Starting phenix.real_space_refine on Wed Mar 4 20:15:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l2m_23133/03_2026/7l2m_23133.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2m_23133/03_2026/7l2m_23133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l2m_23133/03_2026/7l2m_23133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2m_23133/03_2026/7l2m_23133.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l2m_23133/03_2026/7l2m_23133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2m_23133/03_2026/7l2m_23133.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 S 118 5.16 5 Na 3 4.78 5 C 10504 2.51 5 N 2530 2.21 5 O 2826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15981 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3653 Classifications: {'peptide': 446} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 434} Chain breaks: 1 Chain: "C" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3653 Classifications: {'peptide': 446} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 434} Chain breaks: 1 Chain: "D" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3653 Classifications: {'peptide': 446} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 434} Chain breaks: 1 Chain: "B" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3653 Classifications: {'peptide': 446} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 434} Chain breaks: 1 Chain: "E" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 591 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "F" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 591 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {' NA': 1, '6EU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {' NA': 1, '6EU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {' NA': 1, '6EU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.49, per 1000 atoms: 0.22 Number of scatterers: 15981 At special positions: 0 Unit cell: (131.1, 132.24, 114, 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 118 16.00 Na 3 11.00 O 2826 8.00 N 2530 7.00 C 10504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 16 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 23 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 51 " - pdb=" SG CYS E 63 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 71 " distance=2.03 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 16 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 23 " distance=2.04 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 31 " distance=2.04 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 58 " distance=2.04 Simple disulfide: pdb=" SG CYS F 51 " - pdb=" SG CYS F 63 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 71 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 672.6 milliseconds 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 7 sheets defined 60.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.691A pdb=" N TYR A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 4.228A pdb=" N LEU A 365 " --> pdb=" O CYS A 362 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 366 " --> pdb=" O ARG A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 408 through 413 removed outlier: 4.340A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.697A pdb=" N PHE A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.919A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 removed outlier: 3.613A pdb=" N TYR A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.543A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 563 through 575 removed outlier: 3.866A pdb=" N VAL A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 599 removed outlier: 5.174A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.620A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.731A pdb=" N ILE A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 689 removed outlier: 3.976A pdb=" N ASN A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 removed outlier: 3.831A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 353 removed outlier: 3.752A pdb=" N TYR C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 408 through 413 removed outlier: 4.347A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.645A pdb=" N PHE C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.794A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 removed outlier: 3.609A pdb=" N TYR C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 533 through 535 No H-bonds generated for 'chain 'C' and resid 533 through 535' Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.752A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 Processing helix chain 'C' and resid 563 through 576 removed outlier: 3.837A pdb=" N VAL C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 599 removed outlier: 5.151A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 removed outlier: 3.610A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 removed outlier: 3.731A pdb=" N ILE C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 689 removed outlier: 3.950A pdb=" N ASN C 676 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 689 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 712 removed outlier: 3.645A pdb=" N THR C 704 " --> pdb=" O GLN C 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 353 removed outlier: 3.755A pdb=" N TYR D 351 " --> pdb=" O GLY D 347 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 408 through 413 removed outlier: 4.149A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.674A pdb=" N PHE D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.761A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR D 454 " --> pdb=" O ALA D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 removed outlier: 3.607A pdb=" N TYR D 472 " --> pdb=" O THR D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.705A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 Processing helix chain 'D' and resid 563 through 576 removed outlier: 3.835A pdb=" N VAL D 567 " --> pdb=" O GLY D 563 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 599 removed outlier: 5.171A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 removed outlier: 3.615A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 removed outlier: 3.719A pdb=" N ILE D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 689 removed outlier: 3.993A pdb=" N ASN D 676 " --> pdb=" O ILE D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 712 removed outlier: 3.513A pdb=" N ILE D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR D 704 " --> pdb=" O GLN D 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 353 removed outlier: 3.768A pdb=" N TYR B 351 " --> pdb=" O GLY B 347 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 408 through 413 removed outlier: 4.252A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.652A pdb=" N PHE B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 removed outlier: 3.808A pdb=" N ILE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 removed outlier: 3.606A pdb=" N TYR B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.540A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 563 through 576 removed outlier: 3.855A pdb=" N VAL B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 599 removed outlier: 5.165A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.617A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 removed outlier: 3.698A pdb=" N ILE B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 689 removed outlier: 3.965A pdb=" N ASN B 676 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 689 " --> pdb=" O THR B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 712 removed outlier: 3.694A pdb=" N THR B 704 " --> pdb=" O GLN B 700 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 373 removed outlier: 3.624A pdb=" N GLU A 371 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ALA A 373 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 368 through 373 removed outlier: 3.795A pdb=" N GLU C 371 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ALA C 373 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 368 through 373 removed outlier: 3.691A pdb=" N GLU D 371 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA D 373 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 368 through 373 removed outlier: 3.817A pdb=" N GLU B 371 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA B 373 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 21 through 22 Processing sheet with id=AA6, first strand: chain 'E' and resid 61 through 62 Processing sheet with id=AA7, first strand: chain 'F' and resid 21 through 22 843 hydrogen bonds defined for protein. 2472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4750 1.34 - 1.46: 3920 1.46 - 1.58: 7542 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 16392 Sorted by residual: bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 1.329 1.452 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" CAL 6EU A 901 " pdb=" CAM 6EU A 901 " ideal model delta sigma weight residual 1.560 1.517 0.043 2.00e-02 2.50e+03 4.59e+00 ... (remaining 16387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 21549 1.91 - 3.83: 574 3.83 - 5.74: 86 5.74 - 7.66: 5 7.66 - 9.57: 10 Bond angle restraints: 22224 Sorted by residual: angle pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 121.54 130.45 -8.91 1.91e+00 2.74e-01 2.18e+01 angle pdb=" C SER B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" CBM 6EU D 901 " pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 110.82 120.39 -9.57 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CBM 6EU B 901 " pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 110.82 120.38 -9.56 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CBM 6EU A 901 " pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 110.82 120.38 -9.56 3.00e+00 1.11e-01 1.01e+01 ... (remaining 22219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 9284 17.84 - 35.67: 524 35.67 - 53.51: 101 53.51 - 71.34: 21 71.34 - 89.18: 18 Dihedral angle restraints: 9948 sinusoidal: 4238 harmonic: 5710 Sorted by residual: dihedral pdb=" CA PHE B 712 " pdb=" C PHE B 712 " pdb=" N LEU B 713 " pdb=" CA LEU B 713 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA PHE A 712 " pdb=" C PHE A 712 " pdb=" N LEU A 713 " pdb=" CA LEU A 713 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA SER D 722 " pdb=" C SER D 722 " pdb=" N GLY D 723 " pdb=" CA GLY D 723 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 9945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1873 0.048 - 0.096: 531 0.096 - 0.145: 63 0.145 - 0.193: 1 0.193 - 0.241: 4 Chirality restraints: 2472 Sorted by residual: chirality pdb=" CAO 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" CAR 6EU C 901 " pdb=" CAW 6EU C 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.48 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CAO 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAR 6EU A 901 " pdb=" CAW 6EU A 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.48 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CAO 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAR 6EU B 901 " pdb=" CAW 6EU B 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.48 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2469 not shown) Planarity restraints: 2724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 444 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C TYR A 444 " 0.040 2.00e-02 2.50e+03 pdb=" O TYR A 444 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 445 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 438 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C PHE A 438 " 0.039 2.00e-02 2.50e+03 pdb=" O PHE A 438 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A 439 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 442 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C CYS A 442 " -0.038 2.00e-02 2.50e+03 pdb=" O CYS A 442 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 443 " 0.013 2.00e-02 2.50e+03 ... (remaining 2721 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1665 2.74 - 3.28: 16189 3.28 - 3.82: 23901 3.82 - 4.36: 27672 4.36 - 4.90: 47542 Nonbonded interactions: 116969 Sorted by model distance: nonbonded pdb=" OH TYR D 584 " pdb=" OG1 THR D 641 " model vdw 2.196 3.040 nonbonded pdb=" N GLU C 536 " pdb=" OE1 GLU C 536 " model vdw 2.264 3.120 nonbonded pdb=" N GLU D 536 " pdb=" OE1 GLU D 536 " model vdw 2.267 3.120 nonbonded pdb=" OH TYR C 584 " pdb=" OG1 THR C 641 " model vdw 2.270 3.040 nonbonded pdb=" N GLU A 536 " pdb=" OE1 GLU A 536 " model vdw 2.279 3.120 ... (remaining 116964 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 280 through 901) selection = (chain 'B' and resid 280 through 901) selection = (chain 'C' and resid 280 through 901) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue 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: 0.690 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.980 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.007 0.125 16404 Z= 0.323 Angle : 0.780 9.573 22248 Z= 0.412 Chirality : 0.042 0.241 2472 Planarity : 0.004 0.052 2724 Dihedral : 12.367 89.181 6244 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.75 % Allowed : 4.08 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.19), residues: 1914 helix: 1.51 (0.15), residues: 1028 sheet: 0.19 (0.67), residues: 64 loop : -1.98 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 455 TYR 0.014 0.002 TYR A 444 PHE 0.015 0.002 PHE B 304 TRP 0.006 0.001 TRP C 549 HIS 0.004 0.001 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00704 (16392) covalent geometry : angle 0.77824 (22224) SS BOND : bond 0.00433 ( 12) SS BOND : angle 1.67862 ( 24) hydrogen bonds : bond 0.16298 ( 843) hydrogen bonds : angle 6.24115 ( 2472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 541 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ASP cc_start: 0.8199 (m-30) cc_final: 0.7603 (p0) REVERT: A 403 SER cc_start: 0.8282 (p) cc_final: 0.8070 (t) REVERT: A 411 ASP cc_start: 0.7860 (m-30) cc_final: 0.7646 (m-30) REVERT: A 423 GLN cc_start: 0.9048 (tp40) cc_final: 0.8744 (tp-100) REVERT: A 536 GLU cc_start: 0.8830 (mp0) cc_final: 0.8612 (mp0) REVERT: A 551 ASN cc_start: 0.9235 (p0) cc_final: 0.8987 (p0) REVERT: A 576 ASP cc_start: 0.8838 (t0) cc_final: 0.8110 (m-30) REVERT: A 639 LYS cc_start: 0.9339 (mtmt) cc_final: 0.8949 (ttmt) REVERT: A 653 TYR cc_start: 0.8476 (m-10) cc_final: 0.8218 (m-80) REVERT: A 697 TRP cc_start: 0.8712 (t60) cc_final: 0.7839 (t60) REVERT: C 300 ASP cc_start: 0.8174 (m-30) cc_final: 0.7547 (p0) REVERT: C 416 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: C 510 SER cc_start: 0.8933 (m) cc_final: 0.8694 (p) REVERT: C 551 ASN cc_start: 0.9314 (p0) cc_final: 0.9019 (p0) REVERT: C 561 GLN cc_start: 0.8342 (mp10) cc_final: 0.8140 (mp10) REVERT: C 564 ILE cc_start: 0.8941 (tt) cc_final: 0.8592 (mm) REVERT: C 576 ASP cc_start: 0.8836 (t0) cc_final: 0.7845 (m-30) REVERT: C 579 ARG cc_start: 0.6954 (mmt180) cc_final: 0.6522 (mtm-85) REVERT: C 580 PHE cc_start: 0.8835 (t80) cc_final: 0.8600 (t80) REVERT: C 639 LYS cc_start: 0.9339 (mtmt) cc_final: 0.8885 (mttt) REVERT: C 666 TYR cc_start: 0.9551 (t80) cc_final: 0.9335 (t80) REVERT: C 696 ILE cc_start: 0.8867 (mt) cc_final: 0.8603 (mt) REVERT: D 296 ASP cc_start: 0.6407 (p0) cc_final: 0.5900 (p0) REVERT: D 300 ASP cc_start: 0.8082 (m-30) cc_final: 0.7722 (p0) REVERT: D 411 ASP cc_start: 0.8084 (m-30) cc_final: 0.7877 (m-30) REVERT: D 561 GLN cc_start: 0.8436 (mp10) cc_final: 0.8118 (mp10) REVERT: D 576 ASP cc_start: 0.8920 (t0) cc_final: 0.8193 (m-30) REVERT: D 653 TYR cc_start: 0.8586 (m-10) cc_final: 0.8341 (m-80) REVERT: D 666 TYR cc_start: 0.9490 (t80) cc_final: 0.9275 (t80) REVERT: B 560 GLN cc_start: 0.7798 (tp-100) cc_final: 0.7587 (mm-40) REVERT: B 564 ILE cc_start: 0.9042 (tp) cc_final: 0.8807 (mm) REVERT: B 576 ASP cc_start: 0.8891 (t0) cc_final: 0.7988 (m-30) REVERT: B 628 ASN cc_start: 0.8086 (m110) cc_final: 0.7885 (m-40) REVERT: B 636 GLU cc_start: 0.8836 (mm-30) cc_final: 0.7907 (mm-30) REVERT: B 653 TYR cc_start: 0.8544 (m-10) cc_final: 0.8298 (m-80) REVERT: B 697 TRP cc_start: 0.8808 (t60) cc_final: 0.8397 (t60) REVERT: E 21 PHE cc_start: 0.7167 (m-80) cc_final: 0.6825 (m-10) REVERT: E 34 TYR cc_start: 0.7032 (m-80) cc_final: 0.6569 (m-80) REVERT: E 68 ILE cc_start: 0.9495 (mt) cc_final: 0.9240 (pt) REVERT: F 61 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.5895 (pt) REVERT: F 68 ILE cc_start: 0.9427 (mt) cc_final: 0.9175 (pt) outliers start: 13 outliers final: 6 residues processed: 548 average time/residue: 0.1204 time to fit residues: 97.7571 Evaluate side-chains 362 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 354 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS A 494 GLN ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN C 393 ASN C 408 ASN D 301 ASN D 408 ASN D 560 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.190553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128324 restraints weight = 22902.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.124489 restraints weight = 18491.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125228 restraints weight = 16860.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125853 restraints weight = 12354.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.126062 restraints weight = 10932.205| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16404 Z= 0.160 Angle : 0.596 9.569 22248 Z= 0.313 Chirality : 0.040 0.156 2472 Planarity : 0.003 0.053 2724 Dihedral : 7.691 59.887 2522 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.41 % Allowed : 11.84 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.20), residues: 1914 helix: 2.30 (0.16), residues: 1048 sheet: 0.34 (0.67), residues: 64 loop : -1.86 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 575 TYR 0.012 0.001 TYR D 511 PHE 0.014 0.001 PHE B 712 TRP 0.016 0.001 TRP A 740 HIS 0.007 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00358 (16392) covalent geometry : angle 0.59585 (22224) SS BOND : bond 0.00532 ( 12) SS BOND : angle 0.96182 ( 24) hydrogen bonds : bond 0.05598 ( 843) hydrogen bonds : angle 4.03683 ( 2472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 405 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.7841 (m-30) cc_final: 0.7623 (m-30) REVERT: A 421 LEU cc_start: 0.9379 (tp) cc_final: 0.9164 (tp) REVERT: A 423 GLN cc_start: 0.9070 (tp40) cc_final: 0.8713 (tp-100) REVERT: A 560 GLN cc_start: 0.8082 (tp40) cc_final: 0.7415 (mm-40) REVERT: A 561 GLN cc_start: 0.8174 (mp10) cc_final: 0.7967 (mp10) REVERT: A 576 ASP cc_start: 0.8673 (t0) cc_final: 0.8454 (m-30) REVERT: A 636 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8271 (tp30) REVERT: C 300 ASP cc_start: 0.7757 (m-30) cc_final: 0.7481 (p0) REVERT: C 423 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8714 (tm-30) REVERT: C 636 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8360 (tp30) REVERT: D 561 GLN cc_start: 0.8401 (mp10) cc_final: 0.8129 (mp10) REVERT: D 576 ASP cc_start: 0.8796 (t0) cc_final: 0.8200 (m-30) REVERT: D 636 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8331 (tp30) REVERT: B 572 MET cc_start: 0.8405 (mtm) cc_final: 0.8173 (mtm) REVERT: B 576 ASP cc_start: 0.8750 (t0) cc_final: 0.8143 (m-30) REVERT: B 599 ILE cc_start: 0.8707 (tt) cc_final: 0.7871 (tt) REVERT: E 34 TYR cc_start: 0.7081 (m-80) cc_final: 0.6606 (m-80) REVERT: E 56 LYS cc_start: 0.9076 (ptmt) cc_final: 0.8518 (ptpp) REVERT: E 68 ILE cc_start: 0.9426 (mt) cc_final: 0.9083 (pt) REVERT: E 72 GLU cc_start: 0.6956 (pm20) cc_final: 0.6690 (pm20) REVERT: F 14 LYS cc_start: 0.8249 (ptmt) cc_final: 0.7901 (ptpp) REVERT: F 47 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8560 (mm-30) REVERT: F 56 LYS cc_start: 0.8951 (ptmt) cc_final: 0.8358 (ptpp) REVERT: F 68 ILE cc_start: 0.9460 (mt) cc_final: 0.9132 (pt) outliers start: 42 outliers final: 27 residues processed: 426 average time/residue: 0.1090 time to fit residues: 71.0611 Evaluate side-chains 378 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 351 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 69 optimal weight: 0.0770 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 165 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 141 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.197680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.133790 restraints weight = 22274.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.133514 restraints weight = 15038.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.134033 restraints weight = 11264.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134609 restraints weight = 9819.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134561 restraints weight = 9233.303| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16404 Z= 0.114 Angle : 0.532 9.551 22248 Z= 0.284 Chirality : 0.039 0.154 2472 Planarity : 0.003 0.048 2724 Dihedral : 5.996 58.526 2512 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.36 % Allowed : 14.14 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.20), residues: 1914 helix: 2.63 (0.16), residues: 1024 sheet: 0.52 (0.70), residues: 64 loop : -1.81 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 701 TYR 0.013 0.001 TYR A 653 PHE 0.013 0.001 PHE A 649 TRP 0.022 0.001 TRP A 740 HIS 0.006 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00242 (16392) covalent geometry : angle 0.53197 (22224) SS BOND : bond 0.00207 ( 12) SS BOND : angle 0.76414 ( 24) hydrogen bonds : bond 0.04301 ( 843) hydrogen bonds : angle 3.71619 ( 2472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 394 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9094 (tp40) cc_final: 0.8723 (tp-100) REVERT: A 503 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8785 (tt) REVERT: A 561 GLN cc_start: 0.7876 (mp10) cc_final: 0.7648 (mp10) REVERT: A 636 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8396 (tp30) REVERT: C 300 ASP cc_start: 0.7729 (m-30) cc_final: 0.7496 (p0) REVERT: C 423 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8725 (tm-30) REVERT: C 503 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8692 (tt) REVERT: C 636 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8461 (tp30) REVERT: D 503 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8707 (tt) REVERT: D 561 GLN cc_start: 0.8384 (mp10) cc_final: 0.7990 (mp10) REVERT: D 636 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8392 (tp30) REVERT: B 433 ILE cc_start: 0.9273 (tp) cc_final: 0.9071 (tt) REVERT: B 503 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8686 (tt) REVERT: E 56 LYS cc_start: 0.9098 (ptmt) cc_final: 0.8534 (ptpp) REVERT: E 68 ILE cc_start: 0.9429 (mt) cc_final: 0.9100 (pt) REVERT: F 5 GLU cc_start: 0.8725 (tt0) cc_final: 0.8496 (tp30) REVERT: F 14 LYS cc_start: 0.8158 (ptmt) cc_final: 0.7824 (ptpp) REVERT: F 56 LYS cc_start: 0.8973 (ptmt) cc_final: 0.8388 (ptpp) REVERT: F 68 ILE cc_start: 0.9417 (mt) cc_final: 0.9084 (pt) outliers start: 41 outliers final: 23 residues processed: 413 average time/residue: 0.1074 time to fit residues: 68.7106 Evaluate side-chains 371 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 344 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain E residue 15 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 9 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 419 ASN D 695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.197431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.131621 restraints weight = 22364.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130725 restraints weight = 15532.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131386 restraints weight = 11616.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131844 restraints weight = 10512.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132044 restraints weight = 9102.720| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 16404 Z= 0.110 Angle : 0.519 9.458 22248 Z= 0.276 Chirality : 0.038 0.169 2472 Planarity : 0.003 0.045 2724 Dihedral : 5.745 59.639 2511 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.53 % Allowed : 16.21 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 1914 helix: 2.51 (0.16), residues: 1036 sheet: 0.66 (0.71), residues: 64 loop : -1.76 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 701 TYR 0.013 0.001 TYR C 653 PHE 0.011 0.001 PHE A 649 TRP 0.012 0.001 TRP A 740 HIS 0.008 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00241 (16392) covalent geometry : angle 0.51800 (22224) SS BOND : bond 0.00216 ( 12) SS BOND : angle 1.10499 ( 24) hydrogen bonds : bond 0.04025 ( 843) hydrogen bonds : angle 3.73848 ( 2472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 385 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9063 (tp40) cc_final: 0.8701 (tp-100) REVERT: A 503 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8752 (tt) REVERT: C 423 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8714 (tm-30) REVERT: C 636 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8501 (tp30) REVERT: C 700 GLN cc_start: 0.8736 (mp10) cc_final: 0.8521 (mp10) REVERT: D 503 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8739 (tt) REVERT: D 600 GLU cc_start: 0.6638 (mp0) cc_final: 0.6213 (mm-30) REVERT: D 636 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8402 (tp30) REVERT: B 503 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8669 (tt) REVERT: E 21 PHE cc_start: 0.7028 (m-80) cc_final: 0.6667 (m-10) REVERT: E 56 LYS cc_start: 0.9116 (ptmt) cc_final: 0.8628 (ptpp) REVERT: E 68 ILE cc_start: 0.9379 (mt) cc_final: 0.9059 (pt) REVERT: F 14 LYS cc_start: 0.8133 (ptmt) cc_final: 0.7830 (ptpp) REVERT: F 34 TYR cc_start: 0.7515 (m-10) cc_final: 0.7221 (m-10) REVERT: F 56 LYS cc_start: 0.8992 (ptmt) cc_final: 0.8420 (ptpp) REVERT: F 68 ILE cc_start: 0.9394 (mt) cc_final: 0.9074 (pt) outliers start: 44 outliers final: 28 residues processed: 400 average time/residue: 0.1055 time to fit residues: 65.7597 Evaluate side-chains 373 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 342 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 682 MET Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 13 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 155 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 176 optimal weight: 0.0670 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 HIS D 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.199574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.135720 restraints weight = 21926.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.134699 restraints weight = 15685.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.135153 restraints weight = 12134.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135915 restraints weight = 10946.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135806 restraints weight = 10061.049| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 16404 Z= 0.105 Angle : 0.515 9.164 22248 Z= 0.276 Chirality : 0.038 0.156 2472 Planarity : 0.003 0.042 2724 Dihedral : 5.546 59.104 2511 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.64 % Allowed : 16.26 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.20), residues: 1914 helix: 2.54 (0.16), residues: 1036 sheet: 0.74 (0.72), residues: 64 loop : -1.73 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 701 TYR 0.012 0.001 TYR C 653 PHE 0.010 0.001 PHE B 659 TRP 0.010 0.001 TRP A 740 HIS 0.009 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00229 (16392) covalent geometry : angle 0.51285 (22224) SS BOND : bond 0.00237 ( 12) SS BOND : angle 1.48261 ( 24) hydrogen bonds : bond 0.03796 ( 843) hydrogen bonds : angle 3.72815 ( 2472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 379 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9184 (tp40) cc_final: 0.8813 (tp-100) REVERT: A 503 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8790 (tt) REVERT: A 571 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8675 (tppt) REVERT: C 423 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8726 (tm-30) REVERT: C 503 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8747 (tt) REVERT: D 503 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8777 (tt) REVERT: B 359 GLU cc_start: 0.4130 (tt0) cc_final: 0.3927 (tm-30) REVERT: B 503 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8754 (tt) REVERT: E 56 LYS cc_start: 0.9090 (ptmt) cc_final: 0.8580 (ptpp) REVERT: E 68 ILE cc_start: 0.9405 (mt) cc_final: 0.9044 (pt) REVERT: F 14 LYS cc_start: 0.8316 (ptmt) cc_final: 0.7940 (ptpp) REVERT: F 56 LYS cc_start: 0.9097 (ptmt) cc_final: 0.8441 (ptpp) REVERT: F 68 ILE cc_start: 0.9382 (mt) cc_final: 0.8975 (pt) outliers start: 46 outliers final: 29 residues processed: 401 average time/residue: 0.1056 time to fit residues: 66.0497 Evaluate side-chains 388 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 355 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 13 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 2 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 85 optimal weight: 0.0070 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 HIS D 628 ASN B 628 ASN B 687 ASN F 43 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.196618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131271 restraints weight = 22019.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130224 restraints weight = 15703.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130986 restraints weight = 11855.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131706 restraints weight = 10700.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.131574 restraints weight = 9193.780| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16404 Z= 0.136 Angle : 0.560 8.905 22248 Z= 0.296 Chirality : 0.039 0.167 2472 Planarity : 0.003 0.042 2724 Dihedral : 5.618 54.063 2511 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.51 % Allowed : 17.13 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1914 helix: 2.43 (0.16), residues: 1040 sheet: 0.71 (0.71), residues: 64 loop : -1.76 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 575 TYR 0.025 0.001 TYR E 74 PHE 0.017 0.001 PHE A 649 TRP 0.018 0.001 TRP A 697 HIS 0.010 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00315 (16392) covalent geometry : angle 0.55775 (22224) SS BOND : bond 0.00232 ( 12) SS BOND : angle 1.47070 ( 24) hydrogen bonds : bond 0.04466 ( 843) hydrogen bonds : angle 3.85909 ( 2472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 370 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9176 (tp40) cc_final: 0.8809 (tp-100) REVERT: A 571 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8641 (tppt) REVERT: C 423 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8684 (tm-30) REVERT: C 503 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8816 (tt) REVERT: C 649 PHE cc_start: 0.8023 (m-80) cc_final: 0.7757 (m-80) REVERT: D 636 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8516 (tp30) REVERT: B 359 GLU cc_start: 0.4320 (tt0) cc_final: 0.4086 (tm-30) REVERT: B 533 GLN cc_start: 0.8508 (mp10) cc_final: 0.8266 (mp10) REVERT: B 568 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8031 (mtm) REVERT: E 47 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8338 (mm-30) REVERT: E 56 LYS cc_start: 0.9181 (ptmt) cc_final: 0.8652 (ptpp) REVERT: E 68 ILE cc_start: 0.9389 (mt) cc_final: 0.9048 (pt) REVERT: F 14 LYS cc_start: 0.8444 (ptmt) cc_final: 0.8077 (ptpp) REVERT: F 56 LYS cc_start: 0.9157 (ptmt) cc_final: 0.8517 (ptpp) REVERT: F 68 ILE cc_start: 0.9356 (mt) cc_final: 0.9017 (pt) outliers start: 61 outliers final: 41 residues processed: 396 average time/residue: 0.1057 time to fit residues: 65.4068 Evaluate side-chains 392 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 349 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 682 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 13 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 97 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 0.1980 chunk 151 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 551 ASN D 289 HIS D 700 GLN B 289 HIS E 43 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.194163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129571 restraints weight = 21838.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127720 restraints weight = 15145.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128395 restraints weight = 12522.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128991 restraints weight = 10757.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129009 restraints weight = 9857.495| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 16404 Z= 0.203 Angle : 0.642 12.864 22248 Z= 0.329 Chirality : 0.041 0.155 2472 Planarity : 0.003 0.042 2724 Dihedral : 5.998 42.708 2511 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.39 % Allowed : 16.90 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1914 helix: 2.26 (0.16), residues: 1032 sheet: 0.74 (0.72), residues: 64 loop : -1.91 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 420 TYR 0.017 0.001 TYR E 74 PHE 0.012 0.001 PHE E 67 TRP 0.012 0.001 TRP A 697 HIS 0.004 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00478 (16392) covalent geometry : angle 0.64028 (22224) SS BOND : bond 0.00476 ( 12) SS BOND : angle 1.62888 ( 24) hydrogen bonds : bond 0.05473 ( 843) hydrogen bonds : angle 4.11524 ( 2472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 342 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9208 (tp40) cc_final: 0.8823 (tp-100) REVERT: A 571 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8731 (tppt) REVERT: C 423 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8689 (tm-30) REVERT: C 503 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8767 (tt) REVERT: C 575 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7108 (ttp80) REVERT: D 533 GLN cc_start: 0.8560 (mp10) cc_final: 0.8351 (mp10) REVERT: B 533 GLN cc_start: 0.8553 (mp10) cc_final: 0.8221 (mp10) REVERT: E 47 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8315 (mm-30) REVERT: E 56 LYS cc_start: 0.8829 (ptmt) cc_final: 0.8277 (ptpp) REVERT: E 68 ILE cc_start: 0.9397 (mt) cc_final: 0.9051 (pt) REVERT: F 14 LYS cc_start: 0.8512 (ptmt) cc_final: 0.8138 (ptpp) REVERT: F 17 ASP cc_start: 0.7203 (t0) cc_final: 0.6945 (t70) REVERT: F 43 ASN cc_start: 0.8749 (t0) cc_final: 0.8548 (t0) REVERT: F 56 LYS cc_start: 0.9174 (ptmt) cc_final: 0.8599 (ptpp) REVERT: F 68 ILE cc_start: 0.9357 (mt) cc_final: 0.9055 (pt) outliers start: 59 outliers final: 50 residues processed: 369 average time/residue: 0.1119 time to fit residues: 63.5776 Evaluate side-chains 382 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 330 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 682 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain E residue 15 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 14 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS C 289 HIS D 289 HIS E 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.186852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110462 restraints weight = 24138.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113862 restraints weight = 11947.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115786 restraints weight = 8432.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116776 restraints weight = 7141.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117187 restraints weight = 6617.396| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16404 Z= 0.139 Angle : 0.594 8.910 22248 Z= 0.308 Chirality : 0.040 0.155 2472 Planarity : 0.003 0.047 2724 Dihedral : 5.553 40.523 2511 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.64 % Allowed : 18.45 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.20), residues: 1914 helix: 2.39 (0.16), residues: 1032 sheet: 0.78 (0.73), residues: 64 loop : -1.86 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 701 TYR 0.009 0.001 TYR B 666 PHE 0.011 0.001 PHE A 436 TRP 0.011 0.001 TRP A 697 HIS 0.009 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00321 (16392) covalent geometry : angle 0.59277 (22224) SS BOND : bond 0.00300 ( 12) SS BOND : angle 1.45983 ( 24) hydrogen bonds : bond 0.04617 ( 843) hydrogen bonds : angle 3.92932 ( 2472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 351 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9436 (tp40) cc_final: 0.9016 (tp-100) REVERT: A 571 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8629 (tppt) REVERT: C 423 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8822 (tm-30) REVERT: C 503 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8839 (tt) REVERT: C 649 PHE cc_start: 0.8177 (m-80) cc_final: 0.7947 (m-80) REVERT: D 499 ARG cc_start: 0.8504 (tpp80) cc_final: 0.8155 (tpp-160) REVERT: D 636 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8523 (tp30) REVERT: B 499 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8246 (tpp-160) REVERT: B 533 GLN cc_start: 0.8742 (mp10) cc_final: 0.8485 (mp10) REVERT: E 5 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8170 (mm-30) REVERT: E 47 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8054 (mm-30) REVERT: E 68 ILE cc_start: 0.9481 (mt) cc_final: 0.9057 (pt) REVERT: E 72 GLU cc_start: 0.6442 (pm20) cc_final: 0.6171 (pm20) REVERT: F 14 LYS cc_start: 0.8242 (ptmt) cc_final: 0.7845 (ptpp) REVERT: F 43 ASN cc_start: 0.8953 (t0) cc_final: 0.8741 (t0) REVERT: F 56 LYS cc_start: 0.8888 (ptmt) cc_final: 0.8338 (ptpp) REVERT: F 68 ILE cc_start: 0.9403 (mt) cc_final: 0.9052 (pt) REVERT: F 72 GLU cc_start: 0.6772 (pp20) cc_final: 0.6492 (pp20) outliers start: 46 outliers final: 37 residues processed: 375 average time/residue: 0.1008 time to fit residues: 58.9158 Evaluate side-chains 373 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 335 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 682 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain F residue 13 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 31 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 65 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.185218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108281 restraints weight = 24353.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111856 restraints weight = 12176.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.113551 restraints weight = 8586.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114642 restraints weight = 7327.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114934 restraints weight = 6717.966| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16404 Z= 0.166 Angle : 0.619 8.681 22248 Z= 0.324 Chirality : 0.041 0.164 2472 Planarity : 0.003 0.043 2724 Dihedral : 5.737 47.106 2511 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.64 % Allowed : 19.14 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.20), residues: 1914 helix: 2.27 (0.16), residues: 1036 sheet: 0.73 (0.73), residues: 64 loop : -1.87 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 420 TYR 0.012 0.001 TYR E 74 PHE 0.020 0.001 PHE A 304 TRP 0.008 0.001 TRP D 740 HIS 0.010 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00392 (16392) covalent geometry : angle 0.61745 (22224) SS BOND : bond 0.00350 ( 12) SS BOND : angle 1.58648 ( 24) hydrogen bonds : bond 0.05018 ( 843) hydrogen bonds : angle 4.06079 ( 2472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 348 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9436 (tp40) cc_final: 0.9012 (tp-100) REVERT: C 503 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8861 (tt) REVERT: C 575 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7093 (ttp80) REVERT: D 499 ARG cc_start: 0.8585 (tpp80) cc_final: 0.8273 (tpp-160) REVERT: B 499 ARG cc_start: 0.8607 (tpp80) cc_final: 0.8328 (tpp-160) REVERT: B 533 GLN cc_start: 0.8766 (mp10) cc_final: 0.8451 (mp10) REVERT: E 5 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8200 (mm-30) REVERT: E 34 TYR cc_start: 0.8087 (m-10) cc_final: 0.7727 (m-10) REVERT: E 47 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7894 (mm-30) REVERT: E 68 ILE cc_start: 0.9491 (mt) cc_final: 0.9144 (pt) REVERT: F 14 LYS cc_start: 0.8179 (ptmt) cc_final: 0.7805 (ptpp) REVERT: F 43 ASN cc_start: 0.9061 (t0) cc_final: 0.8797 (t0) REVERT: F 56 LYS cc_start: 0.8906 (ptmt) cc_final: 0.8358 (ptpp) REVERT: F 68 ILE cc_start: 0.9392 (mt) cc_final: 0.9046 (pt) REVERT: F 72 GLU cc_start: 0.6649 (pp20) cc_final: 0.6342 (pp20) outliers start: 46 outliers final: 43 residues processed: 370 average time/residue: 0.1031 time to fit residues: 58.8104 Evaluate side-chains 386 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 341 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 682 MET Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 682 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain F residue 13 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 101 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 87 optimal weight: 30.0000 chunk 4 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 148 optimal weight: 0.6980 chunk 177 optimal weight: 0.2980 chunk 123 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.190472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122016 restraints weight = 23652.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120638 restraints weight = 12621.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120811 restraints weight = 10090.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121353 restraints weight = 9203.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121557 restraints weight = 8376.429| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 16404 Z= 0.114 Angle : 0.591 9.547 22248 Z= 0.310 Chirality : 0.040 0.180 2472 Planarity : 0.003 0.049 2724 Dihedral : 5.426 59.491 2511 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.90 % Allowed : 20.17 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.20), residues: 1914 helix: 2.36 (0.16), residues: 1036 sheet: 0.75 (0.73), residues: 64 loop : -1.83 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 499 TYR 0.011 0.001 TYR A 441 PHE 0.022 0.001 PHE A 304 TRP 0.009 0.001 TRP C 697 HIS 0.010 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00250 (16392) covalent geometry : angle 0.59045 (22224) SS BOND : bond 0.00288 ( 12) SS BOND : angle 1.20493 ( 24) hydrogen bonds : bond 0.03762 ( 843) hydrogen bonds : angle 3.87915 ( 2472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 370 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9417 (tp40) cc_final: 0.8964 (tp-100) REVERT: A 636 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8380 (tp30) REVERT: A 677 MET cc_start: 0.8728 (ttp) cc_final: 0.8523 (ttt) REVERT: C 503 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8821 (tt) REVERT: C 580 PHE cc_start: 0.8630 (t80) cc_final: 0.8354 (t80) REVERT: C 649 PHE cc_start: 0.8215 (m-80) cc_final: 0.7979 (m-80) REVERT: D 499 ARG cc_start: 0.8418 (tpp80) cc_final: 0.8207 (tmt-80) REVERT: D 600 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7484 (mp0) REVERT: B 499 ARG cc_start: 0.8539 (tpp80) cc_final: 0.8205 (tmt-80) REVERT: B 666 TYR cc_start: 0.9323 (t80) cc_final: 0.8923 (t80) REVERT: E 47 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8267 (mm-30) REVERT: E 68 ILE cc_start: 0.9479 (mt) cc_final: 0.9156 (pt) REVERT: F 14 LYS cc_start: 0.7939 (ptmt) cc_final: 0.7581 (ptpp) REVERT: F 43 ASN cc_start: 0.9114 (t0) cc_final: 0.8873 (t0) REVERT: F 56 LYS cc_start: 0.8692 (ptmt) cc_final: 0.8202 (ptpp) REVERT: F 68 ILE cc_start: 0.9372 (mt) cc_final: 0.9017 (pt) REVERT: F 72 GLU cc_start: 0.6746 (pp20) cc_final: 0.6511 (pp20) outliers start: 33 outliers final: 27 residues processed: 388 average time/residue: 0.1090 time to fit residues: 65.3252 Evaluate side-chains 382 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 354 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 682 MET Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 71 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 10.0000 chunk 92 optimal weight: 0.0070 chunk 41 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 HIS E 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.188608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111839 restraints weight = 24409.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115336 restraints weight = 12030.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117308 restraints weight = 8453.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118407 restraints weight = 7148.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118916 restraints weight = 6588.696| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16404 Z= 0.128 Angle : 0.604 8.707 22248 Z= 0.318 Chirality : 0.040 0.180 2472 Planarity : 0.003 0.054 2724 Dihedral : 5.376 57.012 2511 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.95 % Allowed : 20.23 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.20), residues: 1914 helix: 2.31 (0.16), residues: 1040 sheet: 0.74 (0.73), residues: 64 loop : -1.81 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 701 TYR 0.011 0.001 TYR C 584 PHE 0.022 0.001 PHE A 304 TRP 0.008 0.001 TRP C 697 HIS 0.007 0.001 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00295 (16392) covalent geometry : angle 0.60307 (22224) SS BOND : bond 0.00266 ( 12) SS BOND : angle 1.25051 ( 24) hydrogen bonds : bond 0.04226 ( 843) hydrogen bonds : angle 3.96957 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2713.56 seconds wall clock time: 47 minutes 25.92 seconds (2845.92 seconds total)