Starting phenix.real_space_refine on Fri Jul 3 20:39:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l2m_23133/07_2026/7l2m_23133.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2m_23133/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7l2m_23133/07_2026/7l2m_23133.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l2m_23133/07_2026/7l2m_23133.cif" model { file = "/net/cci-nas-00/data/ceres_data/7l2m_23133/07_2026/7l2m_23133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2m_23133/07_2026/7l2m_23133.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l2m_23133/07_2026/7l2m_23133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2m_23133/07_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-6108/lib/python3.11/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: 3.68, per 1000 atoms: 0.23 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: 1.35 Conformation dependent library (CDL) restraints added in 476.7 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: 0.43 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: 2.30 Time building geometry restraints manager: 1.71 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: 9012 17.84 - 35.67: 480 35.67 - 53.51: 89 53.51 - 71.34: 13 71.34 - 89.18: 10 Dihedral angle restraints: 9604 sinusoidal: 3894 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 9601 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.070 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 11.749 89.181 5900 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/Z covalent geometry : bond 0.00704 / 0.32 (16392) covalent geometry : angle 0.77824 / 0.41 (22224) SS BOND : bond 0.00433 / 0.31 ( 12) SS BOND : angle 1.67862 / 1.15 ( 24) hydrogen bonds : bond 0.16298 / 11.15 ( 843) hydrogen bonds : angle 6.24115 / 4.51 ( 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 : 0.359 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: 0.1162 time to fit residues: 94.7245 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 : 0.398 ------------------------------------------------------------------------------- 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... 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 551 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.191077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.129739 restraints weight = 22877.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124739 restraints weight = 17329.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125923 restraints weight = 16539.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126425 restraints weight = 11832.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126692 restraints weight = 10798.970| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16404 Z= 0.159 Angle : 0.598 9.590 22248 Z= 0.313 Chirality : 0.040 0.156 2472 Planarity : 0.003 0.053 2724 Dihedral : 6.472 59.433 2178 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.24 % Allowed : 11.90 % Favored : 85.86 % 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: 0.92 (0.20), residues: 1914 helix: 2.32 (0.16), residues: 1048 sheet: 0.36 (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 0.013 0.001 TYR A 511 PHE 0.015 0.001 PHE B 712 TRP 0.016 0.001 TRP A 740 HIS 0.008 0.001 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (16392) covalent geometry : angle 0.59736 / 0.31 (22224) SS BOND : bond 0.00567 / 0.28 ( 12) SS BOND : angle 0.93452 / 0.71 ( 24) hydrogen bonds : bond 0.05430 / 3.68 ( 843) hydrogen bonds : angle 4.01323 / 2.87 ( 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 444 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 405 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.7859 (m-30) cc_final: 0.7646 (m-30) REVERT: A 421 LEU cc_start: 0.9377 (tp) cc_final: 0.9173 (tp) REVERT: A 423 GLN cc_start: 0.9091 (tp40) cc_final: 0.8731 (tp-100) REVERT: A 560 GLN cc_start: 0.8093 (tp40) cc_final: 0.7393 (mm-40) REVERT: A 561 GLN cc_start: 0.8188 (mp10) cc_final: 0.7982 (mp10) REVERT: A 571 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8490 (mptt) REVERT: A 576 ASP cc_start: 0.8683 (t0) cc_final: 0.8453 (m-30) REVERT: C 300 ASP cc_start: 0.7788 (m-30) cc_final: 0.7500 (p0) REVERT: C 423 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8710 (tm-30) REVERT: C 636 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8355 (tp30) REVERT: D 561 GLN cc_start: 0.8378 (mp10) cc_final: 0.8083 (mp10) REVERT: D 576 ASP cc_start: 0.8802 (t0) cc_final: 0.8044 (m-30) REVERT: B 572 MET cc_start: 0.8418 (mtm) cc_final: 0.8205 (mtm) REVERT: B 576 ASP cc_start: 0.8755 (t0) cc_final: 0.8140 (m-30) REVERT: B 599 ILE cc_start: 0.8725 (tt) cc_final: 0.7900 (tt) REVERT: E 34 TYR cc_start: 0.7067 (m-80) cc_final: 0.6703 (m-80) REVERT: E 56 LYS cc_start: 0.9065 (ptmt) cc_final: 0.8491 (ptpp) REVERT: E 68 ILE cc_start: 0.9430 (mt) cc_final: 0.9081 (pt) REVERT: E 72 GLU cc_start: 0.6952 (pm20) cc_final: 0.6680 (pm20) REVERT: F 14 LYS cc_start: 0.8240 (ptmt) cc_final: 0.7891 (ptpp) REVERT: F 47 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8561 (mm-30) REVERT: F 56 LYS cc_start: 0.8935 (ptmt) cc_final: 0.8340 (ptpp) REVERT: F 68 ILE cc_start: 0.9466 (mt) cc_final: 0.9132 (pt) outliers start: 39 outliers final: 24 residues processed: 423 average time/residue: 0.1044 time to fit residues: 67.6569 Evaluate side-chains 375 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 351 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 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 61 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 69 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4173 r_free = 0.4173 target = 0.194666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130514 restraints weight = 22306.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.128956 restraints weight = 15249.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129785 restraints weight = 12054.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130369 restraints weight = 10578.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130311 restraints weight = 9745.404| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16404 Z= 0.142 Angle : 0.565 9.560 22248 Z= 0.298 Chirality : 0.039 0.154 2472 Planarity : 0.003 0.050 2724 Dihedral : 5.729 56.446 2168 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.22 % Allowed : 13.22 % Favored : 83.56 % 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: 1.05 (0.20), residues: 1914 helix: 2.55 (0.16), residues: 1024 sheet: 0.45 (0.69), residues: 64 loop : -1.86 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 701 TYR 0.015 0.001 TYR A 653 PHE 0.012 0.001 PHE A 712 TRP 0.022 0.001 TRP A 740 HIS 0.007 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (16392) covalent geometry : angle 0.56431 / 0.30 (22224) SS BOND : bond 0.00253 / 0.17 ( 12) SS BOND : angle 0.85223 / 0.61 ( 24) hydrogen bonds : bond 0.04963 / 3.34 ( 843) hydrogen bonds : angle 3.85943 / 2.76 ( 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 431 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 375 time to evaluate : 0.477 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: 0.9048 (tp40) cc_final: 0.8697 (tp-100) REVERT: A 503 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8762 (tt) REVERT: A 576 ASP cc_start: 0.8486 (t0) cc_final: 0.8205 (m-30) REVERT: A 600 GLU cc_start: 0.6907 (mp0) cc_final: 0.6612 (mm-30) REVERT: C 423 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8694 (tm-30) REVERT: C 503 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8690 (tt) REVERT: D 503 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8642 (tt) REVERT: D 561 GLN cc_start: 0.8365 (mp10) cc_final: 0.8023 (mp10) REVERT: D 636 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8394 (tp30) REVERT: B 503 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8652 (tt) REVERT: B 576 ASP cc_start: 0.8654 (t0) cc_final: 0.8405 (t70) REVERT: E 21 PHE cc_start: 0.6799 (m-80) cc_final: 0.6295 (m-10) REVERT: E 34 TYR cc_start: 0.7188 (m-80) cc_final: 0.6756 (m-80) REVERT: E 56 LYS cc_start: 0.9126 (ptmt) cc_final: 0.8558 (ptpp) REVERT: E 68 ILE cc_start: 0.9405 (mt) cc_final: 0.9101 (pt) REVERT: F 14 LYS cc_start: 0.8225 (ptmt) cc_final: 0.7870 (ptpp) REVERT: F 47 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8561 (mm-30) REVERT: F 56 LYS cc_start: 0.9047 (ptmt) cc_final: 0.8528 (ptpp) REVERT: F 68 ILE cc_start: 0.9388 (mt) cc_final: 0.9086 (pt) outliers start: 56 outliers final: 34 residues processed: 396 average time/residue: 0.1091 time to fit residues: 66.6309 Evaluate side-chains 380 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 342 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 433 ILE 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 641 THR 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 503 LEU Chi-restraints excluded: chain C residue 508 VAL 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 447 ILE 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 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 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 B residue 650 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 61 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 9 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 144 optimal weight: 0.0870 chunk 114 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 165 optimal weight: 0.0270 chunk 75 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 419 ASN D 628 ASN D 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.197536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132935 restraints weight = 22225.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.132609 restraints weight = 15544.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133405 restraints weight = 12374.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.133884 restraints weight = 9966.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133830 restraints weight = 8825.192| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 16404 Z= 0.108 Angle : 0.522 9.441 22248 Z= 0.277 Chirality : 0.038 0.164 2472 Planarity : 0.003 0.048 2724 Dihedral : 5.263 54.525 2167 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.47 % Allowed : 15.86 % Favored : 81.67 % 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: 1.11 (0.20), residues: 1914 helix: 2.39 (0.16), residues: 1060 sheet: 0.62 (0.71), residues: 64 loop : -1.72 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 409 TYR 0.013 0.001 TYR C 653 PHE 0.011 0.001 PHE A 649 TRP 0.025 0.001 TRP B 740 HIS 0.008 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (16392) covalent geometry : angle 0.52182 / 0.28 (22224) SS BOND : bond 0.00190 / 0.13 ( 12) SS BOND : angle 0.67053 / 0.47 ( 24) hydrogen bonds : bond 0.04014 / 2.70 ( 843) hydrogen bonds : angle 3.70962 / 2.65 ( 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 431 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 388 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9162 (tp40) cc_final: 0.8802 (tp-100) REVERT: A 503 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8743 (tt) REVERT: C 423 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8695 (tm-30) REVERT: C 503 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8726 (tt) REVERT: C 636 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8478 (tp30) REVERT: D 503 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8740 (tt) REVERT: D 600 GLU cc_start: 0.6570 (mp0) cc_final: 0.6112 (mm-30) REVERT: B 503 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8649 (tt) REVERT: E 34 TYR cc_start: 0.7234 (m-80) cc_final: 0.6914 (m-80) REVERT: E 56 LYS cc_start: 0.9128 (ptmt) cc_final: 0.8650 (ptpp) REVERT: E 68 ILE cc_start: 0.9399 (mt) cc_final: 0.9084 (pt) REVERT: F 14 LYS cc_start: 0.8170 (ptmt) cc_final: 0.7826 (ptpp) REVERT: F 34 TYR cc_start: 0.7506 (m-10) cc_final: 0.7242 (m-10) REVERT: F 56 LYS cc_start: 0.9009 (ptmt) cc_final: 0.8430 (ptpp) REVERT: F 68 ILE cc_start: 0.9407 (mt) cc_final: 0.9083 (pt) outliers start: 43 outliers final: 27 residues processed: 403 average time/residue: 0.1046 time to fit residues: 66.1737 Evaluate side-chains 375 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 344 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ILE 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 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 510 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 641 THR 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 641 THR Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain E residue 13 LYS 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: 2.9990 chunk 58 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 289 HIS B 628 ASN B 687 ASN F 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.194622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129491 restraints weight = 22209.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128351 restraints weight = 15697.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.129216 restraints weight = 12122.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129665 restraints weight = 11136.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.129593 restraints weight = 9528.724| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16404 Z= 0.137 Angle : 0.552 9.168 22248 Z= 0.292 Chirality : 0.039 0.190 2472 Planarity : 0.003 0.048 2724 Dihedral : 5.362 59.567 2167 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.33 % Allowed : 16.15 % Favored : 80.52 % 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: 1.02 (0.20), residues: 1914 helix: 2.31 (0.16), residues: 1060 sheet: 0.64 (0.71), residues: 64 loop : -1.74 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 420 TYR 0.011 0.001 TYR C 653 PHE 0.009 0.001 PHE B 659 TRP 0.015 0.001 TRP A 697 HIS 0.009 0.001 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (16392) covalent geometry : angle 0.55030 / 0.29 (22224) SS BOND : bond 0.00457 / 0.34 ( 12) SS BOND : angle 1.33192 / 0.68 ( 24) hydrogen bonds : bond 0.04512 / 3.03 ( 843) hydrogen bonds : angle 3.87284 / 2.74 ( 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 416 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 358 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9166 (tp40) cc_final: 0.8799 (tp-100) REVERT: C 423 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8675 (tm-30) REVERT: C 503 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8761 (tt) REVERT: D 600 GLU cc_start: 0.6635 (mp0) cc_final: 0.6134 (mm-30) REVERT: B 503 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8756 (tt) REVERT: E 34 TYR cc_start: 0.7265 (m-80) cc_final: 0.6875 (m-80) REVERT: E 56 LYS cc_start: 0.9140 (ptmt) cc_final: 0.8633 (ptpp) REVERT: E 68 ILE cc_start: 0.9401 (mt) cc_final: 0.9095 (pt) REVERT: F 14 LYS cc_start: 0.8294 (ptmt) cc_final: 0.7932 (ptpp) REVERT: F 34 TYR cc_start: 0.7519 (m-10) cc_final: 0.7098 (m-10) REVERT: F 56 LYS cc_start: 0.9179 (ptmt) cc_final: 0.8603 (ptpp) REVERT: F 68 ILE cc_start: 0.9392 (mt) cc_final: 0.9091 (pt) outliers start: 58 outliers final: 40 residues processed: 381 average time/residue: 0.1061 time to fit residues: 63.2978 Evaluate side-chains 364 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 322 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 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 578 CYS Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 641 THR 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 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 D residue 737 ASP 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 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 B residue 685 THR Chi-restraints excluded: chain E residue 13 LYS 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: 9.9990 chunk 163 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 50 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 289 HIS D 700 GLN E 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.187060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117643 restraints weight = 24079.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115440 restraints weight = 14633.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116084 restraints weight = 11078.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116539 restraints weight = 9827.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116948 restraints weight = 8543.090| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16404 Z= 0.121 Angle : 0.560 12.347 22248 Z= 0.291 Chirality : 0.039 0.161 2472 Planarity : 0.003 0.047 2724 Dihedral : 5.230 59.356 2167 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.87 % Allowed : 17.47 % Favored : 79.66 % 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: 1.03 (0.20), residues: 1914 helix: 2.32 (0.16), residues: 1060 sheet: 0.67 (0.72), residues: 64 loop : -1.74 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 420 TYR 0.011 0.001 TYR C 653 PHE 0.011 0.001 PHE A 659 TRP 0.011 0.001 TRP B 740 HIS 0.009 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (16392) covalent geometry : angle 0.55790 / 0.29 (22224) SS BOND : bond 0.00170 / 0.12 ( 12) SS BOND : angle 1.46707 / 0.90 ( 24) hydrogen bonds : bond 0.04213 / 2.83 ( 843) hydrogen bonds : angle 3.83916 / 2.73 ( 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 403 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 353 time to evaluate : 0.622 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: 0.9409 (tp40) cc_final: 0.8995 (tp-100) REVERT: C 423 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8836 (tm-30) REVERT: C 503 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8868 (tt) REVERT: E 13 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8729 (ptpp) REVERT: E 34 TYR cc_start: 0.7095 (m-80) cc_final: 0.6642 (m-80) REVERT: E 47 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7968 (mm-30) REVERT: E 56 LYS cc_start: 0.8607 (ptmt) cc_final: 0.8121 (ptpp) REVERT: E 68 ILE cc_start: 0.9455 (mt) cc_final: 0.9065 (pt) REVERT: F 14 LYS cc_start: 0.7924 (ptmt) cc_final: 0.7591 (ptpp) REVERT: F 17 ASP cc_start: 0.7463 (t0) cc_final: 0.6952 (t0) REVERT: F 56 LYS cc_start: 0.8775 (ptmt) cc_final: 0.8188 (ptpp) REVERT: F 68 ILE cc_start: 0.9428 (mt) cc_final: 0.9064 (pt) outliers start: 50 outliers final: 38 residues processed: 371 average time/residue: 0.1018 time to fit residues: 59.3214 Evaluate side-chains 378 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 338 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 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 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 592 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 641 THR 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 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 437 ASN 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 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 13 LYS 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: 7.9990 chunk 29 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 551 ASN D 289 HIS B 289 HIS F 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.193358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128033 restraints weight = 21776.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.126970 restraints weight = 15018.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.127512 restraints weight = 11674.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128189 restraints weight = 10618.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128170 restraints weight = 9391.028| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16404 Z= 0.185 Angle : 0.622 12.766 22248 Z= 0.321 Chirality : 0.041 0.153 2472 Planarity : 0.003 0.048 2724 Dihedral : 5.248 51.489 2167 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.45 % Allowed : 17.76 % Favored : 78.79 % 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: 2.13 (0.16), residues: 1064 sheet: 0.61 (0.71), residues: 64 loop : -1.77 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 420 TYR 0.015 0.001 TYR C 584 PHE 0.016 0.001 PHE A 649 TRP 0.010 0.001 TRP B 740 HIS 0.004 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (16392) covalent geometry : angle 0.62002 / 0.32 (22224) SS BOND : bond 0.00263 / 0.19 ( 12) SS BOND : angle 1.69909 / 1.20 ( 24) hydrogen bonds : bond 0.05282 / 3.56 ( 843) hydrogen bonds : angle 4.09215 / 2.90 ( 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 399 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 339 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9209 (tp40) cc_final: 0.8817 (tp-100) REVERT: C 423 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8677 (tm-30) REVERT: C 575 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7248 (ttp80) REVERT: D 393 ASN cc_start: 0.8998 (m-40) cc_final: 0.8566 (m110) REVERT: D 401 TYR cc_start: 0.7305 (m-80) cc_final: 0.6637 (m-80) REVERT: D 636 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8249 (mm-30) REVERT: B 576 ASP cc_start: 0.8505 (t0) cc_final: 0.8275 (t70) REVERT: E 47 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8291 (mm-30) REVERT: E 68 ILE cc_start: 0.9399 (mt) cc_final: 0.9068 (pt) REVERT: E 72 GLU cc_start: 0.6895 (pm20) cc_final: 0.6638 (pm20) REVERT: F 14 LYS cc_start: 0.8529 (ptmt) cc_final: 0.8152 (ptpp) REVERT: F 56 LYS cc_start: 0.9193 (ptmt) cc_final: 0.8624 (ptpp) REVERT: F 68 ILE cc_start: 0.9369 (mt) cc_final: 0.9090 (pt) REVERT: F 72 GLU cc_start: 0.6536 (pp20) cc_final: 0.6301 (pp20) outliers start: 60 outliers final: 53 residues processed: 364 average time/residue: 0.1015 time to fit residues: 57.2848 Evaluate side-chains 382 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 328 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 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 697 TRP 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 480 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 596 VAL Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 641 THR 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 480 LEU 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 599 ILE 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 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 2 CYS Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 43 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 14 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 184 optimal weight: 0.6980 chunk 180 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 123 optimal weight: 0.0970 chunk 158 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 289 HIS D 289 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.188443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116828 restraints weight = 23482.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117498 restraints weight = 13444.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118135 restraints weight = 9228.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.119127 restraints weight = 8340.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119167 restraints weight = 7503.047| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4273 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= 0.111 Angle : 0.581 13.759 22248 Z= 0.300 Chirality : 0.039 0.157 2472 Planarity : 0.003 0.057 2724 Dihedral : 5.115 54.223 2167 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.61 % Allowed : 19.83 % Favored : 78.56 % 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: 1.09 (0.20), residues: 1914 helix: 2.49 (0.16), residues: 1036 sheet: 0.70 (0.73), residues: 64 loop : -1.77 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 499 TYR 0.016 0.001 TYR B 666 PHE 0.012 0.001 PHE D 659 TRP 0.009 0.001 TRP B 740 HIS 0.009 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (16392) covalent geometry : angle 0.57914 / 0.30 (22224) SS BOND : bond 0.00332 / 0.18 ( 12) SS BOND : angle 1.47970 / 1.06 ( 24) hydrogen bonds : bond 0.03995 / 2.68 ( 843) hydrogen bonds : angle 3.81793 / 2.71 ( 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 385 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 357 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9406 (tp40) cc_final: 0.8980 (tp-100) REVERT: C 423 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8819 (tm-30) REVERT: C 575 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7132 (ttp80) REVERT: D 677 MET cc_start: 0.8616 (ttp) cc_final: 0.8395 (ttt) REVERT: B 533 GLN cc_start: 0.8728 (mp10) cc_final: 0.8518 (mp10) REVERT: B 568 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7962 (mtm) REVERT: E 13 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8746 (ptpp) REVERT: E 34 TYR cc_start: 0.6769 (m-80) cc_final: 0.6517 (m-80) REVERT: E 47 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8013 (mm-30) REVERT: E 56 LYS cc_start: 0.8208 (ptmt) cc_final: 0.7782 (ptpp) REVERT: E 68 ILE cc_start: 0.9469 (mt) cc_final: 0.9054 (pt) REVERT: F 14 LYS cc_start: 0.8069 (ptmt) cc_final: 0.7674 (ptpp) REVERT: F 56 LYS cc_start: 0.8746 (ptmt) cc_final: 0.8211 (ptpp) REVERT: F 68 ILE cc_start: 0.9441 (mt) cc_final: 0.9092 (pt) outliers start: 28 outliers final: 20 residues processed: 372 average time/residue: 0.1077 time to fit residues: 61.9351 Evaluate side-chains 360 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 337 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 460 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 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 510 SER Chi-restraints excluded: chain C residue 575 ARG 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 592 SER Chi-restraints excluded: chain B residue 339 LEU 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 592 SER Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 21 PHE 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: 9.9990 chunk 109 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 70 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 HIS D 289 HIS E 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.186158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110006 restraints weight = 23697.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113688 restraints weight = 11725.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115388 restraints weight = 8178.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116329 restraints weight = 6946.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116648 restraints weight = 6366.772| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16404 Z= 0.151 Angle : 0.606 11.821 22248 Z= 0.315 Chirality : 0.040 0.165 2472 Planarity : 0.004 0.051 2724 Dihedral : 5.133 47.779 2167 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.13 % Allowed : 19.60 % Favored : 78.28 % 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: 2.32 (0.16), residues: 1040 sheet: 0.66 (0.72), residues: 64 loop : -1.81 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 499 TYR 0.015 0.001 TYR B 666 PHE 0.018 0.001 PHE A 304 TRP 0.012 0.001 TRP D 740 HIS 0.010 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (16392) covalent geometry : angle 0.60478 / 0.31 (22224) SS BOND : bond 0.00517 / 0.20 ( 12) SS BOND : angle 1.47609 / 1.09 ( 24) hydrogen bonds : bond 0.04751 / 3.20 ( 843) hydrogen bonds : angle 4.00494 / 2.83 ( 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 391 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 354 time to evaluate : 0.397 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: 0.9430 (tp40) cc_final: 0.9005 (tp-100) REVERT: C 423 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8822 (tm-30) REVERT: C 533 GLN cc_start: 0.8742 (mp10) cc_final: 0.8493 (mp10) REVERT: C 575 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7165 (ttp80) REVERT: B 393 ASN cc_start: 0.8742 (m-40) cc_final: 0.8437 (m-40) REVERT: B 568 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7867 (mtm) REVERT: E 13 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8780 (ptpp) REVERT: E 17 ASP cc_start: 0.7204 (t0) cc_final: 0.6921 (t0) REVERT: E 21 PHE cc_start: 0.6922 (m-80) cc_final: 0.6484 (m-80) REVERT: E 34 TYR cc_start: 0.6929 (m-80) cc_final: 0.6662 (m-80) REVERT: E 47 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8062 (mm-30) REVERT: E 68 ILE cc_start: 0.9479 (mt) cc_final: 0.9050 (pt) REVERT: F 14 LYS cc_start: 0.8129 (ptmt) cc_final: 0.7768 (ptpp) REVERT: F 56 LYS cc_start: 0.8883 (ptmt) cc_final: 0.8248 (ptpp) REVERT: F 61 LEU cc_start: 0.7629 (mp) cc_final: 0.7148 (mt) REVERT: F 68 ILE cc_start: 0.9456 (mt) cc_final: 0.9101 (pt) REVERT: F 72 GLU cc_start: 0.6538 (pp20) cc_final: 0.6261 (pp20) outliers start: 37 outliers final: 30 residues processed: 371 average time/residue: 0.1123 time to fit residues: 64.4010 Evaluate side-chains 375 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 342 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 592 SER Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 650 THR 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 510 SER Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 599 ILE 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 592 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain B residue 339 LEU 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 592 SER Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain F residue 21 PHE 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: 0.9980 chunk 113 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 chunk 4 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 498 GLN E 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.185039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108587 restraints weight = 24378.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112267 restraints weight = 12056.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113976 restraints weight = 8410.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115113 restraints weight = 7156.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115397 restraints weight = 6544.735| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16404 Z= 0.166 Angle : 0.636 12.690 22248 Z= 0.329 Chirality : 0.040 0.184 2472 Planarity : 0.004 0.050 2724 Dihedral : 5.175 47.231 2167 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.36 % Allowed : 19.66 % Favored : 77.99 % 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: 2.24 (0.16), residues: 1036 sheet: 0.66 (0.72), residues: 64 loop : -1.90 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 499 TYR 0.018 0.001 TYR B 666 PHE 0.026 0.001 PHE A 304 TRP 0.010 0.001 TRP D 740 HIS 0.010 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (16392) covalent geometry : angle 0.63351 / 0.33 (22224) SS BOND : bond 0.00235 / 0.14 ( 12) SS BOND : angle 1.68838 / 0.97 ( 24) hydrogen bonds : bond 0.04922 / 3.32 ( 843) hydrogen bonds : angle 4.07597 / 2.87 ( 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 393 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 352 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9423 (tp40) cc_final: 0.8984 (tp-100) REVERT: A 562 MET cc_start: 0.7495 (mtt) cc_final: 0.7006 (mtt) REVERT: A 644 MET cc_start: 0.8395 (ptp) cc_final: 0.8187 (ptp) REVERT: A 700 GLN cc_start: 0.9244 (mm-40) cc_final: 0.9036 (mm-40) REVERT: C 423 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8833 (tm-30) REVERT: C 575 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7178 (ttp80) REVERT: D 684 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8133 (tm-30) REVERT: B 393 ASN cc_start: 0.8792 (m-40) cc_final: 0.8436 (m-40) REVERT: B 499 ARG cc_start: 0.8381 (tpt90) cc_final: 0.8129 (tmt-80) REVERT: B 568 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7877 (mtm) REVERT: E 17 ASP cc_start: 0.7069 (t0) cc_final: 0.6768 (t0) REVERT: E 21 PHE cc_start: 0.7005 (m-80) cc_final: 0.6699 (m-80) REVERT: E 47 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8156 (mm-30) REVERT: E 68 ILE cc_start: 0.9491 (mt) cc_final: 0.9144 (pt) REVERT: F 14 LYS cc_start: 0.8146 (ptmt) cc_final: 0.7776 (ptpp) REVERT: F 61 LEU cc_start: 0.7013 (mp) cc_final: 0.6679 (mt) REVERT: F 68 ILE cc_start: 0.9453 (mt) cc_final: 0.9101 (pt) REVERT: F 72 GLU cc_start: 0.6504 (pp20) cc_final: 0.6231 (pp20) outliers start: 41 outliers final: 35 residues processed: 371 average time/residue: 0.1082 time to fit residues: 62.1339 Evaluate side-chains 384 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 347 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 650 THR 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 510 SER Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 599 ILE 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 498 GLN Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 437 ASN 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 568 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 43 ASN 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: 0.4980 chunk 41 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 110 optimal weight: 0.4980 chunk 133 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.185041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108663 restraints weight = 24272.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112259 restraints weight = 12160.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113921 restraints weight = 8559.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115329 restraints weight = 7305.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115445 restraints weight = 6610.197| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 16404 Z= 0.202 Angle : 0.902 59.200 22248 Z= 0.514 Chirality : 0.051 1.424 2472 Planarity : 0.005 0.140 2724 Dihedral : 5.181 47.285 2167 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.13 % Allowed : 19.77 % Favored : 78.10 % Cbeta Deviations : 0.11 % 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: 0.81 (0.20), residues: 1914 helix: 2.25 (0.16), residues: 1036 sheet: 0.67 (0.72), residues: 64 loop : -1.90 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG C 499 TYR 0.020 0.001 TYR E 22 PHE 0.030 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/Z covalent geometry : bond 0.00453 / 0.20 (16392) covalent geometry : angle 0.89939 / 0.51 (22224) SS BOND : bond 0.00550 / 0.32 ( 12) SS BOND : angle 2.31762 / 1.87 ( 24) hydrogen bonds : bond 0.04956 / 3.35 ( 843) hydrogen bonds : angle 4.08010 / 2.87 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2650.24 seconds wall clock time: 46 minutes 33.07 seconds (2793.07 seconds total)