Starting phenix.real_space_refine on Thu Sep 18 00:42:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yo4_39435/09_2025/8yo4_39435.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yo4_39435/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yo4_39435/09_2025/8yo4_39435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yo4_39435/09_2025/8yo4_39435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yo4_39435/09_2025/8yo4_39435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yo4_39435/09_2025/8yo4_39435.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.104 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.02, per 1000 atoms: 0.24 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: 1.07 Conformation dependent library (CDL) restraints added in 605.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.55 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: 2.43 Time building geometry restraints manager: 1.42 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: 1.560 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.850 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.000 ------------------------------------------------------------------------------- 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= 0.129 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 : 9.58 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG A 351 TYR 0.018 0.001 TYR C 567 PHE 0.017 0.001 PHE B 350 TRP 0.011 0.001 TRP C 604 HIS 0.005 0.001 HIS C 432 Details of bonding type rmsd covalent geometry : bond 0.00278 (13052) covalent geometry : angle 0.56988 (17790) hydrogen bonds : bond 0.16769 ( 441) hydrogen bonds : angle 6.12385 ( 1170) *********************** 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 : 0.402 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: 0.1204 time to fit residues: 26.4337 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 : 0.388 ------------------------------------------------------------------------------- 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 98 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 55 optimal weight: 10.0000 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS C 621 HIS C 642 GLN ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.161051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114819 restraints weight = 15590.083| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.52 r_work: 0.3130 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 13052 Z= 0.348 Angle : 0.715 9.885 17790 Z= 0.384 Chirality : 0.047 0.163 1928 Planarity : 0.005 0.077 2110 Dihedral : 16.441 145.528 2130 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 5.07 % Allowed : 27.73 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.21), residues: 1444 helix: -0.59 (0.23), residues: 514 sheet: -2.72 (0.39), residues: 166 loop : -1.80 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 427 TYR 0.027 0.002 TYR C 567 PHE 0.024 0.002 PHE C 581 TRP 0.013 0.002 TRP C 673 HIS 0.008 0.002 HIS C 432 Details of bonding type rmsd covalent geometry : bond 0.00827 (13052) covalent geometry : angle 0.71491 (17790) hydrogen bonds : bond 0.04716 ( 441) hydrogen bonds : angle 5.03957 ( 1170) *********************** 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 226 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 162 time to evaluate : 0.333 Fit side-chains REVERT: A 252 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: A 347 GLU cc_start: 0.7873 (tt0) cc_final: 0.7465 (tm-30) REVERT: C 456 LYS cc_start: 0.7472 (tptp) cc_final: 0.7168 (ttmm) REVERT: C 474 PHE cc_start: 0.8239 (m-10) cc_final: 0.7835 (m-10) REVERT: B 11 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7568 (mt) REVERT: B 238 TYR cc_start: 0.8679 (m-80) cc_final: 0.8258 (m-80) REVERT: B 361 LYS cc_start: 0.7947 (tttm) cc_final: 0.7396 (mtmt) REVERT: B 433 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7151 (tm-30) REVERT: D 406 ASP cc_start: 0.7741 (p0) cc_final: 0.7476 (p0) REVERT: D 430 GLU cc_start: 0.8088 (pm20) cc_final: 0.7472 (mm-30) REVERT: D 472 LYS cc_start: 0.8945 (pptt) cc_final: 0.8707 (pptt) outliers start: 64 outliers final: 40 residues processed: 216 average time/residue: 0.1078 time to fit residues: 33.3213 Evaluate side-chains 194 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 134 GLU Chi-restraints excluded: chain A residue 159 LEU 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 257 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 352 LEU 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 A residue 438 LEU Chi-restraints excluded: chain C residue 403 CYS 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 484 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 658 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 91 optimal weight: 0.0070 chunk 54 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 48 optimal weight: 0.0770 chunk 146 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3939 r_free = 0.3939 target = 0.168461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123739 restraints weight = 15494.090| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.53 r_work: 0.3287 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13052 Z= 0.119 Angle : 0.532 8.361 17790 Z= 0.293 Chirality : 0.039 0.202 1928 Planarity : 0.004 0.065 2110 Dihedral : 16.263 145.208 2130 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.01 % Allowed : 30.03 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.21), residues: 1444 helix: -0.20 (0.23), residues: 528 sheet: -2.41 (0.41), residues: 156 loop : -1.75 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 351 TYR 0.021 0.001 TYR C 567 PHE 0.018 0.001 PHE A 401 TRP 0.010 0.001 TRP D 673 HIS 0.003 0.001 HIS C 432 Details of bonding type rmsd covalent geometry : bond 0.00261 (13052) covalent geometry : angle 0.53172 (17790) hydrogen bonds : bond 0.03462 ( 441) hydrogen bonds : angle 4.62526 ( 1170) *********************** 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 199 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.428 Fit side-chains REVERT: C 456 LYS cc_start: 0.7375 (tptp) cc_final: 0.7084 (ttmt) REVERT: C 633 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.5989 (mt-10) REVERT: B 11 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7501 (mt) REVERT: B 223 PHE cc_start: 0.8642 (m-10) cc_final: 0.8326 (m-10) REVERT: B 238 TYR cc_start: 0.8250 (m-80) cc_final: 0.7866 (m-80) REVERT: B 361 LYS cc_start: 0.7911 (tttm) cc_final: 0.7406 (mtmt) REVERT: B 433 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7153 (tm-30) REVERT: B 437 ASP cc_start: 0.7993 (t0) cc_final: 0.7793 (m-30) REVERT: D 406 ASP cc_start: 0.7669 (p0) cc_final: 0.7432 (p0) REVERT: D 427 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8092 (mtm110) REVERT: D 430 GLU cc_start: 0.7955 (pm20) cc_final: 0.7450 (mm-30) REVERT: D 472 LYS cc_start: 0.8903 (pptt) cc_final: 0.8606 (pptt) REVERT: D 659 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7196 (t80) outliers start: 38 outliers final: 20 residues processed: 192 average time/residue: 0.1120 time to fit residues: 30.4509 Evaluate side-chains 172 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN 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 430 VAL 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 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 633 GLU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 394 LYS 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 431 LEU Chi-restraints excluded: chain D residue 493 ILE 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 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.168511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.124067 restraints weight = 15473.189| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.51 r_work: 0.3264 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13052 Z= 0.124 Angle : 0.526 7.126 17790 Z= 0.288 Chirality : 0.040 0.221 1928 Planarity : 0.003 0.061 2110 Dihedral : 16.178 144.792 2128 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.04 % Allowed : 29.00 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.21), residues: 1444 helix: -0.04 (0.23), residues: 528 sheet: -2.31 (0.41), residues: 156 loop : -1.69 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 351 TYR 0.021 0.001 TYR C 567 PHE 0.019 0.001 PHE A 401 TRP 0.008 0.001 TRP D 673 HIS 0.012 0.001 HIS D 432 Details of bonding type rmsd covalent geometry : bond 0.00282 (13052) covalent geometry : angle 0.52642 (17790) hydrogen bonds : bond 0.03256 ( 441) hydrogen bonds : angle 4.48566 ( 1170) *********************** 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: 51 poor density : 154 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: C 456 LYS cc_start: 0.7391 (tptp) cc_final: 0.7135 (ttmt) REVERT: C 474 PHE cc_start: 0.8129 (m-10) cc_final: 0.7788 (m-10) REVERT: C 530 LYS cc_start: 0.6698 (OUTLIER) cc_final: 0.6321 (pttt) REVERT: C 551 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8199 (m-40) REVERT: B 11 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7504 (mt) REVERT: B 223 PHE cc_start: 0.8650 (m-10) cc_final: 0.8337 (m-10) REVERT: B 238 TYR cc_start: 0.8250 (m-80) cc_final: 0.7872 (m-80) REVERT: B 361 LYS cc_start: 0.7879 (tttm) cc_final: 0.7396 (mtmt) REVERT: B 413 GLU cc_start: 0.8849 (tp30) cc_final: 0.8560 (mm-30) REVERT: B 433 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7133 (tm-30) REVERT: D 406 ASP cc_start: 0.7635 (p0) cc_final: 0.7418 (p0) REVERT: D 472 LYS cc_start: 0.8919 (pptt) cc_final: 0.8514 (pptt) REVERT: D 597 GLN cc_start: 0.7837 (pm20) cc_final: 0.7524 (pm20) REVERT: D 659 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.7238 (t80) outliers start: 51 outliers final: 33 residues processed: 196 average time/residue: 0.1038 time to fit residues: 29.2327 Evaluate side-chains 183 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 370 VAL Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 404 THR 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 C residue 594 ILE Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 634 LYS 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 B residue 400 ILE Chi-restraints excluded: chain D residue 409 THR 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 493 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 34 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 86 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3940 r_free = 0.3940 target = 0.168686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124206 restraints weight = 15501.360| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.48 r_work: 0.3278 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13052 Z= 0.128 Angle : 0.522 7.511 17790 Z= 0.285 Chirality : 0.039 0.225 1928 Planarity : 0.003 0.059 2110 Dihedral : 16.153 144.489 2128 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 3.80 % Allowed : 28.53 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.21), residues: 1444 helix: 0.04 (0.23), residues: 528 sheet: -2.22 (0.42), residues: 156 loop : -1.65 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 351 TYR 0.020 0.001 TYR C 567 PHE 0.018 0.001 PHE A 401 TRP 0.008 0.001 TRP D 673 HIS 0.007 0.001 HIS C 621 Details of bonding type rmsd covalent geometry : bond 0.00295 (13052) covalent geometry : angle 0.52174 (17790) hydrogen bonds : bond 0.03132 ( 441) hydrogen bonds : angle 4.38155 ( 1170) *********************** 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 201 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 398 MET cc_start: 0.7687 (ttm) cc_final: 0.7119 (ttm) REVERT: A 426 LYS cc_start: 0.6889 (mtmm) cc_final: 0.6568 (mtmm) REVERT: C 456 LYS cc_start: 0.7401 (tptp) cc_final: 0.7111 (ttmt) REVERT: C 474 PHE cc_start: 0.8184 (m-10) cc_final: 0.7924 (m-10) REVERT: C 530 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6331 (pttt) REVERT: B 11 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7483 (mt) REVERT: B 223 PHE cc_start: 0.8666 (m-10) cc_final: 0.8354 (m-10) REVERT: B 238 TYR cc_start: 0.8342 (m-80) cc_final: 0.7929 (m-80) REVERT: B 361 LYS cc_start: 0.7861 (tttm) cc_final: 0.7399 (mtmt) REVERT: B 413 GLU cc_start: 0.8813 (tp30) cc_final: 0.8551 (mm-30) REVERT: B 433 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7040 (tm-30) REVERT: D 406 ASP cc_start: 0.7712 (p0) cc_final: 0.7481 (p0) REVERT: D 597 GLN cc_start: 0.7904 (pm20) cc_final: 0.7565 (pm20) outliers start: 48 outliers final: 33 residues processed: 194 average time/residue: 0.1204 time to fit residues: 33.1973 Evaluate side-chains 184 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 404 THR 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 432 HIS 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 C residue 629 LEU Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 400 ILE 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 431 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 607 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 0.0470 chunk 124 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 135 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3954 r_free = 0.3954 target = 0.170081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125384 restraints weight = 15454.426| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.53 r_work: 0.3312 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1326 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= 0.116 Angle : 0.519 10.332 17790 Z= 0.284 Chirality : 0.039 0.246 1928 Planarity : 0.003 0.056 2110 Dihedral : 16.114 144.202 2128 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.69 % Favored : 92.24 % Rotamer: Outliers : 4.12 % Allowed : 28.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.22), residues: 1444 helix: 0.14 (0.23), residues: 543 sheet: -2.20 (0.42), residues: 159 loop : -1.62 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 351 TYR 0.018 0.001 TYR C 567 PHE 0.022 0.001 PHE B 350 TRP 0.008 0.001 TRP D 673 HIS 0.004 0.001 HIS D 432 Details of bonding type rmsd covalent geometry : bond 0.00262 (13052) covalent geometry : angle 0.51920 (17790) hydrogen bonds : bond 0.03011 ( 441) hydrogen bonds : angle 4.31672 ( 1170) *********************** 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 206 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 229 MET cc_start: 0.8873 (ptt) cc_final: 0.8542 (ptt) REVERT: A 256 PHE cc_start: 0.8000 (m-80) cc_final: 0.7649 (m-80) REVERT: A 421 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: C 456 LYS cc_start: 0.7441 (tptp) cc_final: 0.7148 (ttmt) REVERT: C 474 PHE cc_start: 0.8122 (m-10) cc_final: 0.7865 (m-10) REVERT: C 530 LYS cc_start: 0.6705 (OUTLIER) cc_final: 0.5877 (tptt) REVERT: B 11 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7505 (mt) REVERT: B 77 GLU cc_start: 0.7717 (pp20) cc_final: 0.7432 (pp20) REVERT: B 223 PHE cc_start: 0.8657 (m-10) cc_final: 0.8328 (m-10) REVERT: B 238 TYR cc_start: 0.8294 (m-80) cc_final: 0.7852 (m-80) REVERT: B 299 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7935 (pt0) REVERT: B 361 LYS cc_start: 0.7819 (tttm) cc_final: 0.7246 (mtmt) REVERT: B 413 GLU cc_start: 0.8838 (tp30) cc_final: 0.8571 (mm-30) REVERT: B 433 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7186 (tm-30) REVERT: D 406 ASP cc_start: 0.7737 (p0) cc_final: 0.7498 (p0) REVERT: D 427 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8160 (mtm110) REVERT: D 430 GLU cc_start: 0.8046 (pm20) cc_final: 0.7721 (mm-30) REVERT: D 472 LYS cc_start: 0.8834 (pptt) cc_final: 0.8112 (pptt) REVERT: D 547 MET cc_start: 0.7331 (mtp) cc_final: 0.7113 (ttm) REVERT: D 597 GLN cc_start: 0.7911 (pm20) cc_final: 0.7567 (pm20) outliers start: 52 outliers final: 35 residues processed: 197 average time/residue: 0.1123 time to fit residues: 31.8703 Evaluate side-chains 182 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 322 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 421 GLU 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 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 629 LEU Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 299 GLU 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 B residue 400 ILE 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 431 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 618 LEU 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 139 optimal weight: 0.4980 chunk 41 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS C 621 HIS C 642 GLN D 432 HIS ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.168440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123875 restraints weight = 15487.970| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.52 r_work: 0.3288 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13052 Z= 0.146 Angle : 0.540 9.526 17790 Z= 0.293 Chirality : 0.040 0.262 1928 Planarity : 0.003 0.057 2110 Dihedral : 16.132 144.026 2128 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.24 % Favored : 91.69 % Rotamer: Outliers : 3.80 % Allowed : 28.37 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.21), residues: 1444 helix: 0.12 (0.24), residues: 524 sheet: -2.18 (0.42), residues: 156 loop : -1.66 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 218 TYR 0.030 0.001 TYR C 567 PHE 0.028 0.001 PHE B 350 TRP 0.008 0.001 TRP D 673 HIS 0.017 0.001 HIS D 432 Details of bonding type rmsd covalent geometry : bond 0.00340 (13052) covalent geometry : angle 0.54028 (17790) hydrogen bonds : bond 0.03151 ( 441) hydrogen bonds : angle 4.34439 ( 1170) *********************** 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 197 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 ARG cc_start: 0.8726 (ptp-110) cc_final: 0.8316 (mtm110) REVERT: A 229 MET cc_start: 0.8884 (ptt) cc_final: 0.8625 (ptt) REVERT: A 319 ASN cc_start: 0.8890 (t0) cc_final: 0.8601 (t0) REVERT: A 421 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: C 456 LYS cc_start: 0.7471 (tptp) cc_final: 0.7200 (ttmt) REVERT: C 474 PHE cc_start: 0.8130 (m-10) cc_final: 0.7887 (m-10) REVERT: C 530 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.5837 (tptt) REVERT: C 633 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.6144 (mt-10) REVERT: B 11 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7512 (mt) REVERT: B 77 GLU cc_start: 0.7702 (pp20) cc_final: 0.7396 (pp20) REVERT: B 223 PHE cc_start: 0.8659 (m-10) cc_final: 0.8345 (m-10) REVERT: B 238 TYR cc_start: 0.8401 (m-80) cc_final: 0.7964 (m-80) REVERT: B 361 LYS cc_start: 0.7733 (tttm) cc_final: 0.7243 (mtmt) REVERT: B 409 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7088 (mttt) REVERT: B 413 GLU cc_start: 0.8859 (tp30) cc_final: 0.8584 (mm-30) REVERT: B 433 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7143 (tm-30) REVERT: D 406 ASP cc_start: 0.7734 (p0) cc_final: 0.7484 (p0) REVERT: D 427 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8260 (mtm110) REVERT: D 432 HIS cc_start: 0.8340 (OUTLIER) cc_final: 0.8080 (m170) REVERT: D 547 MET cc_start: 0.7345 (mtp) cc_final: 0.7140 (ttm) REVERT: D 597 GLN cc_start: 0.7899 (pm20) cc_final: 0.7540 (pm20) outliers start: 48 outliers final: 36 residues processed: 190 average time/residue: 0.1211 time to fit residues: 32.6758 Evaluate side-chains 190 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 370 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 421 GLU 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 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 629 LEU Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 211 ILE 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 B residue 400 ILE Chi-restraints excluded: chain B residue 409 LYS 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 431 LEU Chi-restraints excluded: chain D residue 432 HIS Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 607 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 101 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 139 optimal weight: 0.0060 chunk 118 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- 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 ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.166201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121216 restraints weight = 15364.458| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.46 r_work: 0.3249 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13052 Z= 0.192 Angle : 0.568 8.985 17790 Z= 0.308 Chirality : 0.041 0.266 1928 Planarity : 0.004 0.057 2110 Dihedral : 16.189 144.030 2128 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.52 % Favored : 91.41 % Rotamer: Outliers : 4.12 % Allowed : 28.45 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.21), residues: 1444 helix: 0.04 (0.23), residues: 524 sheet: -2.05 (0.44), residues: 146 loop : -1.69 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 351 TYR 0.033 0.002 TYR C 567 PHE 0.043 0.002 PHE B 350 TRP 0.009 0.001 TRP C 673 HIS 0.020 0.001 HIS D 432 Details of bonding type rmsd covalent geometry : bond 0.00454 (13052) covalent geometry : angle 0.56804 (17790) hydrogen bonds : bond 0.03396 ( 441) hydrogen bonds : angle 4.41948 ( 1170) *********************** 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 207 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 155 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 82 ASP cc_start: 0.7900 (m-30) cc_final: 0.7630 (m-30) REVERT: A 229 MET cc_start: 0.8899 (ptt) cc_final: 0.8600 (ptt) REVERT: A 252 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: C 456 LYS cc_start: 0.7519 (tptp) cc_final: 0.7251 (ttmt) REVERT: C 474 PHE cc_start: 0.8134 (m-10) cc_final: 0.7908 (m-10) REVERT: C 530 LYS cc_start: 0.6597 (OUTLIER) cc_final: 0.6293 (pttt) REVERT: B 11 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7546 (mt) REVERT: B 77 GLU cc_start: 0.7716 (pp20) cc_final: 0.7412 (pp20) REVERT: B 238 TYR cc_start: 0.8507 (m-80) cc_final: 0.8181 (m-80) REVERT: B 361 LYS cc_start: 0.7825 (tttm) cc_final: 0.7447 (mtmt) REVERT: B 409 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7112 (mttt) REVERT: B 413 GLU cc_start: 0.8854 (tp30) cc_final: 0.8579 (mm-30) REVERT: B 433 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7038 (tm-30) REVERT: D 406 ASP cc_start: 0.7797 (p0) cc_final: 0.7545 (p0) REVERT: D 427 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8193 (mtm110) REVERT: D 430 GLU cc_start: 0.7926 (pm20) cc_final: 0.7717 (mm-30) REVERT: D 472 LYS cc_start: 0.8870 (pptt) cc_final: 0.8206 (pptt) REVERT: D 597 GLN cc_start: 0.7892 (pm20) cc_final: 0.7515 (pm20) REVERT: D 661 MET cc_start: 0.8816 (tmm) cc_final: 0.8531 (tmm) outliers start: 52 outliers final: 37 residues processed: 199 average time/residue: 0.1141 time to fit residues: 32.2750 Evaluate side-chains 192 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 370 VAL Chi-restraints excluded: chain A residue 404 THR 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 432 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 211 ILE 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 B residue 400 ILE Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 607 THR 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 62 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.168028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123908 restraints weight = 15400.251| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.37 r_work: 0.3270 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13052 Z= 0.135 Angle : 0.538 9.101 17790 Z= 0.292 Chirality : 0.040 0.278 1928 Planarity : 0.003 0.055 2110 Dihedral : 16.164 143.815 2128 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.83 % Favored : 92.11 % Rotamer: Outliers : 3.80 % Allowed : 28.84 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.21), residues: 1444 helix: 0.11 (0.24), residues: 524 sheet: -1.98 (0.44), residues: 146 loop : -1.65 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 351 TYR 0.028 0.001 TYR C 567 PHE 0.035 0.001 PHE B 350 TRP 0.009 0.001 TRP D 673 HIS 0.012 0.001 HIS D 432 Details of bonding type rmsd covalent geometry : bond 0.00313 (13052) covalent geometry : angle 0.53839 (17790) hydrogen bonds : bond 0.03136 ( 441) hydrogen bonds : angle 4.34397 ( 1170) *********************** 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 204 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.7858 (m-30) cc_final: 0.7608 (m-30) REVERT: A 218 ARG cc_start: 0.8598 (ptp-110) cc_final: 0.8229 (mtm110) REVERT: A 229 MET cc_start: 0.8900 (ptt) cc_final: 0.8623 (ptt) REVERT: A 319 ASN cc_start: 0.8929 (t0) cc_final: 0.8653 (t0) REVERT: A 421 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: C 456 LYS cc_start: 0.7486 (tptp) cc_final: 0.7206 (ttmt) REVERT: C 474 PHE cc_start: 0.8072 (m-10) cc_final: 0.7860 (m-10) REVERT: C 530 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6391 (pttt) REVERT: C 547 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7618 (mtt) REVERT: B 11 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7494 (mt) REVERT: B 77 GLU cc_start: 0.7696 (pp20) cc_final: 0.7368 (pp20) REVERT: B 223 PHE cc_start: 0.8639 (m-10) cc_final: 0.8332 (m-10) REVERT: B 238 TYR cc_start: 0.8412 (m-80) cc_final: 0.8093 (m-80) REVERT: B 361 LYS cc_start: 0.7783 (tttm) cc_final: 0.7415 (mtmt) REVERT: B 409 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7055 (mttt) REVERT: B 413 GLU cc_start: 0.8863 (tp30) cc_final: 0.8597 (mm-30) REVERT: B 433 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7038 (tm-30) REVERT: D 406 ASP cc_start: 0.7702 (p0) cc_final: 0.7469 (p0) REVERT: D 427 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7967 (mtm110) REVERT: D 430 GLU cc_start: 0.7891 (pm20) cc_final: 0.7651 (mm-30) REVERT: D 547 MET cc_start: 0.7365 (mtp) cc_final: 0.7149 (ttm) REVERT: D 597 GLN cc_start: 0.7895 (pm20) cc_final: 0.7523 (pm20) REVERT: D 661 MET cc_start: 0.8805 (tmm) cc_final: 0.8497 (tmm) outliers start: 48 outliers final: 37 residues processed: 195 average time/residue: 0.1144 time to fit residues: 32.3855 Evaluate side-chains 193 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 370 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 421 GLU 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 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 500 VAL Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain B residue 11 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 377 GLU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 409 LYS 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 431 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 607 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 43 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 120 optimal weight: 0.0020 chunk 145 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.168404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123792 restraints weight = 15541.379| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.51 r_work: 0.3271 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13052 Z= 0.144 Angle : 0.543 9.108 17790 Z= 0.295 Chirality : 0.040 0.278 1928 Planarity : 0.004 0.055 2110 Dihedral : 16.163 143.585 2128 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.83 % Favored : 92.11 % Rotamer: Outliers : 3.88 % Allowed : 29.08 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.21), residues: 1444 helix: 0.13 (0.24), residues: 524 sheet: -1.98 (0.44), residues: 146 loop : -1.67 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 351 TYR 0.028 0.001 TYR C 567 PHE 0.032 0.001 PHE B 350 TRP 0.009 0.001 TRP D 673 HIS 0.011 0.001 HIS D 432 Details of bonding type rmsd covalent geometry : bond 0.00336 (13052) covalent geometry : angle 0.54298 (17790) hydrogen bonds : bond 0.03124 ( 441) hydrogen bonds : angle 4.34308 ( 1170) ********************** 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 205 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 ARG cc_start: 0.8608 (ptp-110) cc_final: 0.8248 (mtm110) REVERT: A 229 MET cc_start: 0.8882 (ptt) cc_final: 0.8610 (ptt) REVERT: A 252 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: A 319 ASN cc_start: 0.8907 (t0) cc_final: 0.8637 (t0) REVERT: A 351 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7624 (tpp80) REVERT: A 421 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: C 456 LYS cc_start: 0.7522 (tptp) cc_final: 0.7253 (ttmt) REVERT: C 474 PHE cc_start: 0.8078 (m-10) cc_final: 0.7855 (m-10) REVERT: C 530 LYS cc_start: 0.6580 (OUTLIER) cc_final: 0.6256 (pttt) REVERT: C 547 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7624 (mtt) REVERT: B 11 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7523 (mt) REVERT: B 77 GLU cc_start: 0.7700 (pp20) cc_final: 0.7396 (pp20) REVERT: B 223 PHE cc_start: 0.8642 (m-10) cc_final: 0.8334 (m-10) REVERT: B 238 TYR cc_start: 0.8442 (m-80) cc_final: 0.8111 (m-80) REVERT: B 361 LYS cc_start: 0.7792 (tttm) cc_final: 0.7436 (mtmt) REVERT: B 409 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.7057 (mttt) REVERT: B 413 GLU cc_start: 0.8844 (tp30) cc_final: 0.8591 (mm-30) REVERT: B 433 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7029 (tm-30) REVERT: D 406 ASP cc_start: 0.7726 (p0) cc_final: 0.7488 (p0) REVERT: D 427 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8098 (mtm110) REVERT: D 529 MET cc_start: 0.6511 (ptp) cc_final: 0.5588 (ttt) REVERT: D 597 GLN cc_start: 0.7891 (pm20) cc_final: 0.7517 (pm20) REVERT: D 661 MET cc_start: 0.8843 (tmm) cc_final: 0.8537 (tmm) outliers start: 49 outliers final: 40 residues processed: 197 average time/residue: 0.1095 time to fit residues: 31.1486 Evaluate side-chains 201 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 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 370 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 421 GLU 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 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 493 ILE Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain B residue 11 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 377 GLU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 409 LYS 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 431 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 607 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 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** D 621 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.168823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.125179 restraints weight = 15373.027| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.49 r_work: 0.3307 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13052 Z= 0.124 Angle : 0.531 8.871 17790 Z= 0.289 Chirality : 0.039 0.273 1928 Planarity : 0.003 0.054 2110 Dihedral : 16.132 143.340 2128 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.55 % Favored : 92.38 % Rotamer: Outliers : 3.96 % Allowed : 29.24 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.21), residues: 1444 helix: 0.21 (0.24), residues: 524 sheet: -1.90 (0.44), residues: 146 loop : -1.64 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 351 TYR 0.026 0.001 TYR C 567 PHE 0.029 0.001 PHE B 350 TRP 0.009 0.001 TRP D 673 HIS 0.008 0.001 HIS D 432 Details of bonding type rmsd covalent geometry : bond 0.00287 (13052) covalent geometry : angle 0.53129 (17790) hydrogen bonds : bond 0.02971 ( 441) hydrogen bonds : angle 4.28535 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3769.69 seconds wall clock time: 65 minutes 12.33 seconds (3912.33 seconds total)