Starting phenix.real_space_refine on Thu Aug 6 00:57:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yo4_39435/08_2026/8yo4_39435.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yo4_39435/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yo4_39435/08_2026/8yo4_39435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yo4_39435/08_2026/8yo4_39435.map" model { file = "/net/cci-nas-00/data/ceres_data/8yo4_39435/08_2026/8yo4_39435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yo4_39435/08_2026/8yo4_39435.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 4 5.21 5 S 44 5.16 5 C 7953 2.51 5 N 2157 2.21 5 O 2492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 2.92, per 1000 atoms: 0.23 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: 0.95 Conformation dependent library (CDL) restraints added in 528.4 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: 1.31 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: 2.05 Time building geometry restraints manager: 1.31 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: 17241 1.59 - 3.18: 486 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.830 Find NCS groups from input model: 0.130 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.750 ------------------------------------------------------------------------------- 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 : 0.608 7.950 17790 Z= 0.423 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 0.60768 / 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 : 0.482 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: 0.1120 time to fit residues: 25.1454 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 : 0.473 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.162806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115943 restraints weight = 15550.705| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.26 r_work: 0.3191 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.0904 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= 0.325 Angle : 0.698 8.846 17790 Z= 0.383 Chirality : 0.047 0.203 1928 Planarity : 0.005 0.074 2110 Dihedral : 16.319 151.672 2130 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % 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: -2.15 (0.21), residues: 1444 helix: -0.52 (0.23), residues: 512 sheet: -2.63 (0.40), residues: 166 loop : -1.78 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 41 TYR 0.024 0.002 TYR C 567 PHE 0.024 0.002 PHE C 581 TRP 0.012 0.002 TRP C 673 HIS 0.008 0.001 HIS C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00764 / 0.33 (13052) covalent geometry : angle 0.69798 / 0.38 (17790) hydrogen bonds : bond 0.05021 / 3.25 ( 441) hydrogen bonds : angle 5.07851 / 3.59 ( 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 206 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.380 Fit side-chains REVERT: A 347 GLU cc_start: 0.7744 (tt0) cc_final: 0.7329 (tm-30) REVERT: C 456 LYS cc_start: 0.7302 (tptp) cc_final: 0.7058 (ttmt) REVERT: B 11 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7469 (mt) REVERT: B 361 LYS cc_start: 0.7978 (tttm) cc_final: 0.7462 (mtmt) REVERT: B 433 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7244 (tm-30) outliers start: 52 outliers final: 33 residues processed: 196 average time/residue: 0.1206 time to fit residues: 34.2793 Evaluate side-chains 182 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 227 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 257 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 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 400 ILE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 557 ASP Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 91 optimal weight: 0.5980 chunk 54 optimal weight: 20.0000 chunk 5 optimal weight: 0.0030 chunk 25 optimal weight: 1.9990 chunk 131 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 109 optimal weight: 20.0000 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.168580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123344 restraints weight = 15470.722| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.44 r_work: 0.3276 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13052 Z= 0.125 Angle : 0.558 6.850 17790 Z= 0.312 Chirality : 0.041 0.251 1928 Planarity : 0.004 0.063 2110 Dihedral : 16.219 151.371 2130 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.49 % Allowed : 29.08 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.21), residues: 1444 helix: -0.26 (0.23), residues: 548 sheet: -2.47 (0.40), residues: 164 loop : -1.74 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 351 TYR 0.032 0.001 TYR C 567 PHE 0.018 0.001 PHE B 350 TRP 0.009 0.001 TRP D 673 HIS 0.003 0.001 HIS D 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (13052) covalent geometry : angle 0.55755 / 0.31 (17790) hydrogen bonds : bond 0.03810 / 2.50 ( 441) hydrogen bonds : angle 4.74223 / 3.37 ( 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 206 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.426 Fit side-chains REVERT: A 82 ASP cc_start: 0.7779 (m-30) cc_final: 0.7518 (m-30) REVERT: C 456 LYS cc_start: 0.7215 (tptp) cc_final: 0.6982 (ttmt) REVERT: B 11 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7464 (mt) REVERT: B 223 PHE cc_start: 0.8669 (m-10) cc_final: 0.8346 (m-10) REVERT: B 238 TYR cc_start: 0.8334 (m-80) cc_final: 0.8016 (m-80) REVERT: B 361 LYS cc_start: 0.7952 (tttm) cc_final: 0.7474 (mtmt) REVERT: B 433 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7171 (tm-30) REVERT: D 406 ASP cc_start: 0.7600 (p0) cc_final: 0.7352 (p0) REVERT: D 427 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7970 (mtm110) outliers start: 44 outliers final: 24 residues processed: 195 average time/residue: 0.1254 time to fit residues: 35.1345 Evaluate side-chains 179 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 557 ASP 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 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 442 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: 2.9990 chunk 34 optimal weight: 0.9980 chunk 83 optimal weight: 0.2980 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 92 optimal weight: 0.0000 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.168292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.124059 restraints weight = 15412.294| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.45 r_work: 0.3296 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13052 Z= 0.123 Angle : 0.539 7.063 17790 Z= 0.302 Chirality : 0.041 0.250 1928 Planarity : 0.004 0.060 2110 Dihedral : 16.178 150.592 2130 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 4.04 % Allowed : 29.08 % Favored : 66.88 % 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: -0.09 (0.23), residues: 547 sheet: -2.39 (0.40), residues: 159 loop : -1.68 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 351 TYR 0.019 0.001 TYR C 567 PHE 0.020 0.001 PHE B 350 TRP 0.009 0.001 TRP D 673 HIS 0.016 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (13052) covalent geometry : angle 0.53892 / 0.30 (17790) hydrogen bonds : bond 0.03521 / 2.31 ( 441) hydrogen bonds : angle 4.60286 / 3.27 ( 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 208 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.510 Fit side-chains REVERT: A 82 ASP cc_start: 0.7778 (m-30) cc_final: 0.7561 (m-30) REVERT: A 421 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7309 (tt0) REVERT: C 456 LYS cc_start: 0.7238 (tptp) cc_final: 0.7002 (ttmt) REVERT: C 547 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7658 (mtt) REVERT: C 551 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8189 (m-40) REVERT: B 11 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7477 (mt) REVERT: B 189 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7577 (tt) REVERT: B 223 PHE cc_start: 0.8678 (m-10) cc_final: 0.8363 (m-10) REVERT: B 238 TYR cc_start: 0.8381 (m-80) cc_final: 0.8036 (m-80) REVERT: B 361 LYS cc_start: 0.7910 (tttm) cc_final: 0.7454 (mtmt) REVERT: B 433 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7143 (tm-30) REVERT: D 406 ASP cc_start: 0.7601 (p0) cc_final: 0.7383 (p0) REVERT: D 430 GLU cc_start: 0.8028 (pm20) cc_final: 0.7626 (mm-30) REVERT: D 659 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7258 (t80) outliers start: 51 outliers final: 34 residues processed: 195 average time/residue: 0.1225 time to fit residues: 34.6921 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 : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 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 462 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 557 ASP 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 138 VAL Chi-restraints excluded: chain B residue 189 LEU 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 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: 3.9990 chunk 108 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 138 optimal weight: 0.0970 chunk 86 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.169551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124693 restraints weight = 15481.050| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.50 r_work: 0.3306 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13052 Z= 0.118 Angle : 0.527 8.021 17790 Z= 0.297 Chirality : 0.041 0.262 1928 Planarity : 0.003 0.057 2110 Dihedral : 16.142 149.928 2130 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.04 % Allowed : 28.68 % 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: -1.68 (0.22), residues: 1444 helix: -0.09 (0.23), residues: 549 sheet: -2.30 (0.41), residues: 159 loop : -1.63 (0.21), residues: 736 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 B 350 TRP 0.008 0.001 TRP D 673 HIS 0.007 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (13052) covalent geometry : angle 0.52727 / 0.30 (17790) hydrogen bonds : bond 0.03355 / 2.19 ( 441) hydrogen bonds : angle 4.49518 / 3.20 ( 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 204 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 0.458 Fit side-chains REVERT: A 82 ASP cc_start: 0.7595 (m-30) cc_final: 0.7379 (m-30) REVERT: A 252 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: A 421 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: C 547 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7529 (mtt) REVERT: C 551 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.8000 (m-40) REVERT: C 633 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.5726 (mt-10) REVERT: C 661 MET cc_start: 0.8804 (tmm) cc_final: 0.8582 (tmm) REVERT: B 11 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7323 (mt) REVERT: B 223 PHE cc_start: 0.8537 (m-10) cc_final: 0.8332 (m-10) REVERT: B 238 TYR cc_start: 0.8202 (m-80) cc_final: 0.7886 (m-80) REVERT: B 361 LYS cc_start: 0.7949 (tttm) cc_final: 0.7639 (mtmt) REVERT: B 433 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7071 (tm-30) REVERT: D 406 ASP cc_start: 0.7407 (p0) cc_final: 0.7176 (p0) REVERT: D 430 GLU cc_start: 0.7900 (pm20) cc_final: 0.7659 (mm-30) REVERT: D 597 GLN cc_start: 0.7974 (pm20) cc_final: 0.7635 (pm20) REVERT: D 659 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.7238 (t80) outliers start: 51 outliers final: 31 residues processed: 195 average time/residue: 0.1227 time to fit residues: 34.7045 Evaluate side-chains 183 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 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 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 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 547 MET Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 557 ASP 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 138 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 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 659 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 2 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.168305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123509 restraints weight = 15482.706| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.49 r_work: 0.3287 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13052 Z= 0.144 Angle : 0.546 8.601 17790 Z= 0.305 Chirality : 0.041 0.266 1928 Planarity : 0.003 0.057 2110 Dihedral : 16.165 149.505 2128 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.44 % Allowed : 28.21 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.22), residues: 1444 helix: 0.06 (0.23), residues: 537 sheet: -2.23 (0.41), residues: 159 loop : -1.68 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 351 TYR 0.019 0.001 TYR C 567 PHE 0.028 0.001 PHE B 350 TRP 0.009 0.001 TRP D 673 HIS 0.016 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (13052) covalent geometry : angle 0.54567 / 0.30 (17790) hydrogen bonds : bond 0.03491 / 2.28 ( 441) hydrogen bonds : angle 4.47135 / 3.17 ( 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 204 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 148 time to evaluate : 0.434 Fit side-chains REVERT: A 82 ASP cc_start: 0.7774 (m-30) cc_final: 0.7557 (m-30) REVERT: A 252 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: A 421 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: C 547 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7659 (mtt) REVERT: C 633 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.6136 (mt-10) REVERT: B 11 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7514 (mt) REVERT: B 189 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7563 (tt) REVERT: B 223 PHE cc_start: 0.8654 (m-10) cc_final: 0.8345 (m-10) REVERT: B 238 TYR cc_start: 0.8358 (m-80) cc_final: 0.7978 (m-80) REVERT: B 299 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7949 (pt0) REVERT: B 361 LYS cc_start: 0.7915 (tttm) cc_final: 0.7610 (mtmt) REVERT: B 433 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7077 (tm-30) REVERT: D 406 ASP cc_start: 0.7679 (p0) cc_final: 0.7445 (p0) REVERT: D 430 GLU cc_start: 0.8039 (pm20) cc_final: 0.7656 (mm-30) REVERT: D 597 GLN cc_start: 0.7991 (pm20) cc_final: 0.7630 (pm20) REVERT: D 659 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.7195 (t80) outliers start: 56 outliers final: 38 residues processed: 193 average time/residue: 0.1190 time to fit residues: 33.1062 Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 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 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 557 ASP 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 138 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 398 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 139 optimal weight: 0.0170 chunk 41 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3943 r_free = 0.3943 target = 0.169105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124713 restraints weight = 15478.355| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.64 r_work: 0.3281 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13052 Z= 0.129 Angle : 0.537 8.996 17790 Z= 0.300 Chirality : 0.041 0.279 1928 Planarity : 0.003 0.055 2110 Dihedral : 16.155 149.096 2128 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.28 % Allowed : 28.13 % Favored : 67.59 % 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: -1.59 (0.22), residues: 1444 helix: 0.10 (0.23), residues: 537 sheet: -2.23 (0.41), residues: 159 loop : -1.65 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 351 TYR 0.018 0.001 TYR C 567 PHE 0.017 0.001 PHE B 350 TRP 0.009 0.001 TRP D 673 HIS 0.009 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (13052) covalent geometry : angle 0.53721 / 0.30 (17790) hydrogen bonds : bond 0.03296 / 2.15 ( 441) hydrogen bonds : angle 4.39880 / 3.12 ( 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 204 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 0.363 Fit side-chains REVERT: A 82 ASP cc_start: 0.7723 (m-30) cc_final: 0.7523 (m-30) REVERT: A 252 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: A 421 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: C 547 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7611 (mtt) REVERT: C 633 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.5962 (mt-10) REVERT: B 11 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7507 (mt) REVERT: B 223 PHE cc_start: 0.8675 (m-10) cc_final: 0.8374 (m-10) REVERT: B 238 TYR cc_start: 0.8375 (m-80) cc_final: 0.7991 (m-80) REVERT: B 299 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7929 (pt0) REVERT: B 361 LYS cc_start: 0.7913 (tttm) cc_final: 0.7594 (mtmt) REVERT: B 413 GLU cc_start: 0.8811 (tp30) cc_final: 0.8525 (mm-30) REVERT: B 433 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7015 (tm-30) REVERT: D 406 ASP cc_start: 0.7734 (p0) cc_final: 0.7502 (p0) REVERT: D 430 GLU cc_start: 0.8037 (pm20) cc_final: 0.7659 (mm-30) REVERT: D 597 GLN cc_start: 0.7985 (pm20) cc_final: 0.7612 (pm20) REVERT: D 659 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7205 (t80) outliers start: 54 outliers final: 36 residues processed: 195 average time/residue: 0.1226 time to fit residues: 34.4660 Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 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 547 MET Chi-restraints excluded: chain C residue 557 ASP 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 138 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 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 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: 1.9990 chunk 114 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.9611 > 50:) chunk 85 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 139 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 1 optimal weight: 0.0570 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.168260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123266 restraints weight = 15335.900| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.46 r_work: 0.3240 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13052 Z= 0.142 Angle : 0.550 9.439 17790 Z= 0.306 Chirality : 0.042 0.280 1928 Planarity : 0.004 0.055 2110 Dihedral : 16.168 148.846 2128 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.24 % Favored : 91.69 % Rotamer: Outliers : 4.52 % Allowed : 27.58 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.60 (0.22), residues: 1444 helix: 0.07 (0.23), residues: 547 sheet: -2.24 (0.41), residues: 159 loop : -1.65 (0.21), residues: 738 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 A 401 TRP 0.009 0.001 TRP D 673 HIS 0.007 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (13052) covalent geometry : angle 0.54982 / 0.31 (17790) hydrogen bonds : bond 0.03337 / 2.18 ( 441) hydrogen bonds : angle 4.41592 / 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 210 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 153 time to evaluate : 0.462 Fit side-chains REVERT: A 82 ASP cc_start: 0.7684 (m-30) cc_final: 0.7466 (m-30) REVERT: A 252 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: A 319 ASN cc_start: 0.8873 (t0) cc_final: 0.8582 (t0) REVERT: A 421 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: C 547 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7587 (mtt) REVERT: C 633 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.6104 (mt-10) REVERT: B 11 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7422 (mt) REVERT: B 223 PHE cc_start: 0.8665 (m-10) cc_final: 0.8359 (m-10) REVERT: B 238 TYR cc_start: 0.8414 (m-80) cc_final: 0.7987 (m-80) REVERT: B 299 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7905 (pt0) REVERT: B 361 LYS cc_start: 0.7875 (tttm) cc_final: 0.7547 (mtmt) REVERT: B 413 GLU cc_start: 0.8843 (tp30) cc_final: 0.8551 (mm-30) REVERT: B 433 GLU cc_start: 0.7491 (tm-30) cc_final: 0.6999 (tm-30) REVERT: D 406 ASP cc_start: 0.7744 (p0) cc_final: 0.7515 (p0) REVERT: D 430 GLU cc_start: 0.8015 (pm20) cc_final: 0.7621 (mm-30) REVERT: D 597 GLN cc_start: 0.7919 (pm20) cc_final: 0.7532 (pm20) outliers start: 57 outliers final: 43 residues processed: 200 average time/residue: 0.1042 time to fit residues: 30.3036 Evaluate side-chains 196 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 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 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 557 ASP 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 299 GLU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 62 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 chunk 135 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 116 optimal weight: 0.0010 chunk 83 optimal weight: 0.1980 chunk 1 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.1944 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.170454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125804 restraints weight = 15368.922| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.18 r_work: 0.3330 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13052 Z= 0.108 Angle : 0.530 9.636 17790 Z= 0.296 Chirality : 0.040 0.277 1928 Planarity : 0.004 0.052 2110 Dihedral : 16.104 148.306 2128 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.76 % Favored : 92.17 % Rotamer: Outliers : 3.57 % Allowed : 28.92 % Favored : 67.51 % 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: -1.48 (0.22), residues: 1444 helix: 0.19 (0.24), residues: 535 sheet: -2.18 (0.41), residues: 159 loop : -1.59 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 351 TYR 0.014 0.001 TYR C 532 PHE 0.014 0.001 PHE A 401 TRP 0.009 0.001 TRP D 673 HIS 0.013 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (13052) covalent geometry : angle 0.53025 / 0.30 (17790) hydrogen bonds : bond 0.02994 / 1.98 ( 441) hydrogen bonds : angle 4.33980 / 3.08 ( 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 199 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.497 Fit side-chains REVERT: A 319 ASN cc_start: 0.8883 (t0) cc_final: 0.8614 (t0) REVERT: A 421 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: A 426 LYS cc_start: 0.6845 (mtmm) cc_final: 0.6552 (mtmm) REVERT: C 547 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7573 (mtt) REVERT: B 11 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7428 (mt) REVERT: B 223 PHE cc_start: 0.8637 (m-10) cc_final: 0.8351 (m-10) REVERT: B 238 TYR cc_start: 0.8244 (m-80) cc_final: 0.7814 (m-80) REVERT: B 299 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7816 (pt0) REVERT: B 361 LYS cc_start: 0.7873 (tttm) cc_final: 0.7547 (mtmt) REVERT: B 413 GLU cc_start: 0.8845 (tp30) cc_final: 0.8574 (mm-30) REVERT: B 433 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7095 (tm-30) REVERT: D 406 ASP cc_start: 0.7644 (p0) cc_final: 0.7424 (p0) REVERT: D 430 GLU cc_start: 0.7971 (pm20) cc_final: 0.7629 (mm-30) REVERT: D 597 GLN cc_start: 0.7957 (pm20) cc_final: 0.7583 (pm20) REVERT: D 659 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7290 (t80) outliers start: 45 outliers final: 32 residues processed: 191 average time/residue: 0.1237 time to fit residues: 34.1867 Evaluate side-chains 182 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 229 MET Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 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 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 B residue 11 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 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 493 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 43 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 120 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.168629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.124514 restraints weight = 15500.237| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.46 r_work: 0.3308 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 13052 Z= 0.132 Angle : 0.554 10.811 17790 Z= 0.307 Chirality : 0.041 0.274 1928 Planarity : 0.003 0.052 2110 Dihedral : 16.102 147.872 2126 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.83 % Favored : 92.11 % Rotamer: Outliers : 3.25 % Allowed : 29.08 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.22), residues: 1444 helix: 0.21 (0.23), residues: 547 sheet: -2.15 (0.42), residues: 159 loop : -1.61 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 351 TYR 0.017 0.001 TYR C 567 PHE 0.019 0.001 PHE A 36 TRP 0.009 0.001 TRP D 673 HIS 0.014 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (13052) covalent geometry : angle 0.55429 / 0.31 (17790) hydrogen bonds : bond 0.03115 / 2.03 ( 441) hydrogen bonds : angle 4.33672 / 3.07 ( 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 186 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.420 Fit side-chains REVERT: A 218 ARG cc_start: 0.8552 (ptp-110) cc_final: 0.7903 (mtm110) REVERT: A 319 ASN cc_start: 0.8890 (t0) cc_final: 0.8611 (t0) REVERT: A 421 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: C 547 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7472 (mtt) REVERT: B 11 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7326 (mt) REVERT: B 21 MET cc_start: 0.8483 (mmt) cc_final: 0.7931 (mmm) REVERT: B 223 PHE cc_start: 0.8557 (m-10) cc_final: 0.8356 (m-10) REVERT: B 238 TYR cc_start: 0.8231 (m-80) cc_final: 0.7821 (m-80) REVERT: B 299 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7581 (pt0) REVERT: B 361 LYS cc_start: 0.7928 (tttm) cc_final: 0.7671 (mtmt) REVERT: B 433 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6989 (tm-30) REVERT: D 406 ASP cc_start: 0.7492 (p0) cc_final: 0.7273 (p0) REVERT: D 430 GLU cc_start: 0.7897 (pm20) cc_final: 0.7697 (mm-30) REVERT: D 547 MET cc_start: 0.7467 (ttm) cc_final: 0.7048 (ttt) REVERT: D 597 GLN cc_start: 0.7993 (pm20) cc_final: 0.7634 (pm20) outliers start: 41 outliers final: 34 residues processed: 179 average time/residue: 0.1176 time to fit residues: 30.6543 Evaluate side-chains 182 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 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 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 B residue 11 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 0.6980 chunk 27 optimal weight: 0.0270 chunk 102 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 139 optimal weight: 0.2980 chunk 40 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.171636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.125979 restraints weight = 15363.825| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.29 r_work: 0.3330 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 13052 Z= 0.114 Angle : 0.544 10.816 17790 Z= 0.302 Chirality : 0.041 0.276 1928 Planarity : 0.003 0.051 2110 Dihedral : 16.077 147.496 2126 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 3.33 % Allowed : 29.08 % Favored : 67.59 % 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: -1.39 (0.22), residues: 1444 helix: 0.34 (0.24), residues: 531 sheet: -2.07 (0.42), residues: 159 loop : -1.60 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 351 TYR 0.015 0.001 TYR C 567 PHE 0.019 0.001 PHE A 36 TRP 0.010 0.001 TRP D 673 HIS 0.013 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (13052) covalent geometry : angle 0.54415 / 0.30 (17790) hydrogen bonds : bond 0.02959 / 1.95 ( 441) hydrogen bonds : angle 4.30806 / 3.05 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3641.05 seconds wall clock time: 63 minutes 0.58 seconds (3780.58 seconds total)