Starting phenix.real_space_refine on Wed Sep 17 07:33:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j97_61254/09_2025/9j97_61254.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j97_61254/09_2025/9j97_61254.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 { model { file = "/net/cci-nas-00/data/ceres_data/9j97_61254/09_2025/9j97_61254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j97_61254/09_2025/9j97_61254.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j97_61254/09_2025/9j97_61254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j97_61254/09_2025/9j97_61254.map" } 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= 0.003 sd= 0.142 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 4 5.49 5 S 32 5.16 5 C 4524 2.51 5 N 1054 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 6704 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3272 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 378} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3272 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 378} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'8PE': 1, 'CLR': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'8PE': 1, 'CLR': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.93, per 1000 atoms: 0.29 Number of scatterers: 6704 At special positions: 0 Unit cell: (109.787, 94.569, 79.351, 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 32 16.00 P 4 15.00 O 1090 8.00 N 1054 7.00 C 4524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.05 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 341.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 0 sheets defined 73.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 230 through 257 removed outlier: 3.768A pdb=" N THR A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 295 removed outlier: 4.235A pdb=" N ILE A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.686A pdb=" N ILE A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 337 removed outlier: 3.655A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 319 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 removed outlier: 4.447A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.848A pdb=" N PHE A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 387 removed outlier: 3.883A pdb=" N HIS A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 403 through 420 removed outlier: 4.272A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 419 " --> pdb=" O CYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 Processing helix chain 'A' and resid 454 through 471 removed outlier: 3.701A pdb=" N LEU A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 503 removed outlier: 4.397A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 485 " --> pdb=" O GLY A 481 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 532 removed outlier: 3.862A pdb=" N PHE A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 573 removed outlier: 3.850A pdb=" N VAL A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 598 through 600 No H-bonds generated for 'chain 'A' and resid 598 through 600' Processing helix chain 'A' and resid 602 through 619 removed outlier: 4.011A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 612 " --> pdb=" O ASN A 608 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 257 removed outlier: 3.769A pdb=" N THR B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 295 removed outlier: 4.234A pdb=" N ILE B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG B 293 " --> pdb=" O THR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.686A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 337 removed outlier: 3.655A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 319 " --> pdb=" O HIS B 315 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 4.447A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 376 Processing helix chain 'B' and resid 377 through 383 removed outlier: 3.847A pdb=" N PHE B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 387 removed outlier: 3.884A pdb=" N HIS B 387 " --> pdb=" O ALA B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 387' Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 403 through 420 removed outlier: 4.272A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU B 419 " --> pdb=" O CYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 453 removed outlier: 3.949A pdb=" N VAL B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 471 removed outlier: 3.697A pdb=" N LEU B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 503 removed outlier: 4.397A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 485 " --> pdb=" O GLY B 481 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 532 removed outlier: 3.862A pdb=" N PHE B 511 " --> pdb=" O THR B 507 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR B 525 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 526 " --> pdb=" O SER B 522 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 529 " --> pdb=" O THR B 525 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 574 removed outlier: 3.849A pdb=" N VAL B 567 " --> pdb=" O ILE B 563 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG B 570 " --> pdb=" O ASP B 566 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 580 removed outlier: 3.502A pdb=" N THR B 580 " --> pdb=" O GLN B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 597 removed outlier: 3.610A pdb=" N VAL B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 619 removed outlier: 3.597A pdb=" N ARG B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 604 " --> pdb=" O GLU B 600 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 612 " --> pdb=" O ASN B 608 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 613 " --> pdb=" O PHE B 609 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 1017 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: 0.97 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 144 1.23 - 1.38: 2370 1.38 - 1.52: 3180 1.52 - 1.67: 1186 1.67 - 1.81: 44 Bond restraints: 6924 Sorted by residual: bond pdb=" C ILE B 454 " pdb=" N PRO B 455 " ideal model delta sigma weight residual 1.337 1.495 -0.158 1.11e-02 8.12e+03 2.04e+02 bond pdb=" C ILE A 454 " pdb=" N PRO A 455 " ideal model delta sigma weight residual 1.337 1.493 -0.157 1.11e-02 8.12e+03 2.00e+02 bond pdb=" C ILE B 454 " pdb=" O ILE B 454 " ideal model delta sigma weight residual 1.240 1.086 0.154 1.26e-02 6.30e+03 1.49e+02 bond pdb=" C ILE A 454 " pdb=" O ILE A 454 " ideal model delta sigma weight residual 1.240 1.087 0.153 1.26e-02 6.30e+03 1.47e+02 bond pdb=" C GLY A 621 " pdb=" O GLY A 621 " ideal model delta sigma weight residual 1.234 1.098 0.135 1.20e-02 6.94e+03 1.27e+02 ... (remaining 6919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.47: 9168 4.47 - 8.94: 189 8.94 - 13.41: 37 13.41 - 17.88: 7 17.88 - 22.34: 5 Bond angle restraints: 9406 Sorted by residual: angle pdb=" C ILE B 454 " pdb=" N PRO B 455 " pdb=" CA PRO B 455 " ideal model delta sigma weight residual 119.87 136.95 -17.08 1.04e+00 9.25e-01 2.70e+02 angle pdb=" C ILE A 454 " pdb=" N PRO A 455 " pdb=" CA PRO A 455 " ideal model delta sigma weight residual 119.87 136.83 -16.96 1.04e+00 9.25e-01 2.66e+02 angle pdb=" N ILE A 575 " pdb=" CA ILE A 575 " pdb=" C ILE A 575 " ideal model delta sigma weight residual 110.74 98.41 12.33 9.10e-01 1.21e+00 1.84e+02 angle pdb=" N ILE B 575 " pdb=" CA ILE B 575 " pdb=" C ILE B 575 " ideal model delta sigma weight residual 110.74 98.46 12.28 9.10e-01 1.21e+00 1.82e+02 angle pdb=" CB ARG B 624 " pdb=" CG ARG B 624 " pdb=" CD ARG B 624 " ideal model delta sigma weight residual 111.30 88.96 22.34 2.30e+00 1.89e-01 9.44e+01 ... (remaining 9401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.85: 3645 25.85 - 51.69: 346 51.69 - 77.53: 51 77.53 - 103.38: 8 103.38 - 129.22: 2 Dihedral angle restraints: 4052 sinusoidal: 1738 harmonic: 2314 Sorted by residual: dihedral pdb=" C THR B 580 " pdb=" N THR B 580 " pdb=" CA THR B 580 " pdb=" CB THR B 580 " ideal model delta harmonic sigma weight residual -122.00 -154.80 32.80 0 2.50e+00 1.60e-01 1.72e+02 dihedral pdb=" N THR B 580 " pdb=" C THR B 580 " pdb=" CA THR B 580 " pdb=" CB THR B 580 " ideal model delta harmonic sigma weight residual 123.40 152.59 -29.19 0 2.50e+00 1.60e-01 1.36e+02 dihedral pdb=" C TYR B 518 " pdb=" N TYR B 518 " pdb=" CA TYR B 518 " pdb=" CB TYR B 518 " ideal model delta harmonic sigma weight residual -122.60 -143.16 20.56 0 2.50e+00 1.60e-01 6.76e+01 ... (remaining 4049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.282: 1001 0.282 - 0.563: 14 0.563 - 0.845: 4 0.845 - 1.127: 0 1.127 - 1.408: 1 Chirality restraints: 1020 Sorted by residual: chirality pdb=" CA THR B 580 " pdb=" N THR B 580 " pdb=" C THR B 580 " pdb=" CB THR B 580 " both_signs ideal model delta sigma weight residual False 2.53 1.12 1.41 2.00e-01 2.50e+01 4.96e+01 chirality pdb=" CA TYR B 518 " pdb=" N TYR B 518 " pdb=" C TYR B 518 " pdb=" CB TYR B 518 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA TYR A 518 " pdb=" N TYR A 518 " pdb=" C TYR A 518 " pdb=" CB TYR A 518 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.38e+01 ... (remaining 1017 not shown) Planarity restraints: 1124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 575 " 0.028 2.00e-02 2.50e+03 5.79e-02 3.35e+01 pdb=" C ILE B 575 " -0.100 2.00e-02 2.50e+03 pdb=" O ILE B 575 " 0.038 2.00e-02 2.50e+03 pdb=" N GLN B 576 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 575 " 0.028 2.00e-02 2.50e+03 5.78e-02 3.34e+01 pdb=" C ILE A 575 " -0.100 2.00e-02 2.50e+03 pdb=" O ILE A 575 " 0.038 2.00e-02 2.50e+03 pdb=" N GLN A 576 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 621 " -0.023 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C GLY A 621 " 0.089 2.00e-02 2.50e+03 pdb=" O GLY A 621 " -0.036 2.00e-02 2.50e+03 pdb=" N GLU A 622 " -0.030 2.00e-02 2.50e+03 ... (remaining 1121 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 392 2.70 - 3.25: 6588 3.25 - 3.80: 10038 3.80 - 4.35: 13244 4.35 - 4.90: 22471 Nonbonded interactions: 52733 Sorted by model distance: nonbonded pdb=" CE MET B 489 " pdb=" OG1 THR B 574 " model vdw 2.155 3.460 nonbonded pdb=" NH2 ARG A 548 " pdb=" OE2 GLU A 613 " model vdw 2.155 3.120 nonbonded pdb=" NH2 ARG B 548 " pdb=" OE2 GLU B 613 " model vdw 2.155 3.120 nonbonded pdb=" NE2 GLN B 576 " pdb=" OE1 GLU B 600 " model vdw 2.187 3.120 nonbonded pdb=" CE MET A 489 " pdb=" OG1 THR A 574 " model vdw 2.200 3.460 ... (remaining 52728 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' 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: 1.070 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.090 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 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 : 0.014 0.158 6926 Z= 0.872 Angle : 1.856 55.797 9410 Z= 1.083 Chirality : 0.092 1.408 1020 Planarity : 0.008 0.058 1124 Dihedral : 19.356 129.222 2554 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.85 % Favored : 92.25 % Rotamer: Outliers : 12.25 % Allowed : 13.69 % Favored : 74.06 % Cbeta Deviations : 2.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.11 (0.25), residues: 774 helix: -2.29 (0.18), residues: 550 sheet: None (None), residues: 0 loop : -3.43 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 624 TYR 0.026 0.003 TYR A 443 PHE 0.044 0.002 PHE B 571 TRP 0.017 0.002 TRP B 573 HIS 0.008 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.01371 ( 6924) covalent geometry : angle 1.60137 ( 9406) SS BOND : bond 0.01832 ( 2) SS BOND : angle 45.54622 ( 4) hydrogen bonds : bond 0.20428 ( 339) hydrogen bonds : angle 7.90704 ( 1017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 78 time to evaluate : 0.223 Fit side-chains REVERT: A 272 TYR cc_start: 0.9079 (m-80) cc_final: 0.8853 (m-80) REVERT: A 342 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6475 (tt) REVERT: A 420 GLU cc_start: 0.7454 (tt0) cc_final: 0.7246 (mt-10) REVERT: A 452 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: A 464 LEU cc_start: 0.8434 (mt) cc_final: 0.8180 (mt) REVERT: A 468 ARG cc_start: 0.6783 (ttm170) cc_final: 0.6356 (ttm170) REVERT: A 482 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.6631 (ptmm) REVERT: A 496 TYR cc_start: 0.8072 (t80) cc_final: 0.7793 (t80) REVERT: A 500 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7388 (ttpp) REVERT: A 508 MET cc_start: 0.7484 (tpp) cc_final: 0.7237 (tpt) REVERT: A 532 MET cc_start: 0.8451 (mmm) cc_final: 0.8115 (mmp) REVERT: B 272 TYR cc_start: 0.9074 (m-80) cc_final: 0.8858 (m-80) REVERT: B 342 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6466 (tt) REVERT: B 355 MET cc_start: 0.8869 (mtt) cc_final: 0.8464 (mtm) REVERT: B 452 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: B 464 LEU cc_start: 0.8454 (mt) cc_final: 0.8180 (mt) REVERT: B 468 ARG cc_start: 0.6865 (ttm170) cc_final: 0.6439 (ttm170) REVERT: B 482 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.6778 (ptmm) REVERT: B 496 TYR cc_start: 0.8105 (t80) cc_final: 0.7825 (t80) REVERT: B 500 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7421 (ttpp) REVERT: B 508 MET cc_start: 0.7286 (tpp) cc_final: 0.6983 (tpt) REVERT: B 532 MET cc_start: 0.8444 (mmm) cc_final: 0.8097 (mmp) REVERT: B 559 TYR cc_start: 0.8675 (m-80) cc_final: 0.7991 (m-80) outliers start: 85 outliers final: 64 residues processed: 153 average time/residue: 0.0787 time to fit residues: 16.1938 Evaluate side-chains 146 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 74 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 440 CYS Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 518 TYR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 617 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 ASN B 614 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.149612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.115999 restraints weight = 7391.414| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.04 r_work: 0.3059 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6926 Z= 0.160 Angle : 0.660 6.741 9410 Z= 0.338 Chirality : 0.041 0.148 1020 Planarity : 0.005 0.031 1124 Dihedral : 16.327 120.336 1229 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 8.79 % Allowed : 15.56 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.79 (0.27), residues: 774 helix: -1.04 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -3.79 (0.33), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 624 TYR 0.014 0.002 TYR A 553 PHE 0.020 0.002 PHE B 546 TRP 0.014 0.001 TRP B 457 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6924) covalent geometry : angle 0.65703 ( 9406) SS BOND : bond 0.00121 ( 2) SS BOND : angle 3.15706 ( 4) hydrogen bonds : bond 0.06457 ( 339) hydrogen bonds : angle 5.05776 ( 1017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 82 time to evaluate : 0.235 Fit side-chains REVERT: A 268 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8280 (tt) REVERT: A 272 TYR cc_start: 0.8987 (m-80) cc_final: 0.8672 (m-80) REVERT: A 452 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8366 (tp-100) REVERT: A 468 ARG cc_start: 0.6802 (ttm170) cc_final: 0.6466 (ttm170) REVERT: A 519 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7905 (pt) REVERT: A 532 MET cc_start: 0.9350 (mmm) cc_final: 0.8937 (mmt) REVERT: B 272 TYR cc_start: 0.9028 (m-80) cc_final: 0.8705 (m-80) REVERT: B 468 ARG cc_start: 0.6824 (ttm170) cc_final: 0.6498 (ttm170) REVERT: B 519 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7907 (pt) REVERT: B 532 MET cc_start: 0.9356 (mmm) cc_final: 0.8943 (mmt) outliers start: 61 outliers final: 39 residues processed: 136 average time/residue: 0.0699 time to fit residues: 13.4007 Evaluate side-chains 122 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 80 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 626 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.158619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.114109 restraints weight = 7297.640| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.31 r_work: 0.2954 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6926 Z= 0.149 Angle : 0.635 7.229 9410 Z= 0.324 Chirality : 0.040 0.216 1020 Planarity : 0.004 0.032 1124 Dihedral : 14.069 113.242 1139 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 6.48 % Allowed : 18.88 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.28), residues: 774 helix: -0.44 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -3.54 (0.33), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 448 TYR 0.014 0.001 TYR A 553 PHE 0.021 0.001 PHE A 546 TRP 0.013 0.001 TRP B 607 HIS 0.003 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6924) covalent geometry : angle 0.62866 ( 9406) SS BOND : bond 0.00239 ( 2) SS BOND : angle 4.25906 ( 4) hydrogen bonds : bond 0.05839 ( 339) hydrogen bonds : angle 4.69450 ( 1017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 88 time to evaluate : 0.252 Fit side-chains REVERT: A 272 TYR cc_start: 0.8767 (m-80) cc_final: 0.8290 (m-80) REVERT: A 415 CYS cc_start: 0.6792 (OUTLIER) cc_final: 0.6363 (t) REVERT: A 532 MET cc_start: 0.9129 (mmm) cc_final: 0.8733 (mmp) REVERT: A 543 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: B 272 TYR cc_start: 0.8779 (m-80) cc_final: 0.8332 (m-80) REVERT: B 415 CYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6414 (t) REVERT: B 519 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7657 (pt) REVERT: B 532 MET cc_start: 0.9166 (mmm) cc_final: 0.8783 (mmp) REVERT: B 543 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7652 (pm20) outliers start: 45 outliers final: 30 residues processed: 128 average time/residue: 0.0773 time to fit residues: 13.5906 Evaluate side-chains 118 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 626 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.160141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.115278 restraints weight = 7346.226| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.33 r_work: 0.2953 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6926 Z= 0.140 Angle : 0.601 7.405 9410 Z= 0.305 Chirality : 0.040 0.174 1020 Planarity : 0.004 0.033 1124 Dihedral : 12.778 108.167 1131 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 7.20 % Allowed : 18.44 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.29), residues: 774 helix: 0.02 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -3.15 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.014 0.001 TYR A 553 PHE 0.022 0.001 PHE A 546 TRP 0.013 0.001 TRP B 607 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6924) covalent geometry : angle 0.59825 ( 9406) SS BOND : bond 0.00570 ( 2) SS BOND : angle 2.85606 ( 4) hydrogen bonds : bond 0.05493 ( 339) hydrogen bonds : angle 4.51130 ( 1017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 86 time to evaluate : 0.250 Fit side-chains REVERT: A 272 TYR cc_start: 0.8750 (m-80) cc_final: 0.8189 (m-80) REVERT: A 415 CYS cc_start: 0.6734 (OUTLIER) cc_final: 0.6328 (t) REVERT: A 442 LYS cc_start: 0.6250 (OUTLIER) cc_final: 0.5249 (pttt) REVERT: A 452 GLN cc_start: 0.8476 (tp-100) cc_final: 0.7990 (tp-100) REVERT: A 532 MET cc_start: 0.9130 (mmm) cc_final: 0.8701 (mmp) REVERT: A 543 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: B 272 TYR cc_start: 0.8771 (m-80) cc_final: 0.8211 (m-80) REVERT: B 364 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7790 (mmmt) REVERT: B 415 CYS cc_start: 0.6637 (OUTLIER) cc_final: 0.6249 (t) REVERT: B 514 TRP cc_start: 0.6982 (t60) cc_final: 0.6769 (t60) REVERT: B 532 MET cc_start: 0.9160 (mmm) cc_final: 0.8746 (mmp) outliers start: 50 outliers final: 33 residues processed: 133 average time/residue: 0.0749 time to fit residues: 13.8277 Evaluate side-chains 122 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 84 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 626 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.161749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120389 restraints weight = 7478.963| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.18 r_work: 0.2989 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6926 Z= 0.150 Angle : 0.604 7.498 9410 Z= 0.304 Chirality : 0.040 0.145 1020 Planarity : 0.004 0.034 1124 Dihedral : 11.998 105.049 1125 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 6.77 % Allowed : 19.88 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.30), residues: 774 helix: 0.24 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.94 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.015 0.001 TYR A 553 PHE 0.023 0.001 PHE B 546 TRP 0.010 0.001 TRP B 607 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6924) covalent geometry : angle 0.60240 ( 9406) SS BOND : bond 0.00604 ( 2) SS BOND : angle 2.14608 ( 4) hydrogen bonds : bond 0.05600 ( 339) hydrogen bonds : angle 4.46585 ( 1017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 85 time to evaluate : 0.176 Fit side-chains REVERT: A 272 TYR cc_start: 0.8871 (m-80) cc_final: 0.8369 (m-80) REVERT: A 331 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8283 (tp) REVERT: A 364 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7783 (mmmt) REVERT: A 415 CYS cc_start: 0.6795 (OUTLIER) cc_final: 0.6555 (t) REVERT: A 442 LYS cc_start: 0.6279 (OUTLIER) cc_final: 0.5166 (pttt) REVERT: A 504 HIS cc_start: 0.6498 (OUTLIER) cc_final: 0.6112 (m-70) REVERT: A 532 MET cc_start: 0.9176 (mmm) cc_final: 0.8777 (mmp) REVERT: B 272 TYR cc_start: 0.8847 (m-80) cc_final: 0.8343 (m-80) REVERT: B 331 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8338 (tp) REVERT: B 364 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7827 (mmmt) REVERT: B 415 CYS cc_start: 0.6701 (OUTLIER) cc_final: 0.6414 (t) REVERT: B 442 LYS cc_start: 0.6123 (OUTLIER) cc_final: 0.5255 (pttt) REVERT: B 504 HIS cc_start: 0.6509 (OUTLIER) cc_final: 0.6106 (m-70) REVERT: B 508 MET cc_start: 0.6600 (mmm) cc_final: 0.6141 (mmp) REVERT: B 532 MET cc_start: 0.9154 (mmm) cc_final: 0.8755 (mmp) outliers start: 47 outliers final: 28 residues processed: 129 average time/residue: 0.0755 time to fit residues: 13.5632 Evaluate side-chains 122 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 84 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 504 HIS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 626 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 0.2980 chunk 6 optimal weight: 0.1980 chunk 73 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 576 GLN B 576 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.164431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.123707 restraints weight = 7413.489| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.17 r_work: 0.3050 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6926 Z= 0.115 Angle : 0.558 7.972 9410 Z= 0.279 Chirality : 0.038 0.146 1020 Planarity : 0.004 0.032 1124 Dihedral : 10.975 95.114 1115 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.33 % Allowed : 20.32 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.30), residues: 774 helix: 0.62 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -2.65 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 448 TYR 0.011 0.001 TYR B 553 PHE 0.022 0.001 PHE A 546 TRP 0.009 0.001 TRP A 607 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 6924) covalent geometry : angle 0.55661 ( 9406) SS BOND : bond 0.00534 ( 2) SS BOND : angle 1.84950 ( 4) hydrogen bonds : bond 0.04638 ( 339) hydrogen bonds : angle 4.27384 ( 1017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 0.253 Fit side-chains REVERT: A 272 TYR cc_start: 0.8800 (m-80) cc_final: 0.7862 (m-80) REVERT: A 305 LEU cc_start: 0.7968 (mt) cc_final: 0.7737 (mt) REVERT: A 442 LYS cc_start: 0.6142 (OUTLIER) cc_final: 0.5321 (pttt) REVERT: A 452 GLN cc_start: 0.8608 (tp-100) cc_final: 0.8330 (tp40) REVERT: A 504 HIS cc_start: 0.6318 (OUTLIER) cc_final: 0.6022 (m-70) REVERT: B 272 TYR cc_start: 0.8788 (m-80) cc_final: 0.7862 (m-80) REVERT: B 305 LEU cc_start: 0.7945 (mt) cc_final: 0.7725 (mt) REVERT: B 439 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7198 (mm) REVERT: B 442 LYS cc_start: 0.6046 (OUTLIER) cc_final: 0.5337 (pttt) REVERT: B 504 HIS cc_start: 0.6343 (OUTLIER) cc_final: 0.6019 (m-70) REVERT: B 508 MET cc_start: 0.6326 (mmm) cc_final: 0.5885 (mmp) outliers start: 37 outliers final: 24 residues processed: 130 average time/residue: 0.0798 time to fit residues: 14.3459 Evaluate side-chains 129 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 504 HIS Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 626 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.161747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120043 restraints weight = 7425.289| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.22 r_work: 0.3048 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6926 Z= 0.147 Angle : 0.585 8.565 9410 Z= 0.291 Chirality : 0.039 0.137 1020 Planarity : 0.004 0.033 1124 Dihedral : 10.552 93.670 1106 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.05 % Allowed : 19.45 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.30), residues: 774 helix: 0.71 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.59 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 448 TYR 0.015 0.001 TYR A 553 PHE 0.022 0.001 PHE A 546 TRP 0.009 0.001 TRP A 457 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6924) covalent geometry : angle 0.58382 ( 9406) SS BOND : bond 0.00403 ( 2) SS BOND : angle 1.68433 ( 4) hydrogen bonds : bond 0.05234 ( 339) hydrogen bonds : angle 4.30801 ( 1017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 0.247 Fit side-chains REVERT: A 272 TYR cc_start: 0.8830 (m-80) cc_final: 0.8088 (m-80) REVERT: A 305 LEU cc_start: 0.7988 (mt) cc_final: 0.7778 (mt) REVERT: A 415 CYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6610 (t) REVERT: A 442 LYS cc_start: 0.6324 (OUTLIER) cc_final: 0.5547 (pttt) REVERT: A 452 GLN cc_start: 0.8586 (tp-100) cc_final: 0.8311 (tp40) REVERT: A 504 HIS cc_start: 0.6288 (OUTLIER) cc_final: 0.6029 (m-70) REVERT: B 272 TYR cc_start: 0.8822 (m-80) cc_final: 0.8095 (m-80) REVERT: B 305 LEU cc_start: 0.7952 (mt) cc_final: 0.7744 (mt) REVERT: B 331 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8295 (tp) REVERT: B 415 CYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6522 (t) REVERT: B 442 LYS cc_start: 0.6076 (OUTLIER) cc_final: 0.5441 (pttt) REVERT: B 472 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7744 (ttp-110) REVERT: B 504 HIS cc_start: 0.6337 (OUTLIER) cc_final: 0.6057 (m-70) REVERT: B 508 MET cc_start: 0.6380 (mmm) cc_final: 0.5928 (mmp) outliers start: 42 outliers final: 26 residues processed: 131 average time/residue: 0.0758 time to fit residues: 13.7980 Evaluate side-chains 120 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 504 HIS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 626 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 72 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 387 HIS B 576 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.163223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.119924 restraints weight = 7335.993| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.23 r_work: 0.3081 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6926 Z= 0.130 Angle : 0.569 8.055 9410 Z= 0.285 Chirality : 0.038 0.131 1020 Planarity : 0.004 0.032 1124 Dihedral : 10.055 85.686 1101 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.62 % Allowed : 20.03 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.30), residues: 774 helix: 0.85 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.56 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 548 TYR 0.012 0.001 TYR A 553 PHE 0.022 0.001 PHE A 546 TRP 0.010 0.001 TRP B 607 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6924) covalent geometry : angle 0.56825 ( 9406) SS BOND : bond 0.00367 ( 2) SS BOND : angle 1.77228 ( 4) hydrogen bonds : bond 0.05048 ( 339) hydrogen bonds : angle 4.29650 ( 1017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.249 Fit side-chains REVERT: A 272 TYR cc_start: 0.8721 (m-80) cc_final: 0.7900 (m-80) REVERT: A 305 LEU cc_start: 0.7906 (mt) cc_final: 0.7699 (mt) REVERT: A 331 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8161 (tp) REVERT: A 415 CYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6435 (t) REVERT: A 442 LYS cc_start: 0.6252 (OUTLIER) cc_final: 0.5562 (pttt) REVERT: A 452 GLN cc_start: 0.8456 (tp-100) cc_final: 0.8186 (tp40) REVERT: A 472 ARG cc_start: 0.7886 (ttm110) cc_final: 0.7634 (ttp-110) REVERT: A 504 HIS cc_start: 0.6203 (OUTLIER) cc_final: 0.5967 (m-70) REVERT: B 272 TYR cc_start: 0.8703 (m-80) cc_final: 0.7886 (m-80) REVERT: B 305 LEU cc_start: 0.7870 (mt) cc_final: 0.7667 (mt) REVERT: B 331 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8138 (tp) REVERT: B 411 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8496 (tm-30) REVERT: B 415 CYS cc_start: 0.6787 (OUTLIER) cc_final: 0.6465 (t) REVERT: B 442 LYS cc_start: 0.6079 (OUTLIER) cc_final: 0.5474 (pttt) REVERT: B 472 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7642 (ttp-110) REVERT: B 504 HIS cc_start: 0.6272 (OUTLIER) cc_final: 0.6019 (m-70) REVERT: B 508 MET cc_start: 0.6245 (mmm) cc_final: 0.5838 (mmp) REVERT: B 574 THR cc_start: 0.7698 (p) cc_final: 0.7456 (p) outliers start: 39 outliers final: 28 residues processed: 129 average time/residue: 0.0706 time to fit residues: 12.7253 Evaluate side-chains 125 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 504 HIS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 626 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 0.0470 chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.0040 chunk 49 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.3490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.166778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.125785 restraints weight = 7367.104| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.10 r_work: 0.3079 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6926 Z= 0.113 Angle : 0.563 8.894 9410 Z= 0.277 Chirality : 0.037 0.132 1020 Planarity : 0.004 0.032 1124 Dihedral : 9.622 71.868 1100 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.19 % Allowed : 20.89 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.31), residues: 774 helix: 1.05 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -2.44 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.010 0.001 TYR A 352 PHE 0.020 0.001 PHE A 546 TRP 0.012 0.001 TRP B 607 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6924) covalent geometry : angle 0.56184 ( 9406) SS BOND : bond 0.00310 ( 2) SS BOND : angle 1.50776 ( 4) hydrogen bonds : bond 0.04571 ( 339) hydrogen bonds : angle 4.20384 ( 1017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.276 Fit side-chains REVERT: A 272 TYR cc_start: 0.8783 (m-80) cc_final: 0.7607 (m-80) REVERT: A 331 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8341 (tp) REVERT: A 415 CYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6645 (t) REVERT: A 442 LYS cc_start: 0.6220 (OUTLIER) cc_final: 0.5706 (pttp) REVERT: A 452 GLN cc_start: 0.8532 (tp-100) cc_final: 0.8266 (tp40) REVERT: A 472 ARG cc_start: 0.7941 (ttm110) cc_final: 0.7684 (ttp-110) REVERT: A 504 HIS cc_start: 0.6331 (OUTLIER) cc_final: 0.6084 (m-70) REVERT: B 272 TYR cc_start: 0.8771 (m-80) cc_final: 0.7605 (m-80) REVERT: B 305 LEU cc_start: 0.7957 (mt) cc_final: 0.7739 (mt) REVERT: B 411 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8751 (tm-30) REVERT: B 415 CYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6767 (t) REVERT: B 442 LYS cc_start: 0.6213 (OUTLIER) cc_final: 0.5560 (pttp) REVERT: B 472 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7686 (ttp-110) REVERT: B 504 HIS cc_start: 0.6313 (OUTLIER) cc_final: 0.6106 (m-70) REVERT: B 508 MET cc_start: 0.6258 (mmm) cc_final: 0.5879 (mmp) REVERT: B 555 GLN cc_start: 0.7970 (tp40) cc_final: 0.7183 (mt0) outliers start: 36 outliers final: 26 residues processed: 133 average time/residue: 0.0740 time to fit residues: 13.8427 Evaluate side-chains 127 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 504 HIS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 626 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.0670 chunk 39 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.170354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129395 restraints weight = 7334.923| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.10 r_work: 0.3140 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6926 Z= 0.104 Angle : 0.549 10.055 9410 Z= 0.269 Chirality : 0.037 0.131 1020 Planarity : 0.004 0.034 1124 Dihedral : 9.184 55.293 1100 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.61 % Allowed : 21.76 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.31), residues: 774 helix: 1.35 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -2.29 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 448 TYR 0.010 0.001 TYR A 272 PHE 0.020 0.001 PHE A 546 TRP 0.015 0.001 TRP B 607 HIS 0.002 0.000 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 6924) covalent geometry : angle 0.54887 ( 9406) SS BOND : bond 0.00275 ( 2) SS BOND : angle 1.33323 ( 4) hydrogen bonds : bond 0.04052 ( 339) hydrogen bonds : angle 4.12317 ( 1017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.214 Fit side-chains REVERT: A 272 TYR cc_start: 0.8692 (m-80) cc_final: 0.6963 (m-80) REVERT: A 331 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8232 (tp) REVERT: A 415 CYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6547 (t) REVERT: A 442 LYS cc_start: 0.6247 (OUTLIER) cc_final: 0.5589 (pttp) REVERT: A 452 GLN cc_start: 0.8455 (tp-100) cc_final: 0.8191 (tp40) REVERT: A 472 ARG cc_start: 0.7879 (ttm110) cc_final: 0.7596 (ttp-110) REVERT: A 504 HIS cc_start: 0.6358 (OUTLIER) cc_final: 0.6138 (m-70) REVERT: B 272 TYR cc_start: 0.8678 (m-80) cc_final: 0.6961 (m-80) REVERT: B 305 LEU cc_start: 0.7839 (mt) cc_final: 0.7635 (mt) REVERT: B 415 CYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6613 (t) REVERT: B 442 LYS cc_start: 0.6107 (OUTLIER) cc_final: 0.5525 (pttp) REVERT: B 452 GLN cc_start: 0.8671 (tp-100) cc_final: 0.8169 (tp-100) REVERT: B 472 ARG cc_start: 0.7888 (ttm110) cc_final: 0.7606 (ttp-110) REVERT: B 504 HIS cc_start: 0.6324 (OUTLIER) cc_final: 0.5988 (m-70) REVERT: B 508 MET cc_start: 0.6132 (mmm) cc_final: 0.5907 (mmp) REVERT: B 555 GLN cc_start: 0.7890 (tp40) cc_final: 0.7134 (mt0) outliers start: 32 outliers final: 20 residues processed: 134 average time/residue: 0.0728 time to fit residues: 13.6594 Evaluate side-chains 120 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 504 HIS Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 587 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 59 optimal weight: 0.0040 chunk 23 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.165861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.124680 restraints weight = 7316.997| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.10 r_work: 0.3064 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6926 Z= 0.137 Angle : 0.587 8.937 9410 Z= 0.288 Chirality : 0.039 0.136 1020 Planarity : 0.004 0.031 1124 Dihedral : 9.260 54.234 1098 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.47 % Allowed : 22.19 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.30), residues: 774 helix: 1.13 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.26 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 624 TYR 0.016 0.001 TYR A 553 PHE 0.022 0.001 PHE A 546 TRP 0.008 0.001 TRP B 514 HIS 0.002 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6924) covalent geometry : angle 0.58662 ( 9406) SS BOND : bond 0.00264 ( 2) SS BOND : angle 1.49548 ( 4) hydrogen bonds : bond 0.04973 ( 339) hydrogen bonds : angle 4.19538 ( 1017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1581.99 seconds wall clock time: 27 minutes 54.09 seconds (1674.09 seconds total)