Starting phenix.real_space_refine on Wed Sep 17 16:40:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dil_46912/09_2025/9dil_46912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dil_46912/09_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_46912/09_2025/9dil_46912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dil_46912/09_2025/9dil_46912.map" model { file = "/net/cci-nas-00/data/ceres_data/9dil_46912/09_2025/9dil_46912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dil_46912/09_2025/9dil_46912.cif" } resolution = 3.3 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= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.65, per 1000 atoms: 0.27 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: 1.05 Conformation dependent library (CDL) restraints added in 381.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.31 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: 1.58 Time building geometry restraints manager: 1.35 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.920 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (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 ARG 0.003 0.000 ARG B 653 TYR 0.007 0.001 TYR A 517 PHE 0.006 0.001 PHE A 360 TRP 0.007 0.001 TRP A 551 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9962) covalent geometry : angle 0.51562 (13469) hydrogen bonds : bond 0.14277 ( 469) hydrogen bonds : angle 4.93993 ( 1341) *********************** 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 : 0.420 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: 0.8165 (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: 0.1484 time to fit residues: 39.1796 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 : 0.397 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 458 GLN A 533 ASN A 568 GLN C 587 ASN C 633 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.093780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.071627 restraints weight = 21587.178| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.38 r_work: 0.2808 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9962 Z= 0.131 Angle : 0.594 7.424 13469 Z= 0.281 Chirality : 0.043 0.142 1490 Planarity : 0.004 0.058 1766 Dihedral : 5.808 56.306 1391 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.93 % Allowed : 9.77 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.25), residues: 1226 helix: 1.89 (0.22), residues: 617 sheet: 1.43 (0.43), residues: 142 loop : 0.64 (0.32), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 349 TYR 0.017 0.001 TYR A 203 PHE 0.009 0.001 PHE A 230 TRP 0.012 0.001 TRP A 454 HIS 0.005 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9962) covalent geometry : angle 0.59396 (13469) hydrogen bonds : bond 0.04130 ( 469) hydrogen bonds : angle 3.91726 ( 1341) *********************** 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 185 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.7870 (mtt180) cc_final: 0.7605 (mtt180) REVERT: A 349 ARG cc_start: 0.8587 (tpp80) cc_final: 0.8323 (mmm-85) REVERT: A 561 GLU cc_start: 0.8822 (mp0) cc_final: 0.8538 (mp0) REVERT: B 274 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9183 (mp) REVERT: B 317 HIS cc_start: 0.8802 (m-70) cc_final: 0.8566 (m-70) REVERT: B 359 ARG cc_start: 0.8360 (mtp-110) cc_final: 0.8159 (mtp-110) REVERT: B 398 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8543 (tp-100) REVERT: B 417 GLU cc_start: 0.8585 (tt0) cc_final: 0.7862 (tt0) REVERT: B 458 GLN cc_start: 0.8384 (tm-30) cc_final: 0.7940 (tm-30) REVERT: B 609 ASP cc_start: 0.8806 (m-30) cc_final: 0.8491 (m-30) REVERT: B 760 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8467 (tm-30) REVERT: B 766 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6677 (tpp-160) REVERT: C 581 ASP cc_start: 0.9066 (t0) cc_final: 0.8208 (t0) REVERT: C 583 LYS cc_start: 0.9422 (mtmm) cc_final: 0.8741 (mtmm) REVERT: C 632 LYS cc_start: 0.9268 (ttpp) cc_final: 0.9047 (ttpp) outliers start: 20 outliers final: 7 residues processed: 177 average time/residue: 0.1400 time to fit residues: 32.0595 Evaluate side-chains 156 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 458 GLN 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 62 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.092799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.070795 restraints weight = 21798.361| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.39 r_work: 0.2789 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9962 Z= 0.167 Angle : 0.599 8.324 13469 Z= 0.284 Chirality : 0.043 0.140 1490 Planarity : 0.004 0.064 1766 Dihedral : 5.812 55.798 1388 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.42 % Allowed : 10.35 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.25), residues: 1226 helix: 1.88 (0.21), residues: 613 sheet: 1.24 (0.42), residues: 142 loop : 0.55 (0.31), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 313 TYR 0.019 0.002 TYR A 203 PHE 0.009 0.001 PHE A 230 TRP 0.021 0.001 TRP A 454 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9962) covalent geometry : angle 0.59934 (13469) hydrogen bonds : bond 0.04017 ( 469) hydrogen bonds : angle 3.81606 ( 1341) *********************** 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 177 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8931 (mtmm) REVERT: A 349 ARG cc_start: 0.8644 (tpp80) cc_final: 0.8361 (mmm-85) REVERT: A 402 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8907 (mm-30) REVERT: A 561 GLU cc_start: 0.8893 (mp0) cc_final: 0.8622 (mp0) REVERT: A 706 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8806 (tm-30) REVERT: B 230 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.7577 (t80) REVERT: B 274 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9189 (mp) REVERT: B 359 ARG cc_start: 0.8424 (mtp-110) cc_final: 0.8131 (mtp-110) REVERT: B 398 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8545 (tp-100) REVERT: B 417 GLU cc_start: 0.8633 (tt0) cc_final: 0.7867 (tt0) REVERT: B 458 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8100 (tm-30) REVERT: B 465 ARG cc_start: 0.8700 (mmt180) cc_final: 0.8456 (mmt180) REVERT: B 760 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8482 (tm-30) REVERT: B 766 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.6620 (tpp80) REVERT: C 581 ASP cc_start: 0.9058 (t0) cc_final: 0.8200 (t0) REVERT: C 583 LYS cc_start: 0.9445 (mtmm) cc_final: 0.8704 (mtmm) REVERT: C 632 LYS cc_start: 0.9285 (ttpp) cc_final: 0.9048 (ttpp) outliers start: 25 outliers final: 11 residues processed: 166 average time/residue: 0.1450 time to fit residues: 31.0788 Evaluate side-chains 159 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 606 THR 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 766 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 85 optimal weight: 0.9990 chunk 17 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.094548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.072199 restraints weight = 21790.293| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.50 r_work: 0.2820 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9962 Z= 0.106 Angle : 0.570 9.413 13469 Z= 0.268 Chirality : 0.042 0.133 1490 Planarity : 0.004 0.063 1766 Dihedral : 5.735 55.514 1388 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.93 % Allowed : 11.41 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.25), residues: 1226 helix: 1.95 (0.22), residues: 613 sheet: 1.25 (0.42), residues: 142 loop : 0.49 (0.31), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.015 0.001 TYR C 608 PHE 0.009 0.001 PHE A 230 TRP 0.019 0.001 TRP A 454 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9962) covalent geometry : angle 0.57046 (13469) hydrogen bonds : bond 0.03238 ( 469) hydrogen bonds : angle 3.55148 ( 1341) *********************** 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 176 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8349 (t80) REVERT: A 288 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8935 (mtmm) REVERT: A 322 ARG cc_start: 0.7729 (mtt180) cc_final: 0.7517 (mtt180) REVERT: A 349 ARG cc_start: 0.8649 (tpp80) cc_final: 0.8370 (mmm-85) REVERT: A 402 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8795 (mm-30) REVERT: A 561 GLU cc_start: 0.8915 (mp0) cc_final: 0.8673 (mp0) REVERT: A 639 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9079 (mp) REVERT: A 706 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8810 (tm-30) REVERT: B 230 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.7779 (t80) REVERT: B 274 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9166 (mp) REVERT: B 359 ARG cc_start: 0.8401 (mtp-110) cc_final: 0.8009 (mtp-110) REVERT: B 398 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8085 (tm-30) REVERT: B 402 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8401 (mm-30) REVERT: B 417 GLU cc_start: 0.8671 (tt0) cc_final: 0.7721 (tt0) REVERT: B 458 GLN cc_start: 0.8563 (tm-30) cc_final: 0.7959 (tm-30) REVERT: B 760 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8470 (tm-30) REVERT: B 766 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.6636 (tpp-160) REVERT: C 581 ASP cc_start: 0.9017 (t0) cc_final: 0.8568 (t0) outliers start: 20 outliers final: 6 residues processed: 168 average time/residue: 0.1368 time to fit residues: 30.1844 Evaluate side-chains 161 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 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 766 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.0570 chunk 5 optimal weight: 3.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.093426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.071086 restraints weight = 21791.573| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.48 r_work: 0.2796 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9962 Z= 0.141 Angle : 0.581 6.865 13469 Z= 0.272 Chirality : 0.042 0.137 1490 Planarity : 0.004 0.055 1766 Dihedral : 5.716 55.182 1388 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.93 % Allowed : 11.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.25), residues: 1226 helix: 1.99 (0.22), residues: 614 sheet: 1.07 (0.41), residues: 145 loop : 0.47 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.009 0.001 TYR C 608 PHE 0.009 0.001 PHE A 230 TRP 0.016 0.001 TRP A 454 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9962) covalent geometry : angle 0.58062 (13469) hydrogen bonds : bond 0.03408 ( 469) hydrogen bonds : angle 3.54829 ( 1341) *********************** 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 170 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8938 (mtmm) REVERT: A 322 ARG cc_start: 0.7772 (mtt180) cc_final: 0.7536 (mtt180) REVERT: A 349 ARG cc_start: 0.8696 (tpp80) cc_final: 0.8409 (mmm-85) REVERT: A 561 GLU cc_start: 0.8919 (mp0) cc_final: 0.8647 (mp0) REVERT: A 639 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9080 (mp) REVERT: A 706 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8817 (tm-30) REVERT: B 230 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7810 (t80) REVERT: B 274 ILE cc_start: 0.9522 (OUTLIER) cc_final: 0.9179 (mp) REVERT: B 359 ARG cc_start: 0.8472 (mtp-110) cc_final: 0.8099 (mtp-110) REVERT: B 398 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8227 (tp-100) REVERT: B 402 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8422 (mm-30) REVERT: B 417 GLU cc_start: 0.8706 (tt0) cc_final: 0.7691 (tt0) REVERT: B 458 GLN cc_start: 0.8579 (tm-30) cc_final: 0.7960 (tm-30) REVERT: B 609 ASP cc_start: 0.8812 (m-30) cc_final: 0.8527 (m-30) REVERT: B 760 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 766 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6690 (tpp-160) REVERT: C 581 ASP cc_start: 0.9029 (t0) cc_final: 0.8405 (t0) outliers start: 20 outliers final: 10 residues processed: 160 average time/residue: 0.1309 time to fit residues: 27.3135 Evaluate side-chains 160 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 458 GLN 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 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 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 108 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.093379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.071519 restraints weight = 21873.181| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.38 r_work: 0.2808 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9962 Z= 0.119 Angle : 0.567 6.721 13469 Z= 0.264 Chirality : 0.042 0.138 1490 Planarity : 0.004 0.068 1766 Dihedral : 5.697 54.784 1388 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.03 % Allowed : 12.67 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.25), residues: 1226 helix: 2.02 (0.21), residues: 614 sheet: 1.04 (0.41), residues: 145 loop : 0.44 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 338 TYR 0.020 0.001 TYR C 608 PHE 0.006 0.001 PHE A 230 TRP 0.014 0.001 TRP A 454 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9962) covalent geometry : angle 0.56702 (13469) hydrogen bonds : bond 0.03192 ( 469) hydrogen bonds : angle 3.47545 ( 1341) *********************** 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 170 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8936 (mtmm) REVERT: A 322 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7494 (mtt180) REVERT: A 349 ARG cc_start: 0.8673 (tpp80) cc_final: 0.8398 (mmm-85) REVERT: A 561 GLU cc_start: 0.8900 (mp0) cc_final: 0.8643 (mp0) REVERT: A 639 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9093 (mp) REVERT: B 230 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.7825 (t80) REVERT: B 274 ILE cc_start: 0.9517 (OUTLIER) cc_final: 0.9174 (mp) REVERT: B 359 ARG cc_start: 0.8471 (mtp-110) cc_final: 0.8237 (mtp-110) REVERT: B 398 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8191 (tp-100) REVERT: B 402 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8448 (mm-30) REVERT: B 417 GLU cc_start: 0.8714 (tt0) cc_final: 0.7646 (tt0) REVERT: B 458 GLN cc_start: 0.8640 (tm-30) cc_final: 0.7994 (tm-30) REVERT: B 609 ASP cc_start: 0.8825 (m-30) cc_final: 0.8529 (m-30) REVERT: B 760 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8485 (tm-30) REVERT: B 766 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.6670 (tpp-160) REVERT: C 581 ASP cc_start: 0.9010 (t0) cc_final: 0.8345 (t0) outliers start: 21 outliers final: 9 residues processed: 162 average time/residue: 0.1283 time to fit residues: 27.1266 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 : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 458 GLN 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 467 THR Chi-restraints excluded: chain B residue 766 ARG Chi-restraints excluded: chain C residue 658 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 33 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.094073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.071688 restraints weight = 21872.370| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.50 r_work: 0.2808 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9962 Z= 0.118 Angle : 0.578 7.157 13469 Z= 0.270 Chirality : 0.042 0.151 1490 Planarity : 0.004 0.060 1766 Dihedral : 5.680 54.406 1388 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.84 % Allowed : 12.19 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.25), residues: 1226 helix: 2.05 (0.21), residues: 614 sheet: 0.93 (0.41), residues: 146 loop : 0.45 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 338 TYR 0.016 0.001 TYR C 608 PHE 0.008 0.001 PHE A 230 TRP 0.013 0.001 TRP A 454 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9962) covalent geometry : angle 0.57829 (13469) hydrogen bonds : bond 0.03152 ( 469) hydrogen bonds : angle 3.46930 ( 1341) *********************** 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 166 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8930 (mtmm) REVERT: A 349 ARG cc_start: 0.8686 (tpp80) cc_final: 0.8394 (mmm-85) REVERT: A 546 GLU cc_start: 0.8617 (tp30) cc_final: 0.8408 (tp30) REVERT: A 561 GLU cc_start: 0.8918 (mp0) cc_final: 0.8639 (mp0) REVERT: A 607 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8802 (mm-30) REVERT: A 639 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9084 (mp) REVERT: A 710 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8567 (tm-30) REVERT: B 230 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7867 (t80) REVERT: B 274 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9171 (mp) REVERT: B 359 ARG cc_start: 0.8497 (mtp-110) cc_final: 0.8273 (mtp-110) REVERT: B 398 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8195 (tp-100) REVERT: B 402 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8482 (mm-30) REVERT: B 417 GLU cc_start: 0.8727 (tt0) cc_final: 0.7650 (tt0) REVERT: B 458 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 609 ASP cc_start: 0.8820 (m-30) cc_final: 0.8533 (m-30) REVERT: B 760 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8480 (tm-30) REVERT: B 766 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6528 (tpp80) REVERT: C 581 ASP cc_start: 0.9023 (t0) cc_final: 0.8463 (t0) outliers start: 19 outliers final: 8 residues processed: 158 average time/residue: 0.1194 time to fit residues: 25.1095 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 : 0.397 ------------------------------------------------------------------------------- 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 458 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 95 optimal weight: 0.2980 chunk 73 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.0970 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.094517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.072154 restraints weight = 21877.865| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.51 r_work: 0.2818 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9962 Z= 0.111 Angle : 0.595 12.105 13469 Z= 0.278 Chirality : 0.042 0.173 1490 Planarity : 0.004 0.057 1766 Dihedral : 5.654 54.091 1388 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.25), residues: 1226 helix: 2.07 (0.22), residues: 613 sheet: 0.93 (0.41), residues: 146 loop : 0.45 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 338 TYR 0.009 0.001 TYR C 608 PHE 0.008 0.001 PHE A 230 TRP 0.012 0.001 TRP A 454 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9962) covalent geometry : angle 0.59527 (13469) hydrogen bonds : bond 0.02973 ( 469) hydrogen bonds : angle 3.40287 ( 1341) *********************** 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 166 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.8927 (mtmm) REVERT: A 349 ARG cc_start: 0.8684 (tpp80) cc_final: 0.8387 (mmm-85) REVERT: A 546 GLU cc_start: 0.8748 (tp30) cc_final: 0.8493 (tp30) REVERT: A 561 GLU cc_start: 0.8925 (mp0) cc_final: 0.8662 (mp0) REVERT: A 607 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8850 (mm-30) REVERT: A 710 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8564 (tm-30) REVERT: A 756 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8397 (mm-30) REVERT: B 230 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.7960 (t80) REVERT: B 274 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9163 (mp) REVERT: B 359 ARG cc_start: 0.8499 (mtp-110) cc_final: 0.8164 (mtp-110) REVERT: B 398 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8140 (tp-100) REVERT: B 402 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8546 (mm-30) REVERT: B 417 GLU cc_start: 0.8742 (tt0) cc_final: 0.7638 (tt0) REVERT: B 458 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8155 (tm-30) REVERT: B 609 ASP cc_start: 0.8829 (m-30) cc_final: 0.8543 (m-30) REVERT: B 760 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8469 (tm-30) REVERT: B 766 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.6510 (tpp80) REVERT: C 581 ASP cc_start: 0.9025 (t0) cc_final: 0.8513 (t0) outliers start: 17 outliers final: 10 residues processed: 159 average time/residue: 0.1230 time to fit residues: 26.0293 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 : 0.464 ------------------------------------------------------------------------------- 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 458 GLN 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 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 74 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.094423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.072210 restraints weight = 21705.000| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.48 r_work: 0.2817 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9962 Z= 0.116 Angle : 0.595 10.714 13469 Z= 0.276 Chirality : 0.042 0.164 1490 Planarity : 0.004 0.055 1766 Dihedral : 5.625 53.706 1388 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.55 % Allowed : 13.25 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.25), residues: 1226 helix: 2.10 (0.22), residues: 612 sheet: 0.90 (0.41), residues: 146 loop : 0.44 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 711 TYR 0.011 0.001 TYR C 608 PHE 0.008 0.001 PHE A 230 TRP 0.011 0.001 TRP A 454 HIS 0.002 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9962) covalent geometry : angle 0.59484 (13469) hydrogen bonds : bond 0.03000 ( 469) hydrogen bonds : angle 3.39123 ( 1341) *********************** 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 160 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8931 (mtmm) REVERT: A 349 ARG cc_start: 0.8704 (tpp80) cc_final: 0.8403 (mmm-85) REVERT: A 546 GLU cc_start: 0.8714 (tp30) cc_final: 0.8476 (tp30) REVERT: A 561 GLU cc_start: 0.8920 (mp0) cc_final: 0.8631 (mp0) REVERT: A 607 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8905 (mm-30) REVERT: A 710 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8547 (tm-30) REVERT: B 230 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.7984 (t80) REVERT: B 274 ILE cc_start: 0.9513 (OUTLIER) cc_final: 0.9168 (mp) REVERT: B 359 ARG cc_start: 0.8507 (mtp-110) cc_final: 0.8283 (mtp-110) REVERT: B 398 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8124 (tp-100) REVERT: B 402 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8529 (mm-30) REVERT: B 417 GLU cc_start: 0.8731 (tt0) cc_final: 0.7638 (tt0) REVERT: B 458 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8183 (tm-30) REVERT: B 609 ASP cc_start: 0.8823 (m-30) cc_final: 0.8538 (m-30) REVERT: B 760 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8476 (tm-30) REVERT: B 766 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6515 (tpp80) REVERT: C 581 ASP cc_start: 0.9051 (t0) cc_final: 0.8542 (t0) REVERT: C 662 ASP cc_start: 0.8557 (p0) cc_final: 0.8234 (p0) outliers start: 16 outliers final: 9 residues processed: 152 average time/residue: 0.1318 time to fit residues: 26.5095 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 : 0.425 ------------------------------------------------------------------------------- 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 458 GLN Chi-restraints excluded: chain A residue 474 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 0.4980 chunk 88 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 102 optimal weight: 0.1980 chunk 89 optimal weight: 0.0980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.095389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.073355 restraints weight = 21532.248| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.41 r_work: 0.2845 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9962 Z= 0.107 Angle : 0.616 10.574 13469 Z= 0.288 Chirality : 0.042 0.172 1490 Planarity : 0.004 0.064 1766 Dihedral : 5.615 53.357 1388 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.08 % Rotamer: Outliers : 1.26 % Allowed : 13.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.25), residues: 1226 helix: 2.07 (0.22), residues: 614 sheet: 0.89 (0.41), residues: 146 loop : 0.42 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 338 TYR 0.018 0.001 TYR C 608 PHE 0.007 0.001 PHE A 230 TRP 0.011 0.001 TRP A 454 HIS 0.005 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9962) covalent geometry : angle 0.61621 (13469) hydrogen bonds : bond 0.02786 ( 469) hydrogen bonds : angle 3.36613 ( 1341) ********************** 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 165 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8871 (mtmm) REVERT: A 349 ARG cc_start: 0.8687 (tpp80) cc_final: 0.8385 (mmm-85) REVERT: A 546 GLU cc_start: 0.8699 (tp30) cc_final: 0.8460 (tp30) REVERT: A 561 GLU cc_start: 0.8905 (mp0) cc_final: 0.8659 (mp0) REVERT: A 710 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8563 (tm-30) REVERT: B 230 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8034 (t80) REVERT: B 359 ARG cc_start: 0.8529 (mtp-110) cc_final: 0.8213 (mtp-110) REVERT: B 398 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8114 (tp-100) REVERT: B 402 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8536 (mm-30) REVERT: B 417 GLU cc_start: 0.8714 (tt0) cc_final: 0.7599 (tt0) REVERT: B 458 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8171 (tm-30) REVERT: B 609 ASP cc_start: 0.8799 (m-30) cc_final: 0.8515 (m-30) REVERT: B 760 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8478 (tm-30) REVERT: B 766 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.6528 (tpp80) REVERT: C 581 ASP cc_start: 0.9014 (t0) cc_final: 0.8511 (t0) outliers start: 13 outliers final: 9 residues processed: 159 average time/residue: 0.1320 time to fit residues: 27.8974 Evaluate side-chains 157 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 458 GLN Chi-restraints excluded: chain A residue 474 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 90 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 88 optimal weight: 0.0470 chunk 49 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.095455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.073121 restraints weight = 21735.698| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.49 r_work: 0.2836 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9962 Z= 0.110 Angle : 0.613 10.135 13469 Z= 0.285 Chirality : 0.042 0.148 1490 Planarity : 0.004 0.069 1766 Dihedral : 5.589 53.908 1388 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 1.35 % Allowed : 14.22 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.25), residues: 1226 helix: 2.10 (0.22), residues: 613 sheet: 0.90 (0.41), residues: 146 loop : 0.41 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 711 TYR 0.016 0.001 TYR C 608 PHE 0.010 0.001 PHE A 576 TRP 0.011 0.001 TRP A 454 HIS 0.003 0.000 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9962) covalent geometry : angle 0.61273 (13469) hydrogen bonds : bond 0.02842 ( 469) hydrogen bonds : angle 3.34838 ( 1341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2293.62 seconds wall clock time: 40 minutes 5.47 seconds (2405.47 seconds total)