Starting phenix.real_space_refine on Sun Jun 8 17:40:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dil_46912/06_2025/9dil_46912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dil_46912/06_2025/9dil_46912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dil_46912/06_2025/9dil_46912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dil_46912/06_2025/9dil_46912.map" model { file = "/net/cci-nas-00/data/ceres_data/9dil_46912/06_2025/9dil_46912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dil_46912/06_2025/9dil_46912.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 47 5.16 5 C 6131 2.51 5 N 1728 2.21 5 O 1869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9783 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4418 Classifications: {'peptide': 566} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 535} Chain breaks: 1 Chain: "B" Number of atoms: 4362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4362 Classifications: {'peptide': 559} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 529} Chain breaks: 1 Chain: "C" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 895 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.49, per 1000 atoms: 0.66 Number of scatterers: 9783 At special positions: 0 Unit cell: (92.323, 133.826, 127.897, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 8 15.00 O 1869 8.00 N 1728 7.00 C 6131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2294 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 6 sheets defined 58.6% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 210 through 226 removed outlier: 4.615A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.588A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.703A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 431 removed outlier: 3.761A pdb=" N ASP A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 4.174A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 443' Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.502A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.523A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.575A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.710A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 removed outlier: 4.732A pdb=" N ALA A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.513A pdb=" N ILE A 629 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 713 removed outlier: 3.870A pdb=" N LEU A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR A 688 " --> pdb=" O GLY A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 3.714A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 751 through 765 removed outlier: 4.337A pdb=" N TYR A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 210 through 226 removed outlier: 5.021A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 233 Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.518A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 338 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.765A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.671A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.775A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 431 removed outlier: 3.547A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 444 removed outlier: 4.342A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 494 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.583A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.573A pdb=" N LEU B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.573A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.757A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.537A pdb=" N ASN B 602 " --> pdb=" O ASP B 598 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.585A pdb=" N ILE B 629 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 removed outlier: 3.658A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 680 removed outlier: 3.673A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 710 removed outlier: 3.576A pdb=" N GLU B 689 " --> pdb=" O ALA B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 715 removed outlier: 3.832A pdb=" N GLN B 714 " --> pdb=" O ARG B 711 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 715 " --> pdb=" O GLU B 712 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 711 through 715' Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.883A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 748 through 765 removed outlier: 3.540A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 634 removed outlier: 3.682A pdb=" N MET C 627 " --> pdb=" O TYR C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 655 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 269 removed outlier: 6.706A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 542 removed outlier: 7.297A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 269 removed outlier: 6.574A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE B 241 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 542 removed outlier: 7.375A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 562 through 566 removed outlier: 7.761A pdb=" N THR C 563 " --> pdb=" O PHE C 579 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N PHE C 579 " --> pdb=" O THR C 563 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N SER C 565 " --> pdb=" O LYS C 577 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 590 through 596 469 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3326 1.34 - 1.46: 1699 1.46 - 1.58: 4847 1.58 - 1.69: 12 1.69 - 1.81: 78 Bond restraints: 9962 Sorted by residual: bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C4 ADP B 902 " pdb=" C5 ADP B 902 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.10e+00 bond pdb=" C4 ADP A 902 " pdb=" C5 ADP A 902 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.34e-01 bond pdb=" CB VAL B 493 " pdb=" CG1 VAL B 493 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 5.05e-01 ... (remaining 9957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 13142 1.18 - 2.35: 195 2.35 - 3.53: 80 3.53 - 4.70: 32 4.70 - 5.88: 20 Bond angle restraints: 13469 Sorted by residual: angle pdb=" C ILE A 430 " pdb=" N ASP A 431 " pdb=" CA ASP A 431 " ideal model delta sigma weight residual 121.54 125.54 -4.00 1.91e+00 2.74e-01 4.39e+00 angle pdb=" O2B ADP B 902 " pdb=" PB ADP B 902 " pdb=" O3B ADP B 902 " ideal model delta sigma weight residual 119.90 114.02 5.88 3.00e+00 1.11e-01 3.84e+00 angle pdb=" O1B ADP A 901 " pdb=" PB ADP A 901 " pdb=" O2B ADP A 901 " ideal model delta sigma weight residual 119.90 114.03 5.87 3.00e+00 1.11e-01 3.83e+00 angle pdb=" O1B ADP A 902 " pdb=" PB ADP A 902 " pdb=" O3B ADP A 902 " ideal model delta sigma weight residual 119.90 114.07 5.83 3.00e+00 1.11e-01 3.77e+00 angle pdb=" O2B ADP B 901 " pdb=" PB ADP B 901 " pdb=" O3B ADP B 901 " ideal model delta sigma weight residual 119.90 114.09 5.81 3.00e+00 1.11e-01 3.75e+00 ... (remaining 13464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.42: 5465 11.42 - 22.83: 449 22.83 - 34.25: 134 34.25 - 45.66: 37 45.66 - 57.08: 22 Dihedral angle restraints: 6107 sinusoidal: 2564 harmonic: 3543 Sorted by residual: dihedral pdb=" CA ARG A 700 " pdb=" CB ARG A 700 " pdb=" CG ARG A 700 " pdb=" CD ARG A 700 " ideal model delta sinusoidal sigma weight residual -180.00 -122.92 -57.08 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N ILE B 274 " pdb=" CA ILE B 274 " pdb=" CB ILE B 274 " pdb=" CG1 ILE B 274 " ideal model delta sinusoidal sigma weight residual -180.00 -123.55 -56.45 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" N LEU B 213 " pdb=" CA LEU B 213 " pdb=" CB LEU B 213 " pdb=" CG LEU B 213 " ideal model delta sinusoidal sigma weight residual -180.00 -125.88 -54.12 3 1.50e+01 4.44e-03 9.26e+00 ... (remaining 6104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 829 0.026 - 0.053: 410 0.053 - 0.079: 136 0.079 - 0.106: 69 0.106 - 0.132: 46 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CA VAL A 514 " pdb=" N VAL A 514 " pdb=" C VAL A 514 " pdb=" CB VAL A 514 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 371 " pdb=" N ILE A 371 " pdb=" C ILE A 371 " pdb=" CB ILE A 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE B 371 " pdb=" N ILE B 371 " pdb=" C ILE B 371 " pdb=" CB ILE B 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1487 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 635 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO B 636 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 636 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 636 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 544 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO B 545 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 545 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 545 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 544 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO A 545 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 545 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 545 " 0.025 5.00e-02 4.00e+02 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1278 2.75 - 3.29: 9756 3.29 - 3.82: 15613 3.82 - 4.36: 17915 4.36 - 4.90: 31426 Nonbonded interactions: 75988 Sorted by model distance: nonbonded pdb=" O ASN B 624 " pdb=" OH TYR B 755 " model vdw 2.211 3.040 nonbonded pdb=" OD1 ASP B 373 " pdb=" OG1 THR B 375 " model vdw 2.290 3.040 nonbonded pdb=" OD2 ASP A 333 " pdb=" NH2 ARG A 362 " model vdw 2.351 3.120 nonbonded pdb=" OD2 ASP B 333 " pdb=" NH2 ARG B 362 " model vdw 2.368 3.120 nonbonded pdb=" OD1 ASP B 686 " pdb=" OG SER B 746 " model vdw 2.370 3.040 ... (remaining 75983 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' and (resid 200 through 768 or resid 901 through 902)) selection = chain 'B' } 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: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.890 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 0.026 9962 Z= 0.148 Angle : 0.516 5.878 13469 Z= 0.240 Chirality : 0.042 0.132 1490 Planarity : 0.004 0.056 1766 Dihedral : 10.159 57.077 3813 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.55 % Allowed : 6.09 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.25), residues: 1226 helix: 2.02 (0.22), residues: 606 sheet: 1.63 (0.43), residues: 145 loop : 0.52 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 551 HIS 0.003 0.001 HIS A 406 PHE 0.006 0.001 PHE A 360 TYR 0.007 0.001 TYR A 517 ARG 0.003 0.000 ARG B 653 Details of bonding type rmsd hydrogen bonds : bond 0.14277 ( 469) hydrogen bonds : angle 4.93993 ( 1341) covalent geometry : bond 0.00342 ( 9962) covalent geometry : angle 0.51562 (13469) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 274 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9129 (mp) REVERT: B 609 ASP cc_start: 0.8364 (m-30) cc_final: 0.8061 (m-30) REVERT: B 760 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8177 (tm-30) REVERT: B 766 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6751 (tpp80) REVERT: C 581 ASP cc_start: 0.8529 (t0) cc_final: 0.8166 (t0) REVERT: C 585 TYR cc_start: 0.9174 (m-80) cc_final: 0.8906 (m-10) REVERT: C 608 TYR cc_start: 0.8803 (m-80) cc_final: 0.8480 (m-80) outliers start: 16 outliers final: 3 residues processed: 207 average time/residue: 0.3209 time to fit residues: 84.6910 Evaluate side-chains 153 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 766 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.0000 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 398 GLN A 533 ASN A 568 GLN C 587 ASN C 633 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.093934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.071748 restraints weight = 21533.756| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.40 r_work: 0.2813 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9962 Z= 0.123 Angle : 0.594 7.304 13469 Z= 0.281 Chirality : 0.043 0.144 1490 Planarity : 0.004 0.057 1766 Dihedral : 5.810 56.362 1391 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.84 % Allowed : 9.77 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.25), residues: 1226 helix: 1.88 (0.21), residues: 617 sheet: 1.45 (0.43), residues: 142 loop : 0.64 (0.32), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 454 HIS 0.005 0.001 HIS A 340 PHE 0.009 0.001 PHE A 230 TYR 0.017 0.001 TYR A 203 ARG 0.005 0.000 ARG B 635 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 469) hydrogen bonds : angle 3.89590 ( 1341) covalent geometry : bond 0.00280 ( 9962) covalent geometry : angle 0.59393 (13469) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.7879 (mtt180) cc_final: 0.7609 (mtt180) REVERT: A 349 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8351 (mmm-85) REVERT: A 561 GLU cc_start: 0.8824 (mp0) cc_final: 0.8563 (mp0) REVERT: A 607 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8820 (mm-30) REVERT: A 706 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8806 (tm-30) REVERT: B 274 ILE cc_start: 0.9530 (OUTLIER) cc_final: 0.9179 (mp) REVERT: B 317 HIS cc_start: 0.8802 (m-70) cc_final: 0.8560 (m-70) REVERT: B 398 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8541 (tp-100) REVERT: B 417 GLU cc_start: 0.8638 (tt0) cc_final: 0.7900 (tt0) REVERT: B 458 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8038 (tm-30) REVERT: B 609 ASP cc_start: 0.8808 (m-30) cc_final: 0.8497 (m-30) REVERT: B 760 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8455 (tm-30) REVERT: B 766 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.6674 (tpp-160) REVERT: C 581 ASP cc_start: 0.9061 (t0) cc_final: 0.8191 (t0) REVERT: C 583 LYS cc_start: 0.9420 (mtmm) cc_final: 0.8685 (mtmm) REVERT: C 585 TYR cc_start: 0.9167 (m-80) cc_final: 0.8747 (m-10) REVERT: C 632 LYS cc_start: 0.9272 (ttpp) cc_final: 0.9049 (ttpp) outliers start: 19 outliers final: 6 residues processed: 179 average time/residue: 0.2821 time to fit residues: 65.7474 Evaluate side-chains 158 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 766 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.0010 chunk 78 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 568 GLN B 382 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.094315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.071937 restraints weight = 21851.422| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.50 r_work: 0.2814 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9962 Z= 0.115 Angle : 0.577 8.365 13469 Z= 0.270 Chirality : 0.042 0.142 1490 Planarity : 0.004 0.067 1766 Dihedral : 5.738 56.070 1388 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.22 % Allowed : 10.74 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.25), residues: 1226 helix: 1.95 (0.22), residues: 611 sheet: 1.33 (0.42), residues: 142 loop : 0.58 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 454 HIS 0.004 0.001 HIS A 340 PHE 0.009 0.001 PHE A 230 TYR 0.007 0.001 TYR A 203 ARG 0.006 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 469) hydrogen bonds : angle 3.64996 ( 1341) covalent geometry : bond 0.00266 ( 9962) covalent geometry : angle 0.57711 (13469) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8949 (mtmm) REVERT: A 349 ARG cc_start: 0.8641 (tpp80) cc_final: 0.8338 (mmm-85) REVERT: A 402 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8925 (mm-30) REVERT: A 561 GLU cc_start: 0.8897 (mp0) cc_final: 0.8658 (mp0) REVERT: A 706 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8764 (tm-30) REVERT: B 274 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9176 (mp) REVERT: B 398 GLN cc_start: 0.8886 (tm-30) cc_final: 0.7588 (tm-30) REVERT: B 402 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8217 (mm-30) REVERT: B 417 GLU cc_start: 0.8655 (tt0) cc_final: 0.7831 (tt0) REVERT: B 458 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8081 (tm-30) REVERT: B 465 ARG cc_start: 0.8709 (mmt180) cc_final: 0.8376 (mmt180) REVERT: B 609 ASP cc_start: 0.8796 (m-30) cc_final: 0.8474 (m-30) REVERT: B 760 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8465 (tm-30) REVERT: B 766 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.6630 (tpp-160) REVERT: C 581 ASP cc_start: 0.9053 (t0) cc_final: 0.8193 (t0) REVERT: C 583 LYS cc_start: 0.9421 (mtmm) cc_final: 0.8677 (mtmm) REVERT: C 585 TYR cc_start: 0.9160 (m-80) cc_final: 0.8788 (m-10) outliers start: 23 outliers final: 12 residues processed: 174 average time/residue: 0.2903 time to fit residues: 65.8927 Evaluate side-chains 163 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 766 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 120 optimal weight: 0.8980 chunk 52 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.094608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.072286 restraints weight = 21589.859| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.50 r_work: 0.2823 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9962 Z= 0.108 Angle : 0.563 6.145 13469 Z= 0.262 Chirality : 0.042 0.134 1490 Planarity : 0.004 0.065 1766 Dihedral : 5.679 55.839 1388 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.93 % Allowed : 11.51 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.25), residues: 1226 helix: 2.01 (0.22), residues: 611 sheet: 1.20 (0.42), residues: 143 loop : 0.52 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 454 HIS 0.003 0.001 HIS A 340 PHE 0.008 0.001 PHE A 230 TYR 0.016 0.001 TYR C 608 ARG 0.005 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 469) hydrogen bonds : angle 3.51646 ( 1341) covalent geometry : bond 0.00246 ( 9962) covalent geometry : angle 0.56274 (13469) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.8937 (mtmm) REVERT: A 322 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7517 (mtt180) REVERT: A 349 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8378 (mmm-85) REVERT: A 402 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8802 (mm-30) REVERT: A 561 GLU cc_start: 0.8911 (mp0) cc_final: 0.8681 (mp0) REVERT: A 639 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9040 (mp) REVERT: A 706 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8798 (tm-30) REVERT: B 274 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9168 (mp) REVERT: B 398 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8039 (tm-30) REVERT: B 402 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8406 (mm-30) REVERT: B 417 GLU cc_start: 0.8679 (tt0) cc_final: 0.7714 (tt0) REVERT: B 458 GLN cc_start: 0.8585 (tm-30) cc_final: 0.7970 (tm-30) REVERT: B 465 ARG cc_start: 0.8786 (mmt180) cc_final: 0.8583 (mmt180) REVERT: B 609 ASP cc_start: 0.8785 (m-30) cc_final: 0.8465 (m-30) REVERT: B 760 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8473 (tm-30) REVERT: B 766 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6618 (tpp-160) REVERT: C 581 ASP cc_start: 0.9025 (t0) cc_final: 0.8093 (t0) REVERT: C 583 LYS cc_start: 0.9456 (mtmm) cc_final: 0.8697 (mtmm) REVERT: C 585 TYR cc_start: 0.9184 (m-80) cc_final: 0.8777 (m-10) outliers start: 20 outliers final: 9 residues processed: 167 average time/residue: 0.3034 time to fit residues: 67.3348 Evaluate side-chains 163 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 766 ARG Chi-restraints excluded: chain C residue 616 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.094409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.072116 restraints weight = 21665.342| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.49 r_work: 0.2818 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9962 Z= 0.119 Angle : 0.579 10.558 13469 Z= 0.270 Chirality : 0.042 0.133 1490 Planarity : 0.004 0.056 1766 Dihedral : 5.654 55.585 1388 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.13 % Allowed : 11.70 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.25), residues: 1226 helix: 2.03 (0.22), residues: 615 sheet: 1.10 (0.42), residues: 146 loop : 0.49 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 454 HIS 0.004 0.001 HIS A 340 PHE 0.008 0.001 PHE A 230 TYR 0.009 0.001 TYR C 608 ARG 0.006 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 469) hydrogen bonds : angle 3.45739 ( 1341) covalent geometry : bond 0.00280 ( 9962) covalent geometry : angle 0.57904 (13469) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8331 (t80) REVERT: A 288 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.8929 (mtmm) REVERT: A 322 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7496 (mtt180) REVERT: A 349 ARG cc_start: 0.8672 (tpp80) cc_final: 0.8372 (mmm-85) REVERT: A 561 GLU cc_start: 0.8923 (mp0) cc_final: 0.8653 (mp0) REVERT: A 639 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9068 (mp) REVERT: A 706 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8799 (tm-30) REVERT: B 274 ILE cc_start: 0.9513 (OUTLIER) cc_final: 0.9166 (mp) REVERT: B 398 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8035 (tm-30) REVERT: B 402 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8425 (mm-30) REVERT: B 417 GLU cc_start: 0.8718 (tt0) cc_final: 0.7691 (tt0) REVERT: B 458 GLN cc_start: 0.8603 (tm-30) cc_final: 0.7993 (tm-30) REVERT: B 760 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8478 (tm-30) REVERT: B 766 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6546 (tpp80) REVERT: C 581 ASP cc_start: 0.9018 (t0) cc_final: 0.8071 (t0) REVERT: C 583 LYS cc_start: 0.9462 (mtmm) cc_final: 0.8723 (mtmm) REVERT: C 585 TYR cc_start: 0.9213 (m-80) cc_final: 0.8831 (m-10) outliers start: 22 outliers final: 9 residues processed: 161 average time/residue: 0.3423 time to fit residues: 72.6195 Evaluate side-chains 155 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 766 ARG Chi-restraints excluded: chain C residue 616 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.094242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.071931 restraints weight = 21870.279| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.49 r_work: 0.2812 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9962 Z= 0.123 Angle : 0.580 10.592 13469 Z= 0.268 Chirality : 0.042 0.132 1490 Planarity : 0.004 0.054 1766 Dihedral : 5.644 55.210 1388 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.93 % Allowed : 12.38 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.25), residues: 1226 helix: 2.06 (0.22), residues: 614 sheet: 1.01 (0.41), residues: 146 loop : 0.50 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 454 HIS 0.004 0.001 HIS A 340 PHE 0.009 0.001 PHE A 230 TYR 0.021 0.001 TYR C 608 ARG 0.010 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 469) hydrogen bonds : angle 3.44023 ( 1341) covalent geometry : bond 0.00291 ( 9962) covalent geometry : angle 0.57976 (13469) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8330 (t80) REVERT: A 288 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8940 (mtmm) REVERT: A 349 ARG cc_start: 0.8676 (tpp80) cc_final: 0.8373 (mmm-85) REVERT: A 561 GLU cc_start: 0.8931 (mp0) cc_final: 0.8683 (mp0) REVERT: A 639 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9069 (mp) REVERT: A 706 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8856 (tm-30) REVERT: A 710 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8510 (tm-30) REVERT: B 230 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.7864 (t80) REVERT: B 274 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9166 (mp) REVERT: B 398 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8141 (tp-100) REVERT: B 402 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8440 (mm-30) REVERT: B 417 GLU cc_start: 0.8705 (tt0) cc_final: 0.7623 (tt0) REVERT: B 458 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 760 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8486 (tm-30) REVERT: B 766 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6560 (tpp80) REVERT: C 581 ASP cc_start: 0.9018 (t0) cc_final: 0.8067 (t0) REVERT: C 583 LYS cc_start: 0.9492 (mtmm) cc_final: 0.8741 (mtmm) outliers start: 20 outliers final: 8 residues processed: 155 average time/residue: 0.2925 time to fit residues: 59.8427 Evaluate side-chains 155 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 766 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.094148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.071675 restraints weight = 21934.922| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.51 r_work: 0.2806 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9962 Z= 0.129 Angle : 0.583 10.110 13469 Z= 0.272 Chirality : 0.042 0.154 1490 Planarity : 0.004 0.054 1766 Dihedral : 5.647 54.674 1388 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.13 % Allowed : 12.19 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.25), residues: 1226 helix: 2.07 (0.22), residues: 614 sheet: 0.99 (0.41), residues: 146 loop : 0.48 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 454 HIS 0.003 0.001 HIS A 340 PHE 0.008 0.001 PHE A 230 TYR 0.014 0.001 TYR C 608 ARG 0.006 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 469) hydrogen bonds : angle 3.44348 ( 1341) covalent geometry : bond 0.00304 ( 9962) covalent geometry : angle 0.58323 (13469) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8347 (t80) REVERT: A 288 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8945 (mtmm) REVERT: A 322 ARG cc_start: 0.7776 (mtt180) cc_final: 0.7468 (mtt90) REVERT: A 349 ARG cc_start: 0.8689 (tpp80) cc_final: 0.8381 (mmm-85) REVERT: A 546 GLU cc_start: 0.8592 (tp30) cc_final: 0.8342 (tp30) REVERT: A 561 GLU cc_start: 0.8939 (mp0) cc_final: 0.8659 (mp0) REVERT: A 639 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9080 (mp) REVERT: A 706 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8844 (tm-30) REVERT: A 710 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8506 (tm-30) REVERT: B 230 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.7851 (t80) REVERT: B 274 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9172 (mp) REVERT: B 398 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8132 (tp-100) REVERT: B 402 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8455 (mm-30) REVERT: B 417 GLU cc_start: 0.8726 (tt0) cc_final: 0.7619 (tt0) REVERT: B 458 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8098 (tm-30) REVERT: B 561 GLU cc_start: 0.8794 (pm20) cc_final: 0.8540 (pm20) REVERT: B 609 ASP cc_start: 0.8818 (m-30) cc_final: 0.8534 (m-30) REVERT: B 760 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8492 (tm-30) REVERT: B 766 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.6581 (tpp80) REVERT: C 581 ASP cc_start: 0.9024 (t0) cc_final: 0.8496 (t0) REVERT: C 583 LYS cc_start: 0.9491 (mtmm) cc_final: 0.9241 (mtmm) outliers start: 22 outliers final: 10 residues processed: 161 average time/residue: 0.2998 time to fit residues: 64.2043 Evaluate side-chains 159 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 766 ARG Chi-restraints excluded: chain C residue 658 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 102 optimal weight: 0.0870 chunk 100 optimal weight: 0.0670 chunk 25 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.094813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.072569 restraints weight = 21832.438| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.50 r_work: 0.2825 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9962 Z= 0.103 Angle : 0.576 7.045 13469 Z= 0.268 Chirality : 0.041 0.134 1490 Planarity : 0.004 0.062 1766 Dihedral : 5.606 54.339 1388 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.64 % Allowed : 12.77 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.25), residues: 1226 helix: 2.11 (0.22), residues: 615 sheet: 0.99 (0.42), residues: 146 loop : 0.48 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 454 HIS 0.004 0.001 HIS B 340 PHE 0.008 0.001 PHE A 230 TYR 0.010 0.001 TYR C 608 ARG 0.013 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.02887 ( 469) hydrogen bonds : angle 3.35915 ( 1341) covalent geometry : bond 0.00236 ( 9962) covalent geometry : angle 0.57643 (13469) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8322 (t80) REVERT: A 288 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.8930 (mtmm) REVERT: A 349 ARG cc_start: 0.8676 (tpp80) cc_final: 0.8369 (mmm-85) REVERT: A 561 GLU cc_start: 0.8919 (mp0) cc_final: 0.8657 (mp0) REVERT: A 706 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8845 (tm-30) REVERT: A 710 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8485 (tm-30) REVERT: A 756 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8397 (mm-30) REVERT: B 230 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.7906 (t80) REVERT: B 274 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9156 (mp) REVERT: B 398 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8101 (tp-100) REVERT: B 402 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8457 (mm-30) REVERT: B 417 GLU cc_start: 0.8710 (tt0) cc_final: 0.7588 (tt0) REVERT: B 458 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 561 GLU cc_start: 0.8708 (pm20) cc_final: 0.8401 (pm20) REVERT: B 609 ASP cc_start: 0.8824 (m-30) cc_final: 0.8542 (m-30) REVERT: B 760 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8476 (tm-30) REVERT: B 766 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.6615 (tpp-160) REVERT: C 581 ASP cc_start: 0.9003 (t0) cc_final: 0.8464 (t0) REVERT: C 583 LYS cc_start: 0.9510 (mtmm) cc_final: 0.9244 (mtmm) outliers start: 17 outliers final: 10 residues processed: 162 average time/residue: 0.2745 time to fit residues: 58.5690 Evaluate side-chains 162 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 766 ARG Chi-restraints excluded: chain C residue 658 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 4.9990 chunk 32 optimal weight: 0.0170 chunk 96 optimal weight: 0.1980 chunk 73 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 59 optimal weight: 0.0000 overall best weight: 0.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.095685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.073533 restraints weight = 21760.779| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.43 r_work: 0.2851 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9962 Z= 0.103 Angle : 0.597 11.290 13469 Z= 0.278 Chirality : 0.042 0.164 1490 Planarity : 0.004 0.057 1766 Dihedral : 5.569 54.016 1388 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.64 % Allowed : 13.25 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.25), residues: 1226 helix: 2.09 (0.22), residues: 615 sheet: 0.99 (0.42), residues: 146 loop : 0.47 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 454 HIS 0.002 0.000 HIS A 340 PHE 0.010 0.001 PHE A 230 TYR 0.017 0.001 TYR C 608 ARG 0.004 0.000 ARG A 711 Details of bonding type rmsd hydrogen bonds : bond 0.02729 ( 469) hydrogen bonds : angle 3.34237 ( 1341) covalent geometry : bond 0.00234 ( 9962) covalent geometry : angle 0.59733 (13469) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.8164 (t80) REVERT: A 288 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8876 (mtmm) REVERT: A 349 ARG cc_start: 0.8674 (tpp80) cc_final: 0.8374 (mmm-85) REVERT: A 561 GLU cc_start: 0.8903 (mp0) cc_final: 0.8651 (mp0) REVERT: A 607 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8789 (mm-30) REVERT: A 706 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8850 (tm-30) REVERT: B 230 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.7970 (t80) REVERT: B 359 ARG cc_start: 0.8406 (mtp-110) cc_final: 0.8102 (mtp-110) REVERT: B 398 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8052 (tp-100) REVERT: B 402 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8493 (mm-30) REVERT: B 417 GLU cc_start: 0.8701 (tt0) cc_final: 0.7537 (tt0) REVERT: B 458 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8159 (tm-30) REVERT: B 561 GLU cc_start: 0.8680 (pm20) cc_final: 0.8350 (pm20) REVERT: B 760 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8483 (tm-30) REVERT: B 766 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.6531 (tpp80) REVERT: C 581 ASP cc_start: 0.8996 (t0) cc_final: 0.8464 (t0) REVERT: C 583 LYS cc_start: 0.9510 (mtmm) cc_final: 0.9270 (mtmm) outliers start: 17 outliers final: 11 residues processed: 160 average time/residue: 0.2686 time to fit residues: 57.1636 Evaluate side-chains 161 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 766 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 115 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 101 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 114 optimal weight: 0.0270 chunk 98 optimal weight: 0.2980 chunk 69 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.095964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.073747 restraints weight = 21684.754| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.49 r_work: 0.2846 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9962 Z= 0.103 Angle : 0.604 10.535 13469 Z= 0.280 Chirality : 0.042 0.157 1490 Planarity : 0.004 0.071 1766 Dihedral : 5.534 53.742 1388 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 1.45 % Allowed : 13.54 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.25), residues: 1226 helix: 2.11 (0.21), residues: 615 sheet: 1.00 (0.41), residues: 146 loop : 0.45 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 454 HIS 0.004 0.000 HIS B 340 PHE 0.010 0.001 PHE A 576 TYR 0.009 0.001 TYR C 608 ARG 0.018 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.02700 ( 469) hydrogen bonds : angle 3.32802 ( 1341) covalent geometry : bond 0.00238 ( 9962) covalent geometry : angle 0.60446 (13469) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8160 (t80) REVERT: A 288 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8867 (mtmm) REVERT: A 349 ARG cc_start: 0.8657 (tpp80) cc_final: 0.8348 (mmm-85) REVERT: A 561 GLU cc_start: 0.8924 (mp0) cc_final: 0.8668 (mp0) REVERT: A 706 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8851 (tm-30) REVERT: B 230 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8040 (t80) REVERT: B 274 ILE cc_start: 0.9502 (OUTLIER) cc_final: 0.9140 (mp) REVERT: B 359 ARG cc_start: 0.8409 (mtp-110) cc_final: 0.8109 (mtp-110) REVERT: B 398 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8073 (tp-100) REVERT: B 402 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8519 (mm-30) REVERT: B 417 GLU cc_start: 0.8712 (tt0) cc_final: 0.7591 (tt0) REVERT: B 458 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8191 (tm-30) REVERT: B 561 GLU cc_start: 0.8703 (pm20) cc_final: 0.8362 (pm20) REVERT: B 760 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8483 (tm-30) REVERT: B 766 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.6529 (tpp80) REVERT: C 581 ASP cc_start: 0.8978 (t0) cc_final: 0.8435 (t0) REVERT: C 583 LYS cc_start: 0.9496 (mtmm) cc_final: 0.9222 (mtmm) outliers start: 15 outliers final: 9 residues processed: 159 average time/residue: 0.2894 time to fit residues: 61.0622 Evaluate side-chains 160 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 766 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 60 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 0.0670 chunk 104 optimal weight: 0.0040 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.095490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.073212 restraints weight = 21736.200| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.50 r_work: 0.2845 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9962 Z= 0.108 Angle : 0.599 11.042 13469 Z= 0.278 Chirality : 0.042 0.149 1490 Planarity : 0.004 0.071 1766 Dihedral : 5.524 54.405 1388 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.08 % Rotamer: Outliers : 1.35 % Allowed : 13.93 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.25), residues: 1226 helix: 2.21 (0.22), residues: 608 sheet: 0.96 (0.41), residues: 149 loop : 0.45 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 454 HIS 0.002 0.000 HIS C 653 PHE 0.008 0.001 PHE A 230 TYR 0.011 0.001 TYR C 608 ARG 0.013 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.02746 ( 469) hydrogen bonds : angle 3.32608 ( 1341) covalent geometry : bond 0.00253 ( 9962) covalent geometry : angle 0.59892 (13469) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5125.88 seconds wall clock time: 90 minutes 54.55 seconds (5454.55 seconds total)