Starting phenix.real_space_refine on Fri Jul 3 06:42:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yo4_39435/07_2026/8yo4_39435.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yo4_39435/07_2026/8yo4_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_39435/07_2026/8yo4_39435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yo4_39435/07_2026/8yo4_39435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yo4_39435/07_2026/8yo4_39435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yo4_39435/07_2026/8yo4_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-dev-6108/lib/python3.11/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: 3.03, 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: 0.90 Conformation dependent library (CDL) restraints added in 624.9 milliseconds 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: 1.27 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: 2.13 Time building geometry restraints manager: 1.21 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=" C3' DT E 24 " pdb=" C2' DT E 24 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.69e+00 bond pdb=" C1' DT F 15 " pdb=" N1 DT F 15 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.11e+00 bond pdb=" C3' DC F 21 " pdb=" C2' DC F 21 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.99e+00 bond pdb=" C3' DT F 7 " pdb=" C2' DT F 7 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.07e+00 bond pdb=" C3' DT F 17 " pdb=" C2' DT F 17 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.73e+00 ... (remaining 13047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 17243 1.59 - 3.18: 484 3.18 - 4.77: 47 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=" N3 DT F 5 " pdb=" C4 DT F 5 " pdb=" O4 DT F 5 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT E 8 " pdb=" C4 DT E 8 " pdb=" O4 DT E 8 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT E 22 " pdb=" C4 DT E 22 " pdb=" O4 DT E 22 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT E 12 " pdb=" C4 DT E 12 " pdb=" O4 DT E 12 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (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: 1280 0.036 - 0.072: 485 0.072 - 0.108: 124 0.108 - 0.144: 38 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: 1.110 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.010 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 0.042 13052 Z= 0.240 Angle : 0.607 7.950 17790 Z= 0.422 Chirality : 0.041 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 are 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/Z covalent geometry : bond 0.00332 / 0.24 (13052) covalent geometry : angle 0.60667 / 0.42 (17790) hydrogen bonds : bond 0.16769 / 10.51 ( 441) hydrogen bonds : angle 6.12385 / 4.26 ( 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 : 0.413 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: 0.1178 time to fit residues: 26.0323 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 : 0.434 ------------------------------------------------------------------------------- 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... C 621 HIS C 642 GLN ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.162356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115478 restraints weight = 15552.928| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.28 r_work: 0.3196 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 13052 Z= 0.323 Angle : 0.714 9.349 17790 Z= 0.389 Chirality : 0.047 0.201 1928 Planarity : 0.005 0.074 2110 Dihedral : 16.398 153.491 2130 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 4.91 % Allowed : 28.37 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.21), residues: 1444 helix: -0.59 (0.23), residues: 512 sheet: -2.67 (0.40), residues: 166 loop : -1.79 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 41 TYR 0.025 0.002 TYR C 567 PHE 0.026 0.002 PHE C 581 TRP 0.013 0.002 TRP D 673 HIS 0.007 0.002 HIS C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.32 (13052) covalent geometry : angle 0.71381 / 0.39 (17790) hydrogen bonds : bond 0.05036 / 3.26 ( 441) hydrogen bonds : angle 5.10407 / 3.60 ( 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 221 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 159 time to evaluate : 0.474 Fit side-chains REVERT: A 347 GLU cc_start: 0.7736 (tt0) cc_final: 0.7341 (tm-30) REVERT: C 456 LYS cc_start: 0.7336 (tptp) cc_final: 0.7065 (ttmt) REVERT: C 474 PHE cc_start: 0.8189 (m-10) cc_final: 0.7880 (m-10) REVERT: B 11 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7461 (mt) REVERT: B 361 LYS cc_start: 0.7991 (tttm) cc_final: 0.7474 (mtmt) REVERT: B 433 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7198 (tm-30) REVERT: D 406 ASP cc_start: 0.7629 (p0) cc_final: 0.7365 (p0) outliers start: 62 outliers final: 40 residues processed: 209 average time/residue: 0.1183 time to fit residues: 35.6674 Evaluate side-chains 188 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 ASP 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 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 493 ILE Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 557 ASP 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 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 400 ILE Chi-restraints excluded: chain D residue 420 ILE 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: 0.0050 chunk 54 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 146 optimal weight: 9.9990 chunk 85 optimal weight: 0.4980 chunk 109 optimal weight: 8.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3930 r_free = 0.3930 target = 0.167473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122663 restraints weight = 15485.836| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.51 r_work: 0.3246 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13052 Z= 0.135 Angle : 0.564 7.281 17790 Z= 0.315 Chirality : 0.041 0.238 1928 Planarity : 0.004 0.064 2110 Dihedral : 16.277 152.720 2130 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.17 % Allowed : 29.56 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.21), residues: 1444 helix: -0.32 (0.23), residues: 528 sheet: -2.56 (0.39), residues: 166 loop : -1.72 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 218 TYR 0.029 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/Z covalent geometry : bond 0.00281 / 0.14 (13052) covalent geometry : angle 0.56446 / 0.32 (17790) hydrogen bonds : bond 0.03903 / 2.55 ( 441) hydrogen bonds : angle 4.76745 / 3.38 ( 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 203 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 82 ASP cc_start: 0.7759 (m-30) cc_final: 0.7471 (m-30) REVERT: A 421 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7316 (tt0) REVERT: C 456 LYS cc_start: 0.7215 (tptp) cc_final: 0.6968 (ttmt) REVERT: C 474 PHE cc_start: 0.8154 (m-10) cc_final: 0.7943 (m-10) REVERT: B 11 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7462 (mt) REVERT: B 223 PHE cc_start: 0.8662 (m-10) cc_final: 0.8351 (m-10) REVERT: B 361 LYS cc_start: 0.7977 (tttm) cc_final: 0.7487 (mtmt) REVERT: B 433 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7099 (tm-30) REVERT: D 406 ASP cc_start: 0.7631 (p0) cc_final: 0.7379 (p0) REVERT: D 427 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8270 (mtm110) outliers start: 40 outliers final: 25 residues processed: 193 average time/residue: 0.1152 time to fit residues: 31.9488 Evaluate side-chains 178 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 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 462 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 629 LEU 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 437 ASP 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 618 LEU 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: 0.9980 chunk 83 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 0.0270 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 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 = 0.3911 r_free = 0.3911 target = 0.165784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119436 restraints weight = 15526.702| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.25 r_work: 0.3249 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13052 Z= 0.183 Angle : 0.579 7.379 17790 Z= 0.322 Chirality : 0.043 0.246 1928 Planarity : 0.004 0.063 2110 Dihedral : 16.297 152.202 2130 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 4.28 % Allowed : 28.53 % 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 are not related in a simple way. whole: -1.92 (0.21), residues: 1444 helix: -0.25 (0.23), residues: 528 sheet: -2.45 (0.41), residues: 156 loop : -1.76 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 218 TYR 0.023 0.001 TYR C 567 PHE 0.020 0.001 PHE A 401 TRP 0.010 0.001 TRP D 673 HIS 0.016 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (13052) covalent geometry : angle 0.57857 / 0.32 (17790) hydrogen bonds : bond 0.03887 / 2.53 ( 441) hydrogen bonds : angle 4.70266 / 3.34 ( 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: 54 poor density : 151 time to evaluate : 0.460 Fit side-chains REVERT: A 82 ASP cc_start: 0.7794 (m-30) cc_final: 0.7549 (m-30) REVERT: A 252 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: A 421 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: A 426 LYS cc_start: 0.6907 (mtmm) cc_final: 0.6599 (mtmm) REVERT: C 456 LYS cc_start: 0.7319 (tptp) cc_final: 0.7050 (ttmt) REVERT: C 474 PHE cc_start: 0.8173 (m-10) cc_final: 0.7952 (m-10) REVERT: B 11 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7453 (mt) REVERT: B 189 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7642 (tt) REVERT: B 361 LYS cc_start: 0.7939 (tttm) cc_final: 0.7473 (mtmt) REVERT: B 433 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7108 (tm-30) REVERT: D 430 GLU cc_start: 0.8037 (pm20) cc_final: 0.7522 (mm-30) outliers start: 54 outliers final: 37 residues processed: 196 average time/residue: 0.1150 time to fit residues: 32.5900 Evaluate side-chains 187 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 322 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 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 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 189 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 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 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: 0.7980 chunk 108 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 138 optimal weight: 0.1980 chunk 86 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN ** 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 = 0.3928 r_free = 0.3928 target = 0.167430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123274 restraints weight = 15462.412| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.44 r_work: 0.3245 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13052 Z= 0.126 Angle : 0.539 8.028 17790 Z= 0.303 Chirality : 0.041 0.260 1928 Planarity : 0.004 0.059 2110 Dihedral : 16.256 151.479 2130 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 4.36 % Allowed : 28.92 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.22), residues: 1444 helix: -0.06 (0.23), residues: 547 sheet: -2.41 (0.40), residues: 159 loop : -1.70 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 351 TYR 0.020 0.001 TYR C 567 PHE 0.021 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/Z covalent geometry : bond 0.00262 / 0.13 (13052) covalent geometry : angle 0.53944 / 0.30 (17790) hydrogen bonds : bond 0.03441 / 2.25 ( 441) hydrogen bonds : angle 4.53727 / 3.23 ( 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 208 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 153 time to evaluate : 0.459 Fit side-chains REVERT: A 82 ASP cc_start: 0.7791 (m-30) cc_final: 0.7551 (m-30) REVERT: A 252 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: A 421 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: A 426 LYS cc_start: 0.6841 (mtmm) cc_final: 0.6639 (mtmm) REVERT: C 456 LYS cc_start: 0.7270 (tptp) cc_final: 0.7002 (ttmt) REVERT: B 11 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7466 (mt) REVERT: B 223 PHE cc_start: 0.8634 (m-10) cc_final: 0.8310 (m-10) REVERT: B 361 LYS cc_start: 0.7936 (tttm) cc_final: 0.7606 (mtmt) REVERT: B 413 GLU cc_start: 0.8805 (tp30) cc_final: 0.8509 (mm-30) REVERT: B 433 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7095 (tm-30) REVERT: D 406 ASP cc_start: 0.7619 (p0) cc_final: 0.7402 (p0) REVERT: D 430 GLU cc_start: 0.8007 (pm20) cc_final: 0.7553 (mm-30) REVERT: D 659 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.7177 (t80) outliers start: 55 outliers final: 36 residues processed: 197 average time/residue: 0.1154 time to fit residues: 32.7613 Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 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 583 GLN Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 629 LEU 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 394 LYS Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 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 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: 7.9990 chunk 2 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 0.0040 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN ** 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 = 0.3935 r_free = 0.3935 target = 0.168098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123150 restraints weight = 15509.520| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.43 r_work: 0.3274 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 0.032 13052 Z= 0.129 Angle : 0.536 9.777 17790 Z= 0.301 Chirality : 0.041 0.262 1928 Planarity : 0.003 0.056 2110 Dihedral : 16.224 150.748 2130 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.52 % Favored : 91.41 % Rotamer: Outliers : 4.68 % Allowed : 28.76 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.21), residues: 1444 helix: 0.02 (0.24), residues: 528 sheet: -2.29 (0.41), residues: 156 loop : -1.72 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 351 TYR 0.018 0.001 TYR C 567 PHE 0.023 0.001 PHE C 483 TRP 0.009 0.001 TRP D 673 HIS 0.004 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (13052) covalent geometry : angle 0.53629 / 0.30 (17790) hydrogen bonds : bond 0.03390 / 2.22 ( 441) hydrogen bonds : angle 4.47389 / 3.18 ( 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 210 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 151 time to evaluate : 0.497 Fit side-chains REVERT: A 82 ASP cc_start: 0.7775 (m-30) cc_final: 0.7546 (m-30) REVERT: A 252 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: A 421 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: C 456 LYS cc_start: 0.7373 (tptp) cc_final: 0.7096 (ttmt) REVERT: C 633 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.5999 (mt-10) REVERT: B 11 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7513 (mt) REVERT: B 189 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7553 (tt) REVERT: B 223 PHE cc_start: 0.8669 (m-10) cc_final: 0.8336 (m-10) REVERT: B 238 TYR cc_start: 0.8390 (m-80) cc_final: 0.7975 (m-80) REVERT: B 361 LYS cc_start: 0.7943 (tttm) cc_final: 0.7619 (mtmt) REVERT: B 413 GLU cc_start: 0.8830 (tp30) cc_final: 0.8552 (mm-30) REVERT: B 433 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7087 (tm-30) REVERT: D 406 ASP cc_start: 0.7629 (p0) cc_final: 0.7416 (p0) REVERT: D 430 GLU cc_start: 0.8075 (pm20) cc_final: 0.7655 (mm-30) REVERT: D 597 GLN cc_start: 0.7919 (pm20) cc_final: 0.7563 (pm20) REVERT: D 659 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7172 (t80) outliers start: 59 outliers final: 42 residues processed: 201 average time/residue: 0.1064 time to fit residues: 30.7390 Evaluate side-chains 192 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 79 SER 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 322 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 400 ILE 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 403 CYS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 583 GLN 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 138 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 394 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 139 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 HIS C 621 HIS C 642 GLN ** 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 = 0.3925 r_free = 0.3925 target = 0.167207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122973 restraints weight = 15471.661| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.44 r_work: 0.3267 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1174 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= 0.143 Angle : 0.549 8.783 17790 Z= 0.307 Chirality : 0.041 0.266 1928 Planarity : 0.004 0.057 2110 Dihedral : 16.224 150.298 2130 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.31 % Favored : 91.62 % Rotamer: Outliers : 4.75 % Allowed : 28.45 % 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 are not related in a simple way. whole: -1.69 (0.21), residues: 1444 helix: 0.02 (0.24), residues: 528 sheet: -2.29 (0.41), residues: 156 loop : -1.70 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 351 TYR 0.033 0.001 TYR C 567 PHE 0.029 0.001 PHE B 350 TRP 0.009 0.001 TRP D 673 HIS 0.003 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (13052) covalent geometry : angle 0.54928 / 0.31 (17790) hydrogen bonds : bond 0.03390 / 2.22 ( 441) hydrogen bonds : angle 4.43767 / 3.15 ( 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 210 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 150 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.7788 (m-30) cc_final: 0.7550 (m-30) REVERT: A 252 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7133 (tm-30) REVERT: A 421 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: A 426 LYS cc_start: 0.6871 (mtmm) cc_final: 0.6554 (mtmm) REVERT: C 456 LYS cc_start: 0.7382 (tptp) cc_final: 0.7106 (ttmt) REVERT: C 547 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7693 (mtt) REVERT: C 633 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.6116 (mt-10) REVERT: B 11 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7506 (mt) REVERT: B 223 PHE cc_start: 0.8653 (m-10) cc_final: 0.8325 (m-10) REVERT: B 238 TYR cc_start: 0.8451 (m-80) cc_final: 0.8235 (m-10) REVERT: B 361 LYS cc_start: 0.7939 (tttm) cc_final: 0.7621 (mtmt) REVERT: B 413 GLU cc_start: 0.8866 (tp30) cc_final: 0.8593 (mm-30) REVERT: B 433 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7000 (tm-30) REVERT: D 406 ASP cc_start: 0.7727 (p0) cc_final: 0.7493 (p0) REVERT: D 430 GLU cc_start: 0.8000 (pm20) cc_final: 0.7623 (mm-30) REVERT: D 597 GLN cc_start: 0.7952 (pm20) cc_final: 0.7586 (pm20) outliers start: 60 outliers final: 44 residues processed: 201 average time/residue: 0.1168 time to fit residues: 33.7483 Evaluate side-chains 195 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 79 SER 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 252 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 400 ILE 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 403 CYS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 583 GLN 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 220 THR Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 394 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 442 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 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: 0.9980 chunk 85 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 112 optimal weight: 8.9990 chunk 22 optimal weight: 0.0670 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.168150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124348 restraints weight = 15284.156| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.46 r_work: 0.3265 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13052 Z= 0.126 Angle : 0.537 9.256 17790 Z= 0.301 Chirality : 0.041 0.270 1928 Planarity : 0.004 0.062 2110 Dihedral : 16.205 149.870 2128 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.10 % Favored : 91.83 % Rotamer: Outliers : 4.52 % Allowed : 28.68 % 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 are not related in a simple way. whole: -1.62 (0.22), residues: 1444 helix: 0.07 (0.23), residues: 537 sheet: -2.29 (0.41), residues: 159 loop : -1.65 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 351 TYR 0.028 0.001 TYR C 567 PHE 0.027 0.001 PHE B 350 TRP 0.009 0.001 TRP D 673 HIS 0.004 0.001 HIS C 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (13052) covalent geometry : angle 0.53739 / 0.30 (17790) hydrogen bonds : bond 0.03249 / 2.13 ( 441) hydrogen bonds : angle 4.39847 / 3.13 ( 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 204 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 147 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 82 ASP cc_start: 0.7740 (m-30) cc_final: 0.7491 (m-30) REVERT: A 252 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: A 421 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7198 (tt0) REVERT: A 426 LYS cc_start: 0.6827 (mtmm) cc_final: 0.6447 (mtmm) REVERT: C 456 LYS cc_start: 0.7332 (tptp) cc_final: 0.7045 (ttmt) REVERT: C 547 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7735 (mtt) REVERT: C 633 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.5864 (mt-10) REVERT: B 11 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7454 (mt) REVERT: B 223 PHE cc_start: 0.8630 (m-10) cc_final: 0.8304 (m-10) REVERT: B 238 TYR cc_start: 0.8411 (m-80) cc_final: 0.8179 (m-10) REVERT: B 299 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7910 (pt0) REVERT: B 361 LYS cc_start: 0.7915 (tttm) cc_final: 0.7588 (mtmt) REVERT: B 413 GLU cc_start: 0.8867 (tp30) cc_final: 0.8593 (mm-30) REVERT: B 433 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7074 (tm-30) REVERT: D 406 ASP cc_start: 0.7664 (p0) cc_final: 0.7441 (p0) REVERT: D 430 GLU cc_start: 0.8018 (pm20) cc_final: 0.7657 (mm-30) REVERT: D 597 GLN cc_start: 0.7964 (pm20) cc_final: 0.7602 (pm20) outliers start: 57 outliers final: 46 residues processed: 195 average time/residue: 0.1063 time to fit residues: 30.4561 Evaluate side-chains 198 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 79 SER 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 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 322 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 400 ILE 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 403 CYS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 583 GLN 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 220 THR 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 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 442 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 62 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 122 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 116 optimal weight: 0.0050 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3947 r_free = 0.3947 target = 0.169326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125534 restraints weight = 15415.845| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.43 r_work: 0.3298 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 13052 Z= 0.120 Angle : 0.531 9.476 17790 Z= 0.297 Chirality : 0.040 0.275 1928 Planarity : 0.003 0.054 2110 Dihedral : 16.170 149.256 2128 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.76 % Favored : 92.17 % Rotamer: Outliers : 4.12 % Allowed : 29.08 % 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 are not related in a simple way. whole: -1.52 (0.22), residues: 1444 helix: 0.18 (0.23), residues: 537 sheet: -2.23 (0.41), residues: 159 loop : -1.62 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 351 TYR 0.028 0.001 TYR C 567 PHE 0.024 0.001 PHE B 350 TRP 0.009 0.001 TRP D 673 HIS 0.003 0.001 HIS C 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (13052) covalent geometry : angle 0.53143 / 0.30 (17790) hydrogen bonds : bond 0.03107 / 2.04 ( 441) hydrogen bonds : angle 4.34741 / 3.09 ( 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 201 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 82 ASP cc_start: 0.7617 (m-30) cc_final: 0.7408 (m-30) REVERT: A 252 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7031 (tm-30) REVERT: A 319 ASN cc_start: 0.8855 (t0) cc_final: 0.8571 (t0) REVERT: A 421 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: A 426 LYS cc_start: 0.6879 (mtmm) cc_final: 0.6506 (mtmm) REVERT: C 456 LYS cc_start: 0.7352 (tptp) cc_final: 0.7111 (ttmt) REVERT: C 547 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7625 (mtt) REVERT: B 11 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7346 (mt) REVERT: B 223 PHE cc_start: 0.8521 (m-10) cc_final: 0.8301 (m-10) REVERT: B 238 TYR cc_start: 0.8208 (m-80) cc_final: 0.7818 (m-80) REVERT: B 299 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: B 361 LYS cc_start: 0.7948 (tttm) cc_final: 0.7697 (mtmt) REVERT: B 413 GLU cc_start: 0.8843 (tp30) cc_final: 0.8593 (mm-30) REVERT: B 433 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6989 (tm-30) REVERT: D 406 ASP cc_start: 0.7393 (p0) cc_final: 0.7169 (p0) REVERT: D 597 GLN cc_start: 0.7997 (pm20) cc_final: 0.7652 (pm20) outliers start: 52 outliers final: 43 residues processed: 190 average time/residue: 0.1084 time to fit residues: 29.5809 Evaluate side-chains 190 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 322 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 400 ILE 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 403 CYS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 583 GLN 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 220 THR 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 43 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 120 optimal weight: 0.0270 chunk 145 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 127 optimal weight: 0.0170 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 621 HIS C 642 GLN ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.170107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125769 restraints weight = 15532.444| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.53 r_work: 0.3299 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13052 Z= 0.119 Angle : 0.530 9.440 17790 Z= 0.296 Chirality : 0.041 0.275 1928 Planarity : 0.003 0.053 2110 Dihedral : 16.143 148.635 2128 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.83 % Favored : 92.11 % Rotamer: Outliers : 4.04 % Allowed : 28.92 % 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 are not related in a simple way. whole: -1.47 (0.22), residues: 1444 helix: 0.23 (0.23), residues: 537 sheet: -2.22 (0.41), residues: 159 loop : -1.60 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 351 TYR 0.025 0.001 TYR C 567 PHE 0.022 0.001 PHE B 350 TRP 0.009 0.001 TRP D 673 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (13052) covalent geometry : angle 0.53034 / 0.30 (17790) hydrogen bonds : bond 0.03044 / 2.00 ( 441) hydrogen bonds : angle 4.30718 / 3.06 ( 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 197 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 218 ARG cc_start: 0.8436 (ptp-110) cc_final: 0.8180 (mtm-85) REVERT: A 229 MET cc_start: 0.8828 (ptt) cc_final: 0.8463 (ptt) REVERT: A 252 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: A 319 ASN cc_start: 0.8869 (t0) cc_final: 0.8624 (t0) REVERT: A 421 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: A 426 LYS cc_start: 0.6874 (mtmm) cc_final: 0.6622 (mtmm) REVERT: C 456 LYS cc_start: 0.7357 (tptp) cc_final: 0.7105 (ttmt) REVERT: C 547 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7609 (mtt) REVERT: B 11 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7325 (mt) REVERT: B 223 PHE cc_start: 0.8537 (m-10) cc_final: 0.8328 (m-10) REVERT: B 238 TYR cc_start: 0.8177 (m-80) cc_final: 0.7826 (m-80) REVERT: B 361 LYS cc_start: 0.7748 (tttm) cc_final: 0.7471 (mtmt) REVERT: B 413 GLU cc_start: 0.8850 (tp30) cc_final: 0.8598 (mm-30) REVERT: B 433 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6972 (tm-30) REVERT: D 406 ASP cc_start: 0.7442 (p0) cc_final: 0.7231 (p0) REVERT: D 597 GLN cc_start: 0.7987 (pm20) cc_final: 0.7643 (pm20) outliers start: 51 outliers final: 41 residues processed: 188 average time/residue: 0.1033 time to fit residues: 28.3696 Evaluate side-chains 187 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 322 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 583 GLN 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 220 THR Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 394 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 0.5980 chunk 27 optimal weight: 0.0070 chunk 102 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3949 r_free = 0.3949 target = 0.169544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126112 restraints weight = 15405.682| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.51 r_work: 0.3317 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13052 Z= 0.122 Angle : 0.534 9.278 17790 Z= 0.296 Chirality : 0.041 0.278 1928 Planarity : 0.003 0.053 2110 Dihedral : 16.138 148.351 2128 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 3.96 % Allowed : 29.00 % 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 are not related in a simple way. whole: -1.45 (0.22), residues: 1444 helix: 0.23 (0.23), residues: 547 sheet: -2.21 (0.41), residues: 159 loop : -1.59 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 351 TYR 0.025 0.001 TYR C 567 PHE 0.033 0.001 PHE B 350 TRP 0.009 0.001 TRP D 673 HIS 0.006 0.001 HIS C 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13052) covalent geometry : angle 0.53397 / 0.30 (17790) hydrogen bonds : bond 0.03060 / 2.00 ( 441) hydrogen bonds : angle 4.30090 / 3.06 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3378.55 seconds wall clock time: 58 minutes 33.43 seconds (3513.43 seconds total)