170 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 83 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 78 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.0570 chunk 53 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 642 GLN ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 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 = 0.3972 r_free = 0.3972 target = 0.171629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.126770 restraints weight = 15379.783| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.47 r_work: 0.3320 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13052 Z= 0.147 Angle : 0.515 7.561 17790 Z= 0.284 Chirality : 0.039 0.214 1928 Planarity : 0.003 0.062 2110 Dihedral : 16.071 144.880 2128 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.33 % Allowed : 28.53 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.22), residues: 1444 helix: -0.11 (0.23), residues: 549 sheet: -2.26 (0.42), residues: 157 loop : -1.62 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 673 HIS 0.003 0.001 HIS A 402 PHE 0.016 0.001 PHE A 401 TYR 0.023 0.001 TYR C 567 ARG 0.006 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 1.387 Fit side-chains REVERT: A 387 MET cc_start: 0.7736 (tmm) cc_final: 0.7492 (ttt) REVERT: A 421 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: C 431 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8400 (pp) REVERT: C 456 LYS cc_start: 0.7291 (tptp) cc_final: 0.6991 (ttmm) REVERT: C 530 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6379 (pttt) REVERT: B 223 PHE cc_start: 0.8657 (m-10) cc_final: 0.8349 (m-10) REVERT: B 238 TYR cc_start: 0.8309 (m-80) cc_final: 0.7878 (m-80) REVERT: B 333 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8264 (p) REVERT: B 361 LYS cc_start: 0.7893 (tttm) cc_final: 0.7429 (mtmt) REVERT: B 433 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7094 (tm-30) REVERT: D 406 ASP cc_start: 0.7625 (p0) cc_final: 0.7401 (p0) REVERT: D 430 GLU cc_start: 0.7859 (pm20) cc_final: 0.7619 (mm-30) REVERT: D 597 GLN cc_start: 0.7829 (pm20) cc_final: 0.7561 (pm20) REVERT: D 659 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7288 (t80) outliers start: 42 outliers final: 20 residues processed: 191 average time/residue: 0.2792 time to fit residues: 76.2385 Evaluate side-chains 173 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 659 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 84 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 127 optimal weight: 8.9990 chunk 61 optimal weight: 0.3980 chunk 142 optimal weight: 0.5980 chunk 88 optimal weight: 0.0370 chunk 62 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 116 optimal weight: 0.0030 overall best weight: 0.2868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 621 HIS C 642 GLN ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.172851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128029 restraints weight = 15133.812| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.19 r_work: 0.3342 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13052 Z= 0.134 Angle : 0.496 6.930 17790 Z= 0.273 Chirality : 0.038 0.231 1928 Planarity : 0.003 0.059 2110 Dihedral : 15.998 144.475 2128 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.96 % Allowed : 27.65 % Favored : 68.38 % 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: -1.52 (0.22), residues: 1444 helix: 0.05 (0.23), residues: 547 sheet: -2.14 (0.42), residues: 157 loop : -1.55 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 673 HIS 0.010 0.001 HIS C 621 PHE 0.014 0.001 PHE A 401 TYR 0.019 0.001 TYR C 567 ARG 0.005 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: A 319 ASN cc_start: 0.8832 (t0) cc_final: 0.8516 (t0) REVERT: C 431 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8334 (pp) REVERT: C 456 LYS cc_start: 0.7316 (tptp) cc_final: 0.7001 (ttmm) REVERT: C 530 LYS cc_start: 0.6657 (OUTLIER) cc_final: 0.5927 (tptt) REVERT: C 551 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.8121 (m-40) REVERT: B 21 MET cc_start: 0.8616 (mmt) cc_final: 0.8127 (mmm) REVERT: B 223 PHE cc_start: 0.8649 (m-10) cc_final: 0.8370 (m-10) REVERT: B 238 TYR cc_start: 0.8272 (m-80) cc_final: 0.7839 (m-80) REVERT: B 333 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8265 (p) REVERT: B 361 LYS cc_start: 0.7879 (tttm) cc_final: 0.7422 (mtmt) REVERT: B 413 GLU cc_start: 0.8827 (tp30) cc_final: 0.8531 (mm-30) REVERT: B 433 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7053 (tm-30) REVERT: B 437 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: D 406 ASP cc_start: 0.7584 (p0) cc_final: 0.7367 (p0) REVERT: D 430 GLU cc_start: 0.7752 (pm20) cc_final: 0.7546 (mm-30) REVERT: D 597 GLN cc_start: 0.7867 (pm20) cc_final: 0.7557 (pm20) REVERT: D 659 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7253 (t80) outliers start: 50 outliers final: 25 residues processed: 195 average time/residue: 0.2523 time to fit residues: 70.8583 Evaluate side-chains 179 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 659 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 92 optimal weight: 0.0040 chunk 19 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 621 HIS C 642 GLN ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.170139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125400 restraints weight = 15352.249| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.46 r_work: 0.3273 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13052 Z= 0.195 Angle : 0.521 7.819 17790 Z= 0.284 Chirality : 0.040 0.246 1928 Planarity : 0.003 0.059 2110 Dihedral : 16.021 144.232 2128 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.04 % Allowed : 27.81 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.22), residues: 1444 helix: 0.05 (0.23), residues: 549 sheet: -2.16 (0.42), residues: 157 loop : -1.56 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 673 HIS 0.008 0.001 HIS C 621 PHE 0.018 0.001 PHE A 36 TYR 0.020 0.001 TYR C 567 ARG 0.005 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 1.353 Fit side-chains revert: symmetry clash REVERT: A 218 ARG cc_start: 0.8615 (ptp-110) cc_final: 0.8272 (mtm110) REVERT: A 229 MET cc_start: 0.8879 (ptt) cc_final: 0.8567 (ptt) REVERT: A 319 ASN cc_start: 0.8917 (t0) cc_final: 0.8674 (t0) REVERT: A 407 GLU cc_start: 0.8244 (mp0) cc_final: 0.7801 (mp0) REVERT: C 431 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8024 (pp) REVERT: C 456 LYS cc_start: 0.7412 (tptp) cc_final: 0.7115 (ttmt) REVERT: C 530 LYS cc_start: 0.6588 (OUTLIER) cc_final: 0.5856 (tptt) REVERT: B 189 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7520 (tt) REVERT: B 223 PHE cc_start: 0.8648 (m-10) cc_final: 0.8356 (m-10) REVERT: B 238 TYR cc_start: 0.8465 (m-80) cc_final: 0.8045 (m-80) REVERT: B 333 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8252 (p) REVERT: B 361 LYS cc_start: 0.7882 (tttm) cc_final: 0.7432 (mtmt) REVERT: B 413 GLU cc_start: 0.8838 (tp30) cc_final: 0.8541 (mm-30) REVERT: B 433 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7127 (tm-30) REVERT: D 406 ASP cc_start: 0.7739 (p0) cc_final: 0.7503 (p0) REVERT: D 430 GLU cc_start: 0.7888 (pm20) cc_final: 0.7610 (mm-30) REVERT: D 597 GLN cc_start: 0.7827 (pm20) cc_final: 0.7486 (pm20) REVERT: D 659 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7203 (t80) outliers start: 51 outliers final: 32 residues processed: 196 average time/residue: 0.2694 time to fit residues: 75.8875 Evaluate side-chains 187 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 659 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 138 optimal weight: 0.1980 chunk 102 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 621 HIS C 642 GLN ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.168709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123325 restraints weight = 15571.926| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.24 r_work: 0.3288 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13052 Z= 0.209 Angle : 0.527 8.288 17790 Z= 0.287 Chirality : 0.040 0.254 1928 Planarity : 0.003 0.057 2110 Dihedral : 16.052 144.104 2128 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.28 % Allowed : 27.50 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.22), residues: 1444 helix: 0.08 (0.23), residues: 549 sheet: -2.09 (0.43), residues: 154 loop : -1.53 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 673 HIS 0.008 0.001 HIS C 621 PHE 0.016 0.001 PHE B 350 TYR 0.020 0.001 TYR C 567 ARG 0.006 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 154 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 218 ARG cc_start: 0.8703 (ptp-110) cc_final: 0.8250 (mtm110) REVERT: A 229 MET cc_start: 0.8847 (ptt) cc_final: 0.8553 (ptt) REVERT: A 252 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7085 (tm-30) REVERT: A 319 ASN cc_start: 0.8882 (t0) cc_final: 0.8597 (t0) REVERT: A 407 GLU cc_start: 0.8289 (mp0) cc_final: 0.7689 (mp0) REVERT: C 431 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8060 (pp) REVERT: C 456 LYS cc_start: 0.7386 (tptp) cc_final: 0.7111 (ttmt) REVERT: C 530 LYS cc_start: 0.6624 (OUTLIER) cc_final: 0.5847 (tptt) REVERT: B 223 PHE cc_start: 0.8657 (m-10) cc_final: 0.8355 (m-10) REVERT: B 238 TYR cc_start: 0.8482 (m-80) cc_final: 0.8159 (m-10) REVERT: B 333 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8232 (p) REVERT: B 361 LYS cc_start: 0.7834 (tttm) cc_final: 0.7394 (mtmt) REVERT: B 413 GLU cc_start: 0.8849 (tp30) cc_final: 0.8569 (mm-30) REVERT: B 433 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7180 (tm-30) REVERT: D 406 ASP cc_start: 0.7690 (p0) cc_final: 0.7453 (p0) REVERT: D 430 GLU cc_start: 0.7938 (pm20) cc_final: 0.7678 (mm-30) REVERT: D 597 GLN cc_start: 0.7860 (pm20) cc_final: 0.7496 (pm20) outliers start: 54 outliers final: 37 residues processed: 198 average time/residue: 0.2613 time to fit residues: 74.2039 Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 623 ILE Chi-restraints excluded: chain D residue 659 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 11 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 121 optimal weight: 0.0470 chunk 87 optimal weight: 0.0000 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 621 HIS C 642 GLN ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.171908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128067 restraints weight = 15240.665| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.49 r_work: 0.3319 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13052 Z= 0.149 Angle : 0.503 8.155 17790 Z= 0.275 Chirality : 0.039 0.272 1928 Planarity : 0.003 0.056 2110 Dihedral : 16.008 143.726 2128 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.96 % Allowed : 28.13 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.22), residues: 1444 helix: 0.24 (0.23), residues: 543 sheet: -2.10 (0.42), residues: 159 loop : -1.49 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 673 HIS 0.009 0.001 HIS C 621 PHE 0.023 0.001 PHE B 350 TYR 0.016 0.001 TYR C 567 ARG 0.006 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 163 SER cc_start: 0.8809 (m) cc_final: 0.8545 (t) REVERT: A 218 ARG cc_start: 0.8591 (ptp-110) cc_final: 0.8178 (mtm110) REVERT: A 229 MET cc_start: 0.8861 (ptt) cc_final: 0.8619 (ptt) REVERT: A 319 ASN cc_start: 0.8896 (t0) cc_final: 0.8640 (t0) REVERT: A 407 GLU cc_start: 0.8247 (mp0) cc_final: 0.7657 (mp0) REVERT: C 431 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8109 (pp) REVERT: C 456 LYS cc_start: 0.7440 (tptp) cc_final: 0.7145 (ttmt) REVERT: C 530 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.5825 (tptt) REVERT: C 633 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.5722 (mt-10) REVERT: B 21 MET cc_start: 0.8630 (mmt) cc_final: 0.8136 (mmm) REVERT: B 223 PHE cc_start: 0.8663 (m-10) cc_final: 0.8357 (m-10) REVERT: B 238 TYR cc_start: 0.8433 (m-80) cc_final: 0.8109 (m-10) REVERT: B 333 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8277 (p) REVERT: B 361 LYS cc_start: 0.7810 (tttm) cc_final: 0.7494 (mtmt) REVERT: B 413 GLU cc_start: 0.8860 (tp30) cc_final: 0.8593 (mm-30) REVERT: B 433 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7027 (tm-30) REVERT: D 406 ASP cc_start: 0.7727 (p0) cc_final: 0.7500 (p0) REVERT: D 430 GLU cc_start: 0.7841 (pm20) cc_final: 0.7607 (mm-30) REVERT: D 547 MET cc_start: 0.7588 (ttm) cc_final: 0.7086 (ttt) REVERT: D 597 GLN cc_start: 0.7900 (pm20) cc_final: 0.7536 (pm20) REVERT: D 659 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7343 (t80) outliers start: 50 outliers final: 34 residues processed: 204 average time/residue: 0.2768 time to fit residues: 80.6650 Evaluate side-chains 193 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 659 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 7.9990 chunk 91 optimal weight: 0.0030 chunk 145 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 621 HIS C 642 GLN ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.168496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.123256 restraints weight = 15446.863| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.22 r_work: 0.3260 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13052 Z= 0.223 Angle : 0.535 8.680 17790 Z= 0.292 Chirality : 0.040 0.268 1928 Planarity : 0.003 0.056 2110 Dihedral : 16.055 143.601 2128 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 3.65 % Allowed : 28.45 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.22), residues: 1444 helix: 0.18 (0.23), residues: 545 sheet: -2.13 (0.42), residues: 159 loop : -1.51 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 673 HIS 0.008 0.001 HIS C 621 PHE 0.042 0.001 PHE B 350 TYR 0.020 0.001 TYR C 567 ARG 0.005 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: A 218 ARG cc_start: 0.8654 (ptp-110) cc_final: 0.8211 (mtm110) REVERT: A 229 MET cc_start: 0.8841 (ptt) cc_final: 0.8537 (ptt) REVERT: A 252 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: A 319 ASN cc_start: 0.8921 (t0) cc_final: 0.8656 (t0) REVERT: A 407 GLU cc_start: 0.8247 (mp0) cc_final: 0.7645 (mp0) REVERT: A 421 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: C 456 LYS cc_start: 0.7433 (tptp) cc_final: 0.7144 (ttmt) REVERT: C 530 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.6222 (pttt) REVERT: B 223 PHE cc_start: 0.8666 (m-10) cc_final: 0.8372 (m-10) REVERT: B 238 TYR cc_start: 0.8584 (m-80) cc_final: 0.8172 (m-10) REVERT: B 333 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8251 (p) REVERT: B 361 LYS cc_start: 0.7857 (tttm) cc_final: 0.7530 (mtmt) REVERT: B 413 GLU cc_start: 0.8808 (tp30) cc_final: 0.8560 (mm-30) REVERT: B 433 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7156 (tm-30) REVERT: D 430 GLU cc_start: 0.7949 (pm20) cc_final: 0.7698 (mm-30) REVERT: D 529 MET cc_start: 0.6496 (ptp) cc_final: 0.5655 (ttt) REVERT: D 547 MET cc_start: 0.7643 (ttm) cc_final: 0.7128 (ttt) REVERT: D 597 GLN cc_start: 0.7898 (pm20) cc_final: 0.7522 (pm20) REVERT: D 661 MET cc_start: 0.8786 (tmm) cc_final: 0.8502 (tmm) outliers start: 46 outliers final: 36 residues processed: 197 average time/residue: 0.2580 time to fit residues: 73.6048 Evaluate side-chains 190 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 623 ILE Chi-restraints excluded: chain D residue 659 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.0370 chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 621 HIS C 642 GLN ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.170308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.124488 restraints weight = 15457.301| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.25 r_work: 0.3300 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13052 Z= 0.183 Angle : 0.527 9.131 17790 Z= 0.288 Chirality : 0.039 0.271 1928 Planarity : 0.003 0.054 2110 Dihedral : 16.037 143.504 2128 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.62 % Favored : 92.31 % Rotamer: Outliers : 3.80 % Allowed : 27.89 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.22), residues: 1444 helix: 0.30 (0.23), residues: 543 sheet: -2.08 (0.42), residues: 159 loop : -1.51 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 673 HIS 0.025 0.001 HIS D 432 PHE 0.037 0.001 PHE B 350 TYR 0.018 0.001 TYR C 567 ARG 0.006 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 218 ARG cc_start: 0.8639 (ptp-110) cc_final: 0.8214 (mtm110) REVERT: A 229 MET cc_start: 0.8825 (ptt) cc_final: 0.8534 (ptt) REVERT: A 319 ASN cc_start: 0.8909 (t0) cc_final: 0.8680 (t0) REVERT: A 407 GLU cc_start: 0.8233 (mp0) cc_final: 0.7653 (mp0) REVERT: C 456 LYS cc_start: 0.7405 (tptp) cc_final: 0.7118 (ttmt) REVERT: C 530 LYS cc_start: 0.6504 (OUTLIER) cc_final: 0.6196 (pttt) REVERT: C 633 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.6059 (mt-10) REVERT: B 12 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7672 (mt) REVERT: B 223 PHE cc_start: 0.8646 (m-10) cc_final: 0.8351 (m-10) REVERT: B 238 TYR cc_start: 0.8519 (m-80) cc_final: 0.8173 (m-10) REVERT: B 333 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8254 (p) REVERT: B 361 LYS cc_start: 0.7889 (tttm) cc_final: 0.7457 (mtmt) REVERT: B 401 PHE cc_start: 0.8455 (p90) cc_final: 0.7900 (p90) REVERT: B 413 GLU cc_start: 0.8815 (tp30) cc_final: 0.8568 (mm-30) REVERT: B 433 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7083 (tm-30) REVERT: D 427 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8397 (mtm110) REVERT: D 430 GLU cc_start: 0.7969 (pm20) cc_final: 0.7662 (mm-30) REVERT: D 529 MET cc_start: 0.6498 (ptp) cc_final: 0.5660 (ttt) REVERT: D 547 MET cc_start: 0.7612 (ttm) cc_final: 0.7131 (ttt) REVERT: D 597 GLN cc_start: 0.7925 (pm20) cc_final: 0.7556 (pm20) REVERT: D 661 MET cc_start: 0.8790 (tmm) cc_final: 0.8473 (tmm) outliers start: 48 outliers final: 37 residues processed: 193 average time/residue: 0.2712 time to fit residues: 75.3383 Evaluate side-chains 189 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 659 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 85 optimal weight: 0.0980 chunk 118 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 621 HIS C 642 GLN ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.170280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124813 restraints weight = 15409.208| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.21 r_work: 0.3331 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13052 Z= 0.161 Angle : 0.536 8.924 17790 Z= 0.290 Chirality : 0.040 0.281 1928 Planarity : 0.003 0.053 2110 Dihedral : 16.021 143.298 2128 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.69 % Favored : 92.24 % Rotamer: Outliers : 3.65 % Allowed : 28.05 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.22), residues: 1444 helix: 0.35 (0.23), residues: 541 sheet: -2.03 (0.42), residues: 159 loop : -1.50 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 673 HIS 0.024 0.001 HIS D 432 PHE 0.034 0.001 PHE B 350 TYR 0.017 0.001 TYR C 567 ARG 0.006 0.000 ARG A 351 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 218 ARG cc_start: 0.8613 (ptp-110) cc_final: 0.8200 (mtm110) REVERT: A 229 MET cc_start: 0.8840 (ptt) cc_final: 0.8555 (ptt) REVERT: A 319 ASN cc_start: 0.8920 (t0) cc_final: 0.8668 (t0) REVERT: A 351 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7637 (tpp80) REVERT: A 407 GLU cc_start: 0.8230 (mp0) cc_final: 0.7651 (mp0) REVERT: A 421 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: C 456 LYS cc_start: 0.7376 (tptp) cc_final: 0.7085 (ttmt) REVERT: C 530 LYS cc_start: 0.6438 (OUTLIER) cc_final: 0.5676 (tptt) REVERT: C 633 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.5793 (mt-10) REVERT: B 12 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7647 (mt) REVERT: B 21 MET cc_start: 0.8612 (mmt) cc_final: 0.8099 (mmm) REVERT: B 223 PHE cc_start: 0.8651 (m-10) cc_final: 0.8373 (m-10) REVERT: B 238 TYR cc_start: 0.8474 (m-80) cc_final: 0.8151 (m-10) REVERT: B 333 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8275 (p) REVERT: B 361 LYS cc_start: 0.7745 (tttm) cc_final: 0.7416 (mtmt) REVERT: B 413 GLU cc_start: 0.8823 (tp30) cc_final: 0.8578 (mm-30) REVERT: B 433 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7018 (tm-30) REVERT: D 427 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8223 (mtm110) REVERT: D 547 MET cc_start: 0.7524 (ttm) cc_final: 0.7073 (ttt) REVERT: D 597 GLN cc_start: 0.7922 (pm20) cc_final: 0.7554 (pm20) REVERT: D 661 MET cc_start: 0.8787 (tmm) cc_final: 0.8469 (tmm) outliers start: 46 outliers final: 38 residues processed: 185 average time/residue: 0.2631 time to fit residues: 70.1878 Evaluate side-chains 186 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 659 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 141 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 621 HIS C 642 GLN ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.171463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.125591 restraints weight = 15339.212| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.28 r_work: 0.3322 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13052 Z= 0.179 Angle : 0.532 8.689 17790 Z= 0.289 Chirality : 0.040 0.276 1928 Planarity : 0.003 0.053 2110 Dihedral : 16.011 143.065 2128 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.62 % Favored : 92.31 % Rotamer: Outliers : 3.88 % Allowed : 27.73 % Favored : 68.38 % 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: -1.29 (0.22), residues: 1444 helix: 0.36 (0.23), residues: 541 sheet: -2.03 (0.42), residues: 159 loop : -1.52 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 673 HIS 0.022 0.001 HIS D 432 PHE 0.031 0.001 PHE B 350 TYR 0.018 0.001 TYR C 567 ARG 0.006 0.000 ARG A 351 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8087.43 seconds wall clock time: 145 minutes 45.89 seconds (8745.89 seconds total)