Starting phenix.real_space_refine on Fri Jul 3 16:05:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l2n_23134/07_2026/7l2n_23134.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2n_23134/07_2026/7l2n_23134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l2n_23134/07_2026/7l2n_23134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2n_23134/07_2026/7l2n_23134.map" model { file = "/net/cci-nas-00/data/ceres_data/7l2n_23134/07_2026/7l2n_23134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2n_23134/07_2026/7l2n_23134.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7l2n_23134/07_2026/7l2n_23134.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l2n_23134/07_2026/7l2n_23134.cif" } resolution = 3.09 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 9696 2.51 5 N 2328 2.21 5 O 2608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 14724 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3635 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 433} Chain breaks: 1 Chain: "C" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3635 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 433} Chain breaks: 1 Chain: "D" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3635 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 433} Chain breaks: 1 Chain: "B" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3635 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 433} Chain breaks: 1 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 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: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.59, per 1000 atoms: 0.24 Number of scatterers: 14724 At special positions: 0 Unit cell: (123.84, 122.808, 100.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2608 8.00 N 2328 7.00 C 9696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 779.5 milliseconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 68.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 408 through 413 removed outlier: 4.199A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 429 through 454 Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 557 removed outlier: 3.715A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A 553 " --> pdb=" O TRP A 549 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 599 removed outlier: 4.564A pdb=" N ALA A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.855A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 673 through 712 removed outlier: 5.592A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 408 through 413 removed outlier: 4.143A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.546A pdb=" N PHE C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 552 removed outlier: 3.687A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 550 " --> pdb=" O ALA C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.682A pdb=" N THR C 556 " --> pdb=" O MET C 552 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 552 through 557' Processing helix chain 'C' and resid 563 through 599 removed outlier: 3.969A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 removed outlier: 3.874A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 673 through 712 removed outlier: 5.621A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 294 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 408 through 413 removed outlier: 4.167A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.721A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 557 removed outlier: 4.198A pdb=" N TYR D 555 " --> pdb=" O ASN D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 576 Processing helix chain 'D' and resid 576 through 599 Processing helix chain 'D' and resid 629 through 642 removed outlier: 3.824A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 673 through 712 removed outlier: 5.609A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 408 through 413 removed outlier: 3.998A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.544A pdb=" N PHE B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 552 removed outlier: 3.849A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.563A pdb=" N THR B 556 " --> pdb=" O MET B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 599 removed outlier: 3.873A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.796A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 Processing helix chain 'B' and resid 673 through 712 removed outlier: 5.482A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 373 removed outlier: 6.677A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 368 through 373 removed outlier: 6.536A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.622A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 368 through 373 removed outlier: 6.711A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) 911 hydrogen bonds defined for protein. 2673 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: 2.39 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2268 1.31 - 1.43: 4284 1.43 - 1.56: 8368 1.56 - 1.69: 20 1.69 - 1.81: 152 Bond restraints: 15092 Sorted by residual: bond pdb=" CAM 6EU D 901 " pdb=" OAC 6EU D 901 " ideal model delta sigma weight residual 1.422 1.203 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CAM 6EU B 901 " pdb=" OAC 6EU B 901 " ideal model delta sigma weight residual 1.422 1.204 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CAM 6EU C 901 " pdb=" OAC 6EU C 901 " ideal model delta sigma weight residual 1.422 1.204 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CAM 6EU A 901 " pdb=" OAC 6EU A 901 " ideal model delta sigma weight residual 1.422 1.204 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CAV 6EU D 901 " pdb=" CBB 6EU D 901 " ideal model delta sigma weight residual 1.330 1.516 -0.186 2.00e-02 2.50e+03 8.67e+01 ... (remaining 15087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 20182 2.89 - 5.78: 226 5.78 - 8.67: 28 8.67 - 11.56: 16 11.56 - 14.45: 8 Bond angle restraints: 20460 Sorted by residual: angle pdb=" CAN 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" CAO 6EU C 901 " ideal model delta sigma weight residual 115.38 129.83 -14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" CAN 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAO 6EU B 901 " ideal model delta sigma weight residual 115.38 129.82 -14.44 3.00e+00 1.11e-01 2.32e+01 angle pdb=" CAN 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAO 6EU A 901 " ideal model delta sigma weight residual 115.38 129.72 -14.34 3.00e+00 1.11e-01 2.28e+01 angle pdb=" CAN 6EU D 901 " pdb=" CAJ 6EU D 901 " pdb=" CAO 6EU D 901 " ideal model delta sigma weight residual 115.38 129.68 -14.30 3.00e+00 1.11e-01 2.27e+01 angle pdb=" CAN 6EU D 901 " pdb=" CAJ 6EU D 901 " pdb=" OAA 6EU D 901 " ideal model delta sigma weight residual 110.99 96.80 14.19 3.00e+00 1.11e-01 2.24e+01 ... (remaining 20455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 8267 16.19 - 32.37: 449 32.37 - 48.56: 76 48.56 - 64.74: 14 64.74 - 80.93: 6 Dihedral angle restraints: 8812 sinusoidal: 3548 harmonic: 5264 Sorted by residual: dihedral pdb=" CA LEU C 647 " pdb=" C LEU C 647 " pdb=" N GLU C 648 " pdb=" CA GLU C 648 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LEU A 647 " pdb=" C LEU A 647 " pdb=" N GLU A 648 " pdb=" CA GLU A 648 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LEU B 647 " pdb=" C LEU B 647 " pdb=" N GLU B 648 " pdb=" CA GLU B 648 " ideal model delta harmonic sigma weight residual 180.00 156.66 23.34 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 8809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2280 0.137 - 0.273: 8 0.273 - 0.410: 4 0.410 - 0.546: 8 0.546 - 0.683: 4 Chirality restraints: 2304 Sorted by residual: chirality pdb=" CAJ 6EU B 901 " pdb=" CAK 6EU B 901 " pdb=" CAN 6EU B 901 " pdb=" CAO 6EU B 901 " both_signs ideal model delta sigma weight residual False 2.66 1.97 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CAJ 6EU D 901 " pdb=" CAK 6EU D 901 " pdb=" CAN 6EU D 901 " pdb=" CAO 6EU D 901 " both_signs ideal model delta sigma weight residual False 2.66 1.98 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CAJ 6EU C 901 " pdb=" CAK 6EU C 901 " pdb=" CAN 6EU C 901 " pdb=" CAO 6EU C 901 " both_signs ideal model delta sigma weight residual False 2.66 1.99 0.67 2.00e-01 2.50e+01 1.12e+01 ... (remaining 2301 not shown) Planarity restraints: 2500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM 6EU C 901 " -0.108 2.00e-02 2.50e+03 1.91e-01 3.64e+02 pdb=" CAV 6EU C 901 " 0.330 2.00e-02 2.50e+03 pdb=" CBB 6EU C 901 " -0.112 2.00e-02 2.50e+03 pdb=" CBD 6EU C 901 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU D 901 " -0.108 2.00e-02 2.50e+03 1.89e-01 3.57e+02 pdb=" CAV 6EU D 901 " 0.327 2.00e-02 2.50e+03 pdb=" CBB 6EU D 901 " -0.111 2.00e-02 2.50e+03 pdb=" CBD 6EU D 901 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU B 901 " 0.107 2.00e-02 2.50e+03 1.89e-01 3.56e+02 pdb=" CAV 6EU B 901 " -0.327 2.00e-02 2.50e+03 pdb=" CBB 6EU B 901 " 0.111 2.00e-02 2.50e+03 pdb=" CBD 6EU B 901 " 0.109 2.00e-02 2.50e+03 ... (remaining 2497 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 569 2.71 - 3.26: 15585 3.26 - 3.81: 24738 3.81 - 4.35: 30258 4.35 - 4.90: 51500 Nonbonded interactions: 122650 Sorted by model distance: nonbonded pdb=" NH1 ARG B 557 " pdb=" OE1 GLU B 570 " model vdw 2.167 3.120 nonbonded pdb=" NH1 ARG A 557 " pdb=" OE1 GLU A 570 " model vdw 2.168 3.120 nonbonded pdb=" NH1 ARG D 557 " pdb=" OE1 GLU D 570 " model vdw 2.179 3.120 nonbonded pdb=" N GLU A 458 " pdb=" OE1 GLU A 458 " model vdw 2.288 3.120 nonbonded pdb=" N GLU C 458 " pdb=" OE1 GLU C 458 " model vdw 2.313 3.120 ... (remaining 122645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.440 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.011 0.219 15092 Z= 0.557 Angle : 0.858 14.452 20460 Z= 0.411 Chirality : 0.057 0.683 2304 Planarity : 0.008 0.191 2500 Dihedral : 10.504 80.929 5428 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.25 % Allowed : 1.69 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.30 (0.20), residues: 1764 helix: 1.26 (0.15), residues: 1164 sheet: -2.81 (0.54), residues: 68 loop : -1.78 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 331 TYR 0.013 0.002 TYR C 351 PHE 0.023 0.002 PHE C 304 TRP 0.010 0.001 TRP D 549 HIS 0.006 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.01124 / 0.56 (15092) covalent geometry : angle 0.85771 / 0.41 (20460) hydrogen bonds : bond 0.13189 / 8.56 ( 911) hydrogen bonds : angle 5.54423 / 4.00 ( 2673) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 752 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7934 (mmm) cc_final: 0.7432 (mmm) REVERT: A 313 LEU cc_start: 0.8937 (mt) cc_final: 0.8619 (mt) REVERT: A 356 GLU cc_start: 0.6596 (tt0) cc_final: 0.6352 (tt0) REVERT: A 379 SER cc_start: 0.7939 (m) cc_final: 0.7624 (t) REVERT: A 428 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7461 (mtp-110) REVERT: A 432 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7658 (mmt90) REVERT: A 471 ASP cc_start: 0.7322 (m-30) cc_final: 0.7028 (m-30) REVERT: A 472 TYR cc_start: 0.7732 (m-80) cc_final: 0.7525 (m-80) REVERT: A 627 TYR cc_start: 0.6530 (m-80) cc_final: 0.6127 (m-80) REVERT: A 636 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8448 (mm-30) REVERT: A 644 MET cc_start: 0.8896 (mmm) cc_final: 0.8555 (mmm) REVERT: A 653 TYR cc_start: 0.8691 (p90) cc_final: 0.8360 (p90) REVERT: A 682 MET cc_start: 0.7356 (mtp) cc_final: 0.6542 (mtm) REVERT: A 696 ILE cc_start: 0.8518 (tt) cc_final: 0.8103 (mm) REVERT: C 352 ILE cc_start: 0.8696 (mt) cc_final: 0.8489 (mt) REVERT: C 358 HIS cc_start: 0.6356 (p90) cc_final: 0.5516 (t-90) REVERT: C 379 SER cc_start: 0.7946 (m) cc_final: 0.7715 (t) REVERT: C 393 ASN cc_start: 0.8224 (m-40) cc_final: 0.7506 (m-40) REVERT: C 427 ASP cc_start: 0.8718 (m-30) cc_final: 0.8469 (m-30) REVERT: C 432 ARG cc_start: 0.8027 (mtt90) cc_final: 0.7567 (mmt90) REVERT: C 438 PHE cc_start: 0.9161 (t80) cc_final: 0.8931 (t80) REVERT: C 471 ASP cc_start: 0.7423 (m-30) cc_final: 0.7178 (m-30) REVERT: C 561 GLN cc_start: 0.7383 (mt0) cc_final: 0.6799 (tt0) REVERT: C 571 LYS cc_start: 0.8312 (mtpp) cc_final: 0.8075 (mtpp) REVERT: C 639 LYS cc_start: 0.8509 (mttt) cc_final: 0.8302 (mttm) REVERT: C 644 MET cc_start: 0.8944 (mmm) cc_final: 0.8469 (mmm) REVERT: C 653 TYR cc_start: 0.8697 (p90) cc_final: 0.8345 (p90) REVERT: C 697 TRP cc_start: 0.8272 (t60) cc_final: 0.8069 (t60) REVERT: D 308 MET cc_start: 0.7912 (mmm) cc_final: 0.7484 (mmm) REVERT: D 313 LEU cc_start: 0.8913 (mt) cc_final: 0.8490 (mt) REVERT: D 388 ASP cc_start: 0.6728 (p0) cc_final: 0.6494 (p0) REVERT: D 411 ASP cc_start: 0.8267 (m-30) cc_final: 0.7545 (m-30) REVERT: D 432 ARG cc_start: 0.8035 (mtt90) cc_final: 0.7613 (mmt180) REVERT: D 561 GLN cc_start: 0.7320 (mt0) cc_final: 0.6973 (tt0) REVERT: D 644 MET cc_start: 0.8982 (mmm) cc_final: 0.8580 (mmm) REVERT: D 696 ILE cc_start: 0.8586 (tt) cc_final: 0.8213 (mm) REVERT: D 697 TRP cc_start: 0.7898 (t60) cc_final: 0.7684 (t60) REVERT: D 698 LYS cc_start: 0.8832 (mttm) cc_final: 0.8595 (mttp) REVERT: B 288 LEU cc_start: 0.8975 (mt) cc_final: 0.8644 (mt) REVERT: B 308 MET cc_start: 0.8277 (mmm) cc_final: 0.7745 (mmm) REVERT: B 313 LEU cc_start: 0.9036 (tp) cc_final: 0.8828 (tp) REVERT: B 324 LYS cc_start: 0.7974 (mttt) cc_final: 0.7554 (ptpp) REVERT: B 363 ARG cc_start: 0.7245 (ttt90) cc_final: 0.6667 (mtt90) REVERT: B 379 SER cc_start: 0.7901 (m) cc_final: 0.7595 (t) REVERT: B 381 LEU cc_start: 0.7344 (mp) cc_final: 0.7097 (mp) REVERT: B 408 ASN cc_start: 0.7853 (m-40) cc_final: 0.7604 (t0) REVERT: B 420 ARG cc_start: 0.8385 (tpp80) cc_final: 0.8051 (tpp80) REVERT: B 432 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7587 (mmt180) REVERT: B 471 ASP cc_start: 0.7664 (m-30) cc_final: 0.7447 (m-30) REVERT: B 589 PHE cc_start: 0.8687 (t80) cc_final: 0.8475 (t80) REVERT: B 627 TYR cc_start: 0.6636 (m-80) cc_final: 0.6080 (m-80) REVERT: B 644 MET cc_start: 0.8858 (mmm) cc_final: 0.8438 (mmm) REVERT: B 695 ASN cc_start: 0.7699 (m-40) cc_final: 0.7159 (m-40) outliers start: 4 outliers final: 4 residues processed: 754 average time/residue: 0.1199 time to fit residues: 129.9051 Evaluate side-chains 573 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 569 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0030 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 393 ASN A 687 ASN C 354 GLN ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 HIS D 354 GLN D 393 ASN B 354 GLN B 393 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.161635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118592 restraints weight = 20254.133| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.48 r_work: 0.3256 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15092 Z= 0.158 Angle : 0.594 10.543 20460 Z= 0.313 Chirality : 0.039 0.178 2304 Planarity : 0.003 0.043 2500 Dihedral : 6.033 54.860 2008 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.81 % Allowed : 12.75 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.51 (0.20), residues: 1764 helix: 1.44 (0.15), residues: 1180 sheet: -2.49 (0.54), residues: 72 loop : -1.86 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 721 TYR 0.017 0.001 TYR C 463 PHE 0.023 0.001 PHE A 304 TRP 0.013 0.002 TRP D 426 HIS 0.008 0.001 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (15092) covalent geometry : angle 0.59361 / 0.31 (20460) hydrogen bonds : bond 0.04963 / 3.28 ( 911) hydrogen bonds : angle 4.49255 / 3.27 ( 2673) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 633 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8020 (mmm) cc_final: 0.7507 (mmm) REVERT: A 313 LEU cc_start: 0.9011 (mt) cc_final: 0.8716 (mt) REVERT: A 356 GLU cc_start: 0.6556 (tt0) cc_final: 0.6263 (tt0) REVERT: A 379 SER cc_start: 0.7430 (m) cc_final: 0.7219 (t) REVERT: A 409 ARG cc_start: 0.8336 (ttp-170) cc_final: 0.8124 (ttp-110) REVERT: A 425 LYS cc_start: 0.8269 (tptt) cc_final: 0.7959 (tptt) REVERT: A 427 ASP cc_start: 0.8728 (m-30) cc_final: 0.8475 (m-30) REVERT: A 432 ARG cc_start: 0.8343 (mtt90) cc_final: 0.8090 (mmt180) REVERT: A 472 TYR cc_start: 0.8149 (m-80) cc_final: 0.7469 (m-10) REVERT: A 491 ARG cc_start: 0.8175 (mmm160) cc_final: 0.7862 (mtp180) REVERT: A 533 GLN cc_start: 0.8764 (mt0) cc_final: 0.8527 (mt0) REVERT: A 560 GLN cc_start: 0.8658 (tt0) cc_final: 0.8358 (tp40) REVERT: A 571 LYS cc_start: 0.8953 (mttt) cc_final: 0.8500 (mmtt) REVERT: A 627 TYR cc_start: 0.6870 (m-80) cc_final: 0.6513 (m-80) REVERT: A 644 MET cc_start: 0.9127 (mmm) cc_final: 0.8855 (mmm) REVERT: A 653 TYR cc_start: 0.8550 (p90) cc_final: 0.8205 (p90) REVERT: A 688 LYS cc_start: 0.8596 (mtpt) cc_final: 0.7963 (tptt) REVERT: A 696 ILE cc_start: 0.8454 (tt) cc_final: 0.8179 (mm) REVERT: C 358 HIS cc_start: 0.6646 (p90) cc_final: 0.5799 (t-90) REVERT: C 371 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7661 (mm-30) REVERT: C 379 SER cc_start: 0.8162 (m) cc_final: 0.7923 (t) REVERT: C 393 ASN cc_start: 0.8262 (m-40) cc_final: 0.7736 (m-40) REVERT: C 397 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7217 (tt0) REVERT: C 420 ARG cc_start: 0.8418 (tpp80) cc_final: 0.7641 (tpp80) REVERT: C 427 ASP cc_start: 0.8803 (m-30) cc_final: 0.8586 (m-30) REVERT: C 432 ARG cc_start: 0.8346 (mtt90) cc_final: 0.7975 (mmt180) REVERT: C 472 TYR cc_start: 0.7730 (m-80) cc_final: 0.7438 (m-80) REVERT: C 491 ARG cc_start: 0.8274 (mmm160) cc_final: 0.7937 (mtp180) REVERT: C 560 GLN cc_start: 0.8398 (tt0) cc_final: 0.7907 (tp40) REVERT: C 561 GLN cc_start: 0.7275 (mt0) cc_final: 0.6611 (tt0) REVERT: C 564 ILE cc_start: 0.8766 (tt) cc_final: 0.8507 (tp) REVERT: C 571 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8427 (mtpp) REVERT: C 653 TYR cc_start: 0.8655 (p90) cc_final: 0.8257 (p90) REVERT: C 743 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7434 (ttm170) REVERT: C 746 GLU cc_start: 0.5745 (tt0) cc_final: 0.4694 (tt0) REVERT: D 308 MET cc_start: 0.8073 (mmm) cc_final: 0.7554 (mmm) REVERT: D 313 LEU cc_start: 0.8962 (mt) cc_final: 0.8521 (mt) REVERT: D 397 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7662 (tt0) REVERT: D 420 ARG cc_start: 0.8559 (tpp80) cc_final: 0.7836 (tpp80) REVERT: D 432 ARG cc_start: 0.8336 (mtt90) cc_final: 0.7935 (mmt90) REVERT: D 465 LEU cc_start: 0.8213 (tp) cc_final: 0.7778 (tp) REVERT: D 471 ASP cc_start: 0.8112 (m-30) cc_final: 0.7818 (t0) REVERT: D 472 TYR cc_start: 0.7564 (m-80) cc_final: 0.7219 (m-80) REVERT: D 504 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.6705 (ptpt) REVERT: D 560 GLN cc_start: 0.8349 (tt0) cc_final: 0.8097 (tt0) REVERT: D 561 GLN cc_start: 0.7540 (mt0) cc_final: 0.6954 (tt0) REVERT: D 571 LYS cc_start: 0.8912 (mttt) cc_final: 0.8512 (mmtt) REVERT: D 572 MET cc_start: 0.7988 (mtt) cc_final: 0.7292 (mtt) REVERT: D 644 MET cc_start: 0.9168 (mmm) cc_final: 0.8825 (mmm) REVERT: D 684 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7359 (tm-30) REVERT: D 696 ILE cc_start: 0.8469 (tt) cc_final: 0.8074 (mm) REVERT: D 746 GLU cc_start: 0.5956 (tt0) cc_final: 0.5028 (tt0) REVERT: B 288 LEU cc_start: 0.8914 (mt) cc_final: 0.8704 (mt) REVERT: B 308 MET cc_start: 0.8455 (mmm) cc_final: 0.7947 (mmm) REVERT: B 324 LYS cc_start: 0.8054 (mttt) cc_final: 0.7419 (ptpp) REVERT: B 363 ARG cc_start: 0.7222 (ttt90) cc_final: 0.6638 (mtt90) REVERT: B 379 SER cc_start: 0.7660 (m) cc_final: 0.7308 (t) REVERT: B 381 LEU cc_start: 0.7495 (mp) cc_final: 0.7010 (mp) REVERT: B 420 ARG cc_start: 0.8724 (tpp80) cc_final: 0.8348 (tpp80) REVERT: B 432 ARG cc_start: 0.8333 (mtt90) cc_final: 0.7987 (mmt180) REVERT: B 472 TYR cc_start: 0.7684 (m-80) cc_final: 0.7222 (m-80) REVERT: B 491 ARG cc_start: 0.8185 (mmm160) cc_final: 0.7916 (mtp180) REVERT: B 627 TYR cc_start: 0.7002 (m-80) cc_final: 0.6571 (m-80) REVERT: B 644 MET cc_start: 0.9081 (mmm) cc_final: 0.8780 (mmm) REVERT: B 658 VAL cc_start: 0.9335 (t) cc_final: 0.9088 (p) REVERT: B 695 ASN cc_start: 0.7979 (m-40) cc_final: 0.7202 (t0) REVERT: B 743 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7418 (ttm170) outliers start: 45 outliers final: 26 residues processed: 644 average time/residue: 0.1205 time to fit residues: 114.3737 Evaluate side-chains 583 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 556 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 703 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 393 ASN C 354 GLN ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN D 364 HIS D 393 ASN D 687 ASN B 354 GLN B 393 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.160421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117427 restraints weight = 20648.203| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.51 r_work: 0.3227 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15092 Z= 0.150 Angle : 0.576 6.254 20460 Z= 0.305 Chirality : 0.039 0.186 2304 Planarity : 0.003 0.035 2500 Dihedral : 5.827 55.173 2008 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.94 % Allowed : 15.25 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.48 (0.20), residues: 1764 helix: 1.45 (0.15), residues: 1180 sheet: -2.61 (0.53), residues: 72 loop : -1.95 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 721 TYR 0.013 0.001 TYR C 463 PHE 0.026 0.001 PHE D 304 TRP 0.016 0.002 TRP A 740 HIS 0.006 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (15092) covalent geometry : angle 0.57629 / 0.30 (20460) hydrogen bonds : bond 0.04534 / 3.01 ( 911) hydrogen bonds : angle 4.38733 / 3.20 ( 2673) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 585 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7993 (mmm) cc_final: 0.7721 (mmt) REVERT: A 313 LEU cc_start: 0.9003 (mt) cc_final: 0.8654 (mt) REVERT: A 356 GLU cc_start: 0.6533 (tt0) cc_final: 0.6213 (tt0) REVERT: A 379 SER cc_start: 0.7432 (m) cc_final: 0.7168 (t) REVERT: A 397 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7720 (tt0) REVERT: A 409 ARG cc_start: 0.8225 (ttp-170) cc_final: 0.7630 (ttp-170) REVERT: A 427 ASP cc_start: 0.8776 (m-30) cc_final: 0.8531 (m-30) REVERT: A 432 ARG cc_start: 0.8317 (mtt90) cc_final: 0.7990 (mmt90) REVERT: A 472 TYR cc_start: 0.8159 (m-80) cc_final: 0.7446 (m-10) REVERT: A 491 ARG cc_start: 0.8210 (mmm160) cc_final: 0.7907 (mtp180) REVERT: A 559 PHE cc_start: 0.5834 (t80) cc_final: 0.5156 (m-10) REVERT: A 571 LYS cc_start: 0.8996 (mttt) cc_final: 0.8536 (mmtt) REVERT: A 627 TYR cc_start: 0.6955 (m-80) cc_final: 0.6624 (m-80) REVERT: A 653 TYR cc_start: 0.8479 (p90) cc_final: 0.8130 (p90) REVERT: A 696 ILE cc_start: 0.8495 (tt) cc_final: 0.8269 (mm) REVERT: A 698 LYS cc_start: 0.9176 (mmmt) cc_final: 0.8846 (mmtt) REVERT: C 304 PHE cc_start: 0.7609 (t80) cc_final: 0.7378 (t80) REVERT: C 358 HIS cc_start: 0.6658 (p90) cc_final: 0.5825 (t-90) REVERT: C 397 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7251 (tt0) REVERT: C 409 ARG cc_start: 0.8274 (ttp-170) cc_final: 0.7761 (ttp-170) REVERT: C 420 ARG cc_start: 0.8450 (tpp80) cc_final: 0.7637 (tpp80) REVERT: C 432 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7841 (mmt90) REVERT: C 471 ASP cc_start: 0.8062 (m-30) cc_final: 0.7735 (t0) REVERT: C 472 TYR cc_start: 0.7741 (m-80) cc_final: 0.7359 (m-80) REVERT: C 491 ARG cc_start: 0.8310 (mmm160) cc_final: 0.7946 (mtp180) REVERT: C 560 GLN cc_start: 0.8448 (tt0) cc_final: 0.8138 (tp40) REVERT: C 571 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8470 (mtpp) REVERT: C 653 TYR cc_start: 0.8525 (p90) cc_final: 0.8175 (p90) REVERT: C 743 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7364 (ttm170) REVERT: D 308 MET cc_start: 0.8035 (mmm) cc_final: 0.7695 (mmt) REVERT: D 313 LEU cc_start: 0.8971 (mt) cc_final: 0.8568 (mt) REVERT: D 397 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7604 (tt0) REVERT: D 420 ARG cc_start: 0.8496 (tpp80) cc_final: 0.7812 (tpp80) REVERT: D 422 LEU cc_start: 0.8944 (mt) cc_final: 0.8558 (mt) REVERT: D 429 PHE cc_start: 0.8387 (p90) cc_final: 0.8176 (p90) REVERT: D 432 ARG cc_start: 0.8317 (mtt90) cc_final: 0.8034 (mmt180) REVERT: D 472 TYR cc_start: 0.7745 (m-80) cc_final: 0.7280 (m-80) REVERT: D 560 GLN cc_start: 0.8469 (tt0) cc_final: 0.8155 (tt0) REVERT: D 561 GLN cc_start: 0.7584 (mt0) cc_final: 0.6946 (tt0) REVERT: D 644 MET cc_start: 0.9204 (mmm) cc_final: 0.8217 (mmm) REVERT: D 709 GLU cc_start: 0.8395 (tt0) cc_final: 0.8106 (tt0) REVERT: D 746 GLU cc_start: 0.5864 (tt0) cc_final: 0.4984 (tt0) REVERT: B 288 LEU cc_start: 0.9018 (mt) cc_final: 0.8746 (mt) REVERT: B 293 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7651 (mt-10) REVERT: B 308 MET cc_start: 0.8509 (mmm) cc_final: 0.8004 (mmm) REVERT: B 324 LYS cc_start: 0.8065 (mttt) cc_final: 0.7796 (mmpt) REVERT: B 363 ARG cc_start: 0.7315 (ttt90) cc_final: 0.6569 (mtt90) REVERT: B 379 SER cc_start: 0.7560 (m) cc_final: 0.7267 (t) REVERT: B 381 LEU cc_start: 0.7660 (mp) cc_final: 0.7146 (mp) REVERT: B 397 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7865 (tt0) REVERT: B 409 ARG cc_start: 0.7484 (ptt-90) cc_final: 0.7211 (ptt-90) REVERT: B 420 ARG cc_start: 0.8712 (tpp80) cc_final: 0.8249 (tpp80) REVERT: B 432 ARG cc_start: 0.8374 (mtt90) cc_final: 0.7892 (mmt90) REVERT: B 472 TYR cc_start: 0.7730 (m-80) cc_final: 0.7245 (m-80) REVERT: B 491 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7953 (mtp180) REVERT: B 533 GLN cc_start: 0.8728 (mt0) cc_final: 0.8503 (mt0) REVERT: B 560 GLN cc_start: 0.8239 (tp40) cc_final: 0.7753 (tp40) REVERT: B 627 TYR cc_start: 0.7016 (m-80) cc_final: 0.6556 (m-80) REVERT: B 644 MET cc_start: 0.9106 (mmm) cc_final: 0.8818 (mmm) REVERT: B 658 VAL cc_start: 0.9328 (t) cc_final: 0.9096 (p) REVERT: B 695 ASN cc_start: 0.7797 (m-40) cc_final: 0.7260 (m-40) REVERT: B 743 ARG cc_start: 0.8102 (ttm110) cc_final: 0.7441 (ttm170) outliers start: 47 outliers final: 31 residues processed: 604 average time/residue: 0.1143 time to fit residues: 102.4923 Evaluate side-chains 590 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 559 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 11 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 393 ASN C 354 GLN ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN D 354 GLN D 393 ASN B 354 GLN B 378 HIS B 687 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.158791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113969 restraints weight = 20669.972| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.55 r_work: 0.3193 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15092 Z= 0.216 Angle : 0.609 7.305 20460 Z= 0.320 Chirality : 0.040 0.205 2304 Planarity : 0.004 0.092 2500 Dihedral : 5.786 53.697 2008 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.94 % Allowed : 16.88 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.35 (0.20), residues: 1764 helix: 1.36 (0.15), residues: 1180 sheet: -2.31 (0.50), residues: 68 loop : -2.10 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 409 TYR 0.010 0.001 TYR D 351 PHE 0.025 0.002 PHE D 304 TRP 0.032 0.002 TRP B 697 HIS 0.004 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (15092) covalent geometry : angle 0.60909 / 0.32 (20460) hydrogen bonds : bond 0.04548 / 3.02 ( 911) hydrogen bonds : angle 4.41444 / 3.22 ( 2673) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 571 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8077 (mmm) cc_final: 0.7820 (mmt) REVERT: A 313 LEU cc_start: 0.9028 (mt) cc_final: 0.8653 (mt) REVERT: A 326 GLU cc_start: 0.9041 (mp0) cc_final: 0.8807 (mp0) REVERT: A 356 GLU cc_start: 0.6627 (tt0) cc_final: 0.6341 (tt0) REVERT: A 379 SER cc_start: 0.7391 (m) cc_final: 0.7174 (t) REVERT: A 397 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7729 (tt0) REVERT: A 409 ARG cc_start: 0.8374 (ttp-170) cc_final: 0.8019 (ttp-170) REVERT: A 432 ARG cc_start: 0.8394 (mtt90) cc_final: 0.8033 (mmt90) REVERT: A 472 TYR cc_start: 0.8185 (m-80) cc_final: 0.7357 (m-10) REVERT: A 491 ARG cc_start: 0.8324 (mmm160) cc_final: 0.7909 (mtp180) REVERT: A 559 PHE cc_start: 0.6170 (t80) cc_final: 0.5053 (m-10) REVERT: A 571 LYS cc_start: 0.8946 (mttt) cc_final: 0.8535 (mmtt) REVERT: A 627 TYR cc_start: 0.7102 (m-80) cc_final: 0.6700 (m-80) REVERT: A 653 TYR cc_start: 0.8512 (p90) cc_final: 0.8188 (p90) REVERT: A 677 MET cc_start: 0.8504 (tpp) cc_final: 0.8218 (tpp) REVERT: A 698 LYS cc_start: 0.9249 (mmmt) cc_final: 0.8788 (mttp) REVERT: C 393 ASN cc_start: 0.8274 (m110) cc_final: 0.7807 (m-40) REVERT: C 409 ARG cc_start: 0.8322 (ttp-170) cc_final: 0.7869 (ttp-170) REVERT: C 420 ARG cc_start: 0.8460 (tpp80) cc_final: 0.7689 (tpp80) REVERT: C 432 ARG cc_start: 0.8419 (mtt90) cc_final: 0.8011 (mmt180) REVERT: C 472 TYR cc_start: 0.7814 (m-80) cc_final: 0.7445 (m-80) REVERT: C 560 GLN cc_start: 0.8571 (tt0) cc_final: 0.8343 (tp40) REVERT: C 571 LYS cc_start: 0.8785 (mtpp) cc_final: 0.8558 (mtpp) REVERT: C 653 TYR cc_start: 0.8589 (p90) cc_final: 0.8296 (p90) REVERT: C 709 GLU cc_start: 0.8574 (tt0) cc_final: 0.8291 (tt0) REVERT: C 743 ARG cc_start: 0.7943 (ttm110) cc_final: 0.7344 (ttm170) REVERT: D 308 MET cc_start: 0.8054 (mmm) cc_final: 0.7423 (mmm) REVERT: D 397 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7602 (tt0) REVERT: D 420 ARG cc_start: 0.8521 (tpp80) cc_final: 0.7897 (tpp80) REVERT: D 422 LEU cc_start: 0.8911 (mt) cc_final: 0.8582 (mt) REVERT: D 432 ARG cc_start: 0.8420 (mtt90) cc_final: 0.7990 (mmt90) REVERT: D 471 ASP cc_start: 0.8426 (t0) cc_final: 0.7746 (t0) REVERT: D 504 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.6846 (ptpt) REVERT: D 560 GLN cc_start: 0.8601 (tt0) cc_final: 0.8381 (tp40) REVERT: D 561 GLN cc_start: 0.7698 (mt0) cc_final: 0.6903 (tt0) REVERT: D 684 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7446 (tm-30) REVERT: D 698 LYS cc_start: 0.9229 (mmmt) cc_final: 0.8922 (mmtt) REVERT: D 746 GLU cc_start: 0.5723 (tt0) cc_final: 0.5029 (tt0) REVERT: B 288 LEU cc_start: 0.9080 (mt) cc_final: 0.8669 (mt) REVERT: B 293 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7645 (mt-10) REVERT: B 308 MET cc_start: 0.8469 (mmm) cc_final: 0.7991 (mmm) REVERT: B 324 LYS cc_start: 0.8102 (mttt) cc_final: 0.7867 (mmpt) REVERT: B 363 ARG cc_start: 0.7355 (ttt90) cc_final: 0.6558 (mtt90) REVERT: B 397 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7816 (tt0) REVERT: B 409 ARG cc_start: 0.7537 (ptt-90) cc_final: 0.7281 (ptt-90) REVERT: B 420 ARG cc_start: 0.8721 (tpp80) cc_final: 0.8299 (tpp80) REVERT: B 432 ARG cc_start: 0.8406 (mtt90) cc_final: 0.7970 (mmt90) REVERT: B 471 ASP cc_start: 0.8429 (t0) cc_final: 0.7879 (t0) REVERT: B 533 GLN cc_start: 0.8778 (mt0) cc_final: 0.8537 (mt0) REVERT: B 560 GLN cc_start: 0.8295 (tt0) cc_final: 0.7841 (tp40) REVERT: B 627 TYR cc_start: 0.7254 (m-80) cc_final: 0.6745 (m-80) REVERT: B 658 VAL cc_start: 0.9348 (t) cc_final: 0.9132 (p) REVERT: B 695 ASN cc_start: 0.7950 (m-40) cc_final: 0.7416 (m-40) REVERT: B 697 TRP cc_start: 0.8597 (t60) cc_final: 0.8082 (t60) outliers start: 63 outliers final: 39 residues processed: 597 average time/residue: 0.1169 time to fit residues: 102.5165 Evaluate side-chains 583 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 543 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 110 optimal weight: 0.0980 chunk 147 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 154 optimal weight: 0.0000 chunk 145 optimal weight: 0.6980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 393 ASN A 560 GLN C 354 GLN D 354 GLN D 393 ASN B 354 GLN B 393 ASN B 628 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.161172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117254 restraints weight = 20487.174| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.55 r_work: 0.3225 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15092 Z= 0.134 Angle : 0.587 8.118 20460 Z= 0.305 Chirality : 0.038 0.193 2304 Planarity : 0.003 0.074 2500 Dihedral : 5.586 52.998 2008 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.56 % Allowed : 18.12 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.33 (0.20), residues: 1764 helix: 1.36 (0.15), residues: 1180 sheet: -2.27 (0.51), residues: 68 loop : -2.16 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 409 TYR 0.011 0.001 TYR C 463 PHE 0.027 0.001 PHE D 304 TRP 0.010 0.001 TRP D 426 HIS 0.003 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15092) covalent geometry : angle 0.58708 / 0.30 (20460) hydrogen bonds : bond 0.04170 / 2.78 ( 911) hydrogen bonds : angle 4.37701 / 3.19 ( 2673) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 575 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8072 (mmm) cc_final: 0.7501 (mmm) REVERT: A 313 LEU cc_start: 0.9008 (mt) cc_final: 0.8667 (mt) REVERT: A 356 GLU cc_start: 0.6646 (tt0) cc_final: 0.6411 (tt0) REVERT: A 379 SER cc_start: 0.7385 (m) cc_final: 0.7112 (t) REVERT: A 409 ARG cc_start: 0.8321 (ttp-170) cc_final: 0.7967 (ttp-170) REVERT: A 432 ARG cc_start: 0.8330 (mtt90) cc_final: 0.8006 (mmt90) REVERT: A 472 TYR cc_start: 0.8186 (m-80) cc_final: 0.7325 (m-10) REVERT: A 559 PHE cc_start: 0.6096 (t80) cc_final: 0.4960 (m-10) REVERT: A 571 LYS cc_start: 0.8931 (mttt) cc_final: 0.8507 (mmtt) REVERT: A 572 MET cc_start: 0.8346 (ttm) cc_final: 0.7722 (ttm) REVERT: A 627 TYR cc_start: 0.7083 (m-80) cc_final: 0.6686 (m-80) REVERT: A 644 MET cc_start: 0.9154 (mmm) cc_final: 0.8889 (mmm) REVERT: A 696 ILE cc_start: 0.8487 (tt) cc_final: 0.8244 (mm) REVERT: A 698 LYS cc_start: 0.9238 (mmmt) cc_final: 0.8966 (mmtt) REVERT: C 356 GLU cc_start: 0.7018 (tt0) cc_final: 0.6451 (tt0) REVERT: C 393 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7853 (m-40) REVERT: C 409 ARG cc_start: 0.8269 (ttp-170) cc_final: 0.7845 (ttp-170) REVERT: C 420 ARG cc_start: 0.8428 (tpp80) cc_final: 0.7656 (tpp80) REVERT: C 432 ARG cc_start: 0.8366 (mtt90) cc_final: 0.7910 (mmt90) REVERT: C 472 TYR cc_start: 0.7817 (m-80) cc_final: 0.7409 (m-80) REVERT: C 559 PHE cc_start: 0.4976 (t80) cc_final: 0.4768 (m-10) REVERT: C 571 LYS cc_start: 0.8787 (mtpp) cc_final: 0.8567 (mtpp) REVERT: C 698 LYS cc_start: 0.9252 (ttmm) cc_final: 0.9047 (mmmt) REVERT: C 709 GLU cc_start: 0.8611 (tt0) cc_final: 0.8371 (tt0) REVERT: C 743 ARG cc_start: 0.7926 (ttm110) cc_final: 0.7341 (ttm170) REVERT: D 308 MET cc_start: 0.8023 (mmm) cc_final: 0.7382 (mmm) REVERT: D 397 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7577 (tt0) REVERT: D 420 ARG cc_start: 0.8484 (tpp80) cc_final: 0.7837 (tpp80) REVERT: D 422 LEU cc_start: 0.8809 (mt) cc_final: 0.8407 (mt) REVERT: D 429 PHE cc_start: 0.8247 (p90) cc_final: 0.7956 (p90) REVERT: D 432 ARG cc_start: 0.8369 (mtt90) cc_final: 0.7963 (mmt90) REVERT: D 471 ASP cc_start: 0.8375 (t0) cc_final: 0.7660 (t0) REVERT: D 561 GLN cc_start: 0.7585 (mt0) cc_final: 0.6841 (tt0) REVERT: D 644 MET cc_start: 0.9216 (mmm) cc_final: 0.8907 (mmm) REVERT: D 698 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8963 (mttp) REVERT: D 746 GLU cc_start: 0.5621 (tt0) cc_final: 0.4922 (tt0) REVERT: B 288 LEU cc_start: 0.8909 (mt) cc_final: 0.8609 (mt) REVERT: B 293 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7608 (mt-10) REVERT: B 308 MET cc_start: 0.8365 (mmm) cc_final: 0.7870 (mmm) REVERT: B 324 LYS cc_start: 0.8104 (mttt) cc_final: 0.7847 (mmpt) REVERT: B 363 ARG cc_start: 0.7280 (ttt90) cc_final: 0.6507 (mtt90) REVERT: B 397 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7829 (tt0) REVERT: B 409 ARG cc_start: 0.7527 (ptt-90) cc_final: 0.7260 (ptt-90) REVERT: B 420 ARG cc_start: 0.8673 (tpp80) cc_final: 0.8295 (tpp80) REVERT: B 432 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7944 (mmt90) REVERT: B 471 ASP cc_start: 0.8267 (t0) cc_final: 0.7944 (t0) REVERT: B 532 SER cc_start: 0.9285 (m) cc_final: 0.9018 (t) REVERT: B 627 TYR cc_start: 0.7241 (m-80) cc_final: 0.6704 (m-80) REVERT: B 644 MET cc_start: 0.9121 (mmm) cc_final: 0.8828 (mmm) REVERT: B 658 VAL cc_start: 0.9311 (t) cc_final: 0.9101 (p) REVERT: B 695 ASN cc_start: 0.7839 (m-40) cc_final: 0.7333 (m-40) REVERT: B 697 TRP cc_start: 0.8585 (t60) cc_final: 0.7903 (t60) outliers start: 57 outliers final: 38 residues processed: 599 average time/residue: 0.1123 time to fit residues: 100.7300 Evaluate side-chains 597 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 558 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 120 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 393 ASN C 354 GLN C 560 GLN D 354 GLN D 393 ASN B 354 GLN B 393 ASN B 560 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.161283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116976 restraints weight = 20621.687| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.58 r_work: 0.3224 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15092 Z= 0.144 Angle : 0.579 8.505 20460 Z= 0.304 Chirality : 0.039 0.197 2304 Planarity : 0.003 0.067 2500 Dihedral : 5.481 53.381 2008 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.81 % Allowed : 18.19 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.34 (0.20), residues: 1764 helix: 1.37 (0.15), residues: 1180 sheet: -2.23 (0.52), residues: 68 loop : -2.18 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 500 TYR 0.015 0.001 TYR C 653 PHE 0.028 0.001 PHE D 304 TRP 0.012 0.002 TRP A 426 HIS 0.003 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (15092) covalent geometry : angle 0.57947 / 0.30 (20460) hydrogen bonds : bond 0.04099 / 2.74 ( 911) hydrogen bonds : angle 4.39806 / 3.22 ( 2673) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 569 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8112 (mmm) cc_final: 0.7537 (mmm) REVERT: A 313 LEU cc_start: 0.9014 (mt) cc_final: 0.8692 (mt) REVERT: A 356 GLU cc_start: 0.6711 (tt0) cc_final: 0.6473 (tt0) REVERT: A 379 SER cc_start: 0.7382 (m) cc_final: 0.7115 (t) REVERT: A 409 ARG cc_start: 0.8349 (ttp-170) cc_final: 0.8107 (ttp-170) REVERT: A 432 ARG cc_start: 0.8432 (mtt90) cc_final: 0.8099 (mmt180) REVERT: A 472 TYR cc_start: 0.8236 (m-80) cc_final: 0.7760 (m-80) REVERT: A 559 PHE cc_start: 0.5976 (t80) cc_final: 0.4878 (m-10) REVERT: A 571 LYS cc_start: 0.8927 (mttt) cc_final: 0.8503 (mmtt) REVERT: A 627 TYR cc_start: 0.7183 (m-80) cc_final: 0.6772 (m-80) REVERT: A 644 MET cc_start: 0.9159 (mmm) cc_final: 0.8920 (mmm) REVERT: A 696 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8226 (mm) REVERT: A 698 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8852 (mttp) REVERT: C 393 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7795 (m-40) REVERT: C 409 ARG cc_start: 0.8281 (ttp-170) cc_final: 0.7950 (ttp-170) REVERT: C 420 ARG cc_start: 0.8431 (tpp80) cc_final: 0.7635 (tpp80) REVERT: C 432 ARG cc_start: 0.8397 (mtt90) cc_final: 0.7980 (mmt90) REVERT: C 471 ASP cc_start: 0.8471 (t0) cc_final: 0.8166 (t0) REVERT: C 472 TYR cc_start: 0.7836 (m-80) cc_final: 0.7477 (m-80) REVERT: C 559 PHE cc_start: 0.5019 (t80) cc_final: 0.4804 (m-10) REVERT: C 560 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8222 (tp40) REVERT: C 627 TYR cc_start: 0.7165 (m-80) cc_final: 0.6656 (m-80) REVERT: C 716 MET cc_start: 0.1895 (ttp) cc_final: 0.1279 (ptt) REVERT: C 738 TYR cc_start: 0.3689 (OUTLIER) cc_final: 0.2089 (p90) REVERT: C 743 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7342 (ttm170) REVERT: D 308 MET cc_start: 0.8033 (mmm) cc_final: 0.7805 (mmt) REVERT: D 397 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7577 (tt0) REVERT: D 409 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7615 (ttp-170) REVERT: D 420 ARG cc_start: 0.8572 (tpp80) cc_final: 0.7922 (tpp80) REVERT: D 422 LEU cc_start: 0.8769 (mt) cc_final: 0.8375 (mt) REVERT: D 432 ARG cc_start: 0.8423 (mtt90) cc_final: 0.8021 (mmt90) REVERT: D 435 TYR cc_start: 0.9235 (m-10) cc_final: 0.9008 (m-10) REVERT: D 471 ASP cc_start: 0.8286 (t0) cc_final: 0.7637 (t0) REVERT: D 561 GLN cc_start: 0.7352 (mt0) cc_final: 0.6842 (pm20) REVERT: D 698 LYS cc_start: 0.9208 (mmmt) cc_final: 0.8936 (mttp) REVERT: D 738 TYR cc_start: 0.3660 (OUTLIER) cc_final: 0.2087 (p90) REVERT: D 746 GLU cc_start: 0.5637 (tt0) cc_final: 0.4952 (tt0) REVERT: B 293 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7607 (mt-10) REVERT: B 308 MET cc_start: 0.8356 (mmm) cc_final: 0.8108 (mmt) REVERT: B 324 LYS cc_start: 0.8116 (mttt) cc_final: 0.7863 (mmpt) REVERT: B 363 ARG cc_start: 0.7291 (ttt90) cc_final: 0.6497 (mtt90) REVERT: B 397 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7813 (tt0) REVERT: B 420 ARG cc_start: 0.8700 (tpp80) cc_final: 0.8387 (tpp80) REVERT: B 422 LEU cc_start: 0.8810 (mt) cc_final: 0.8411 (mt) REVERT: B 432 ARG cc_start: 0.8364 (mtt90) cc_final: 0.7941 (mmt90) REVERT: B 471 ASP cc_start: 0.8346 (t0) cc_final: 0.7836 (t0) REVERT: B 532 SER cc_start: 0.9287 (m) cc_final: 0.9026 (t) REVERT: B 627 TYR cc_start: 0.7228 (m-80) cc_final: 0.6703 (m-80) REVERT: B 658 VAL cc_start: 0.9305 (t) cc_final: 0.9099 (p) REVERT: B 695 ASN cc_start: 0.7829 (m-40) cc_final: 0.7479 (m-40) outliers start: 61 outliers final: 44 residues processed: 597 average time/residue: 0.1159 time to fit residues: 103.5818 Evaluate side-chains 603 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 554 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 738 TYR Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 738 TYR Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 140 optimal weight: 7.9990 chunk 147 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 393 ASN C 354 GLN C 393 ASN C 687 ASN D 354 GLN D 393 ASN B 354 GLN B 393 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.161643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.117302 restraints weight = 20465.446| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.58 r_work: 0.3225 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15092 Z= 0.144 Angle : 0.598 10.293 20460 Z= 0.311 Chirality : 0.039 0.194 2304 Planarity : 0.003 0.069 2500 Dihedral : 5.438 53.246 2008 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.44 % Allowed : 19.50 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.33 (0.20), residues: 1764 helix: 1.36 (0.15), residues: 1180 sheet: -2.21 (0.52), residues: 68 loop : -2.18 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 409 TYR 0.010 0.001 TYR B 309 PHE 0.027 0.001 PHE C 304 TRP 0.016 0.002 TRP C 697 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (15092) covalent geometry : angle 0.59782 / 0.31 (20460) hydrogen bonds : bond 0.04044 / 2.69 ( 911) hydrogen bonds : angle 4.41074 / 3.23 ( 2673) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 565 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8088 (mmm) cc_final: 0.7512 (mmm) REVERT: A 313 LEU cc_start: 0.9025 (mt) cc_final: 0.8684 (mt) REVERT: A 379 SER cc_start: 0.7375 (m) cc_final: 0.7114 (t) REVERT: A 397 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7687 (tt0) REVERT: A 409 ARG cc_start: 0.8381 (ttp-170) cc_final: 0.8123 (ttp-170) REVERT: A 432 ARG cc_start: 0.8438 (mtt90) cc_final: 0.8110 (mmt180) REVERT: A 472 TYR cc_start: 0.8170 (m-80) cc_final: 0.7663 (m-80) REVERT: A 559 PHE cc_start: 0.5926 (t80) cc_final: 0.4853 (m-10) REVERT: A 571 LYS cc_start: 0.8899 (mttt) cc_final: 0.8465 (mmtt) REVERT: A 627 TYR cc_start: 0.7235 (m-80) cc_final: 0.6750 (m-80) REVERT: A 644 MET cc_start: 0.9148 (mmm) cc_final: 0.8878 (mmm) REVERT: A 696 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8207 (mm) REVERT: A 698 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8870 (mttp) REVERT: C 393 ASN cc_start: 0.8352 (m-40) cc_final: 0.7944 (m-40) REVERT: C 409 ARG cc_start: 0.8221 (ttp-170) cc_final: 0.7877 (ttp-170) REVERT: C 420 ARG cc_start: 0.8394 (tpp80) cc_final: 0.7633 (tpp80) REVERT: C 432 ARG cc_start: 0.8376 (mtt90) cc_final: 0.7967 (mmt90) REVERT: C 471 ASP cc_start: 0.8466 (t0) cc_final: 0.8167 (t0) REVERT: C 472 TYR cc_start: 0.7874 (m-80) cc_final: 0.7487 (m-80) REVERT: C 627 TYR cc_start: 0.7187 (m-80) cc_final: 0.6705 (m-80) REVERT: C 738 TYR cc_start: 0.3636 (OUTLIER) cc_final: 0.2129 (p90) REVERT: C 743 ARG cc_start: 0.7921 (ttm110) cc_final: 0.7369 (ttm170) REVERT: D 308 MET cc_start: 0.8036 (mmm) cc_final: 0.7820 (mmt) REVERT: D 397 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7550 (tt0) REVERT: D 409 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7806 (ttp-110) REVERT: D 420 ARG cc_start: 0.8582 (tpp80) cc_final: 0.7953 (tpp80) REVERT: D 422 LEU cc_start: 0.8789 (mt) cc_final: 0.8419 (mt) REVERT: D 432 ARG cc_start: 0.8380 (mtt90) cc_final: 0.8109 (mmt180) REVERT: D 471 ASP cc_start: 0.8281 (t0) cc_final: 0.7680 (t0) REVERT: D 561 GLN cc_start: 0.7228 (mt0) cc_final: 0.6884 (pm20) REVERT: D 562 MET cc_start: 0.8317 (mtt) cc_final: 0.7896 (mtt) REVERT: D 698 LYS cc_start: 0.9177 (mmmt) cc_final: 0.8966 (mttp) REVERT: D 738 TYR cc_start: 0.3651 (OUTLIER) cc_final: 0.2076 (p90) REVERT: D 746 GLU cc_start: 0.5663 (tt0) cc_final: 0.5019 (tt0) REVERT: B 288 LEU cc_start: 0.8990 (mt) cc_final: 0.8695 (mt) REVERT: B 293 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7595 (mt-10) REVERT: B 308 MET cc_start: 0.8314 (mmm) cc_final: 0.7988 (mmt) REVERT: B 363 ARG cc_start: 0.7280 (ttt90) cc_final: 0.6504 (mtt90) REVERT: B 397 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7791 (tt0) REVERT: B 420 ARG cc_start: 0.8693 (tpp80) cc_final: 0.8309 (tpp80) REVERT: B 432 ARG cc_start: 0.8330 (mtt90) cc_final: 0.7938 (mmt90) REVERT: B 471 ASP cc_start: 0.8345 (t0) cc_final: 0.7945 (t0) REVERT: B 532 SER cc_start: 0.9290 (m) cc_final: 0.9032 (t) REVERT: B 627 TYR cc_start: 0.7263 (m-80) cc_final: 0.6722 (m-80) REVERT: B 644 MET cc_start: 0.9125 (mmm) cc_final: 0.8839 (mmm) REVERT: B 695 ASN cc_start: 0.7834 (m-40) cc_final: 0.7294 (m-40) outliers start: 55 outliers final: 47 residues processed: 593 average time/residue: 0.1132 time to fit residues: 101.0041 Evaluate side-chains 597 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 547 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 738 TYR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 705 ILE Chi-restraints excluded: chain D residue 738 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 54 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 97 optimal weight: 0.0060 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 393 ASN C 354 GLN D 354 GLN D 393 ASN B 354 GLN B 393 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.160806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.117549 restraints weight = 20632.953| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.55 r_work: 0.3234 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15092 Z= 0.141 Angle : 0.615 12.627 20460 Z= 0.320 Chirality : 0.039 0.194 2304 Planarity : 0.003 0.063 2500 Dihedral : 5.379 50.034 2008 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.50 % Allowed : 19.50 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.29 (0.20), residues: 1764 helix: 1.32 (0.15), residues: 1180 sheet: -2.15 (0.53), residues: 68 loop : -2.17 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 409 TYR 0.010 0.001 TYR C 309 PHE 0.029 0.001 PHE C 304 TRP 0.015 0.002 TRP C 740 HIS 0.003 0.001 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (15092) covalent geometry : angle 0.61493 / 0.32 (20460) hydrogen bonds : bond 0.03992 / 2.66 ( 911) hydrogen bonds : angle 4.46542 / 3.28 ( 2673) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 550 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8088 (mmm) cc_final: 0.7509 (mmm) REVERT: A 313 LEU cc_start: 0.9013 (mt) cc_final: 0.8720 (mt) REVERT: A 379 SER cc_start: 0.7355 (m) cc_final: 0.7098 (t) REVERT: A 409 ARG cc_start: 0.8365 (ttp-170) cc_final: 0.8111 (ttp-170) REVERT: A 432 ARG cc_start: 0.8429 (mtt90) cc_final: 0.8104 (mmt180) REVERT: A 472 TYR cc_start: 0.8184 (m-80) cc_final: 0.7680 (m-80) REVERT: A 559 PHE cc_start: 0.5948 (t80) cc_final: 0.4803 (m-10) REVERT: A 571 LYS cc_start: 0.8867 (mttt) cc_final: 0.8421 (mmtt) REVERT: A 627 TYR cc_start: 0.7249 (m-80) cc_final: 0.6779 (m-80) REVERT: A 644 MET cc_start: 0.9140 (mmm) cc_final: 0.8820 (mmm) REVERT: A 653 TYR cc_start: 0.8504 (p90) cc_final: 0.8264 (p90) REVERT: A 696 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8185 (mm) REVERT: A 698 LYS cc_start: 0.9176 (mmmt) cc_final: 0.8869 (mttp) REVERT: C 393 ASN cc_start: 0.8314 (m-40) cc_final: 0.7673 (m-40) REVERT: C 409 ARG cc_start: 0.8192 (ttp-170) cc_final: 0.7920 (ttp-170) REVERT: C 420 ARG cc_start: 0.8389 (tpp80) cc_final: 0.7591 (tpp80) REVERT: C 432 ARG cc_start: 0.8378 (mtt90) cc_final: 0.7959 (mmt90) REVERT: C 471 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8156 (t0) REVERT: C 472 TYR cc_start: 0.7849 (m-80) cc_final: 0.7448 (m-80) REVERT: C 627 TYR cc_start: 0.7194 (m-80) cc_final: 0.6674 (m-80) REVERT: C 716 MET cc_start: 0.1671 (ttp) cc_final: 0.0996 (ptp) REVERT: C 738 TYR cc_start: 0.3705 (OUTLIER) cc_final: 0.2160 (p90) REVERT: C 743 ARG cc_start: 0.7958 (ttm110) cc_final: 0.7425 (ttm170) REVERT: D 308 MET cc_start: 0.8054 (mmm) cc_final: 0.7737 (mmt) REVERT: D 397 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7575 (tt0) REVERT: D 409 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7811 (ttp-110) REVERT: D 420 ARG cc_start: 0.8562 (tpp80) cc_final: 0.8024 (tpp80) REVERT: D 422 LEU cc_start: 0.8761 (mt) cc_final: 0.8390 (mt) REVERT: D 432 ARG cc_start: 0.8392 (mtt90) cc_final: 0.8119 (mmt180) REVERT: D 471 ASP cc_start: 0.8319 (t0) cc_final: 0.7905 (t0) REVERT: D 560 GLN cc_start: 0.8530 (tp40) cc_final: 0.7793 (tp40) REVERT: D 561 GLN cc_start: 0.7483 (mt0) cc_final: 0.6923 (pm20) REVERT: D 562 MET cc_start: 0.8433 (mtt) cc_final: 0.7929 (mtt) REVERT: D 644 MET cc_start: 0.9199 (mmm) cc_final: 0.8483 (mmm) REVERT: D 698 LYS cc_start: 0.9171 (mmmt) cc_final: 0.8924 (mttp) REVERT: D 738 TYR cc_start: 0.3606 (OUTLIER) cc_final: 0.2113 (p90) REVERT: B 293 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7560 (mt-10) REVERT: B 308 MET cc_start: 0.8284 (mmm) cc_final: 0.8031 (mmt) REVERT: B 363 ARG cc_start: 0.7258 (ttt90) cc_final: 0.6486 (mtt90) REVERT: B 397 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7762 (tt0) REVERT: B 420 ARG cc_start: 0.8693 (tpp80) cc_final: 0.8332 (tpp80) REVERT: B 423 GLN cc_start: 0.8969 (tp40) cc_final: 0.8618 (tp-100) REVERT: B 432 ARG cc_start: 0.8328 (mtt90) cc_final: 0.7965 (mmt180) REVERT: B 471 ASP cc_start: 0.8365 (t0) cc_final: 0.7972 (t0) REVERT: B 532 SER cc_start: 0.9289 (m) cc_final: 0.9038 (t) REVERT: B 627 TYR cc_start: 0.7289 (m-80) cc_final: 0.6758 (m-80) REVERT: B 644 MET cc_start: 0.9119 (mmm) cc_final: 0.8836 (mmm) outliers start: 56 outliers final: 48 residues processed: 578 average time/residue: 0.1085 time to fit residues: 93.7679 Evaluate side-chains 588 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 536 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 738 TYR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 705 ILE Chi-restraints excluded: chain D residue 738 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 393 ASN D 354 GLN D 393 ASN B 354 GLN B 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.160486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.117235 restraints weight = 20665.129| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.52 r_work: 0.3230 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15092 Z= 0.158 Angle : 0.645 16.817 20460 Z= 0.332 Chirality : 0.040 0.276 2304 Planarity : 0.003 0.059 2500 Dihedral : 5.370 50.265 2008 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.56 % Allowed : 19.88 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.30 (0.20), residues: 1764 helix: 1.32 (0.15), residues: 1180 sheet: -2.06 (0.55), residues: 68 loop : -2.17 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 409 TYR 0.010 0.001 TYR C 309 PHE 0.029 0.001 PHE C 304 TRP 0.015 0.002 TRP D 740 HIS 0.003 0.001 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (15092) covalent geometry : angle 0.64496 / 0.33 (20460) hydrogen bonds : bond 0.04037 / 2.69 ( 911) hydrogen bonds : angle 4.51908 / 3.32 ( 2673) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 539 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8066 (mmm) cc_final: 0.7483 (mmm) REVERT: A 313 LEU cc_start: 0.9033 (mt) cc_final: 0.8746 (mt) REVERT: A 379 SER cc_start: 0.7443 (m) cc_final: 0.7212 (t) REVERT: A 397 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7577 (tt0) REVERT: A 409 ARG cc_start: 0.8377 (ttp-170) cc_final: 0.8117 (ttp-170) REVERT: A 432 ARG cc_start: 0.8423 (mtt90) cc_final: 0.8114 (mmt180) REVERT: A 472 TYR cc_start: 0.8203 (m-80) cc_final: 0.7695 (m-80) REVERT: A 532 SER cc_start: 0.9292 (m) cc_final: 0.9007 (t) REVERT: A 559 PHE cc_start: 0.5964 (t80) cc_final: 0.4838 (m-10) REVERT: A 562 MET cc_start: 0.8001 (mmp) cc_final: 0.7579 (mmt) REVERT: A 627 TYR cc_start: 0.7293 (m-80) cc_final: 0.6835 (m-80) REVERT: A 644 MET cc_start: 0.9141 (mmm) cc_final: 0.8864 (mmm) REVERT: A 653 TYR cc_start: 0.8450 (p90) cc_final: 0.8215 (p90) REVERT: A 696 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8233 (mm) REVERT: A 698 LYS cc_start: 0.9169 (mmmt) cc_final: 0.8943 (mttp) REVERT: C 393 ASN cc_start: 0.8359 (m-40) cc_final: 0.8059 (m-40) REVERT: C 409 ARG cc_start: 0.8207 (ttp-170) cc_final: 0.7863 (ttp-170) REVERT: C 420 ARG cc_start: 0.8401 (tpp80) cc_final: 0.7602 (tpp80) REVERT: C 423 GLN cc_start: 0.8862 (tp40) cc_final: 0.8478 (tp-100) REVERT: C 432 ARG cc_start: 0.8400 (mtt90) cc_final: 0.7963 (mmt90) REVERT: C 471 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8150 (t0) REVERT: C 472 TYR cc_start: 0.7847 (m-80) cc_final: 0.7443 (m-80) REVERT: C 627 TYR cc_start: 0.7248 (m-80) cc_final: 0.6748 (m-80) REVERT: C 716 MET cc_start: 0.1985 (ttp) cc_final: 0.1320 (ptp) REVERT: C 743 ARG cc_start: 0.7954 (ttm110) cc_final: 0.7422 (ttm170) REVERT: D 308 MET cc_start: 0.8049 (mmm) cc_final: 0.7824 (mmt) REVERT: D 397 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7570 (tt0) REVERT: D 409 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7748 (ttp-170) REVERT: D 420 ARG cc_start: 0.8559 (tpp80) cc_final: 0.8019 (tpp80) REVERT: D 422 LEU cc_start: 0.8779 (mt) cc_final: 0.8415 (mt) REVERT: D 432 ARG cc_start: 0.8409 (mtt90) cc_final: 0.8127 (mmt180) REVERT: D 471 ASP cc_start: 0.8348 (t0) cc_final: 0.7931 (t0) REVERT: D 561 GLN cc_start: 0.7555 (mt0) cc_final: 0.6934 (pm20) REVERT: D 562 MET cc_start: 0.8421 (mtt) cc_final: 0.7868 (mtt) REVERT: D 738 TYR cc_start: 0.3448 (OUTLIER) cc_final: 0.2015 (p90) REVERT: B 293 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7571 (mt-10) REVERT: B 308 MET cc_start: 0.8275 (mmm) cc_final: 0.7951 (mmt) REVERT: B 363 ARG cc_start: 0.7278 (ttt90) cc_final: 0.6487 (mtt90) REVERT: B 397 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7785 (tt0) REVERT: B 409 ARG cc_start: 0.7628 (ptt-90) cc_final: 0.7404 (ptt-90) REVERT: B 420 ARG cc_start: 0.8682 (tpp80) cc_final: 0.8285 (tpp80) REVERT: B 423 GLN cc_start: 0.8978 (tp40) cc_final: 0.8625 (tp-100) REVERT: B 432 ARG cc_start: 0.8328 (mtt90) cc_final: 0.7964 (mmt180) REVERT: B 471 ASP cc_start: 0.8388 (t0) cc_final: 0.7939 (t0) REVERT: B 532 SER cc_start: 0.9285 (m) cc_final: 0.9035 (t) REVERT: B 627 TYR cc_start: 0.7296 (m-80) cc_final: 0.6775 (m-80) REVERT: B 644 MET cc_start: 0.9128 (mmm) cc_final: 0.8836 (mmm) REVERT: B 746 GLU cc_start: 0.6268 (tt0) cc_final: 0.5667 (tt0) outliers start: 57 outliers final: 51 residues processed: 564 average time/residue: 0.1071 time to fit residues: 90.9890 Evaluate side-chains 592 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 538 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 705 ILE Chi-restraints excluded: chain D residue 738 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 74 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 0.0470 chunk 151 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 393 ASN D 354 GLN D 393 ASN B 354 GLN B 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.161023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.117495 restraints weight = 20636.984| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.56 r_work: 0.3239 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15092 Z= 0.147 Angle : 0.641 12.428 20460 Z= 0.332 Chirality : 0.040 0.275 2304 Planarity : 0.003 0.056 2500 Dihedral : 5.328 49.818 2008 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.50 % Allowed : 20.44 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.28 (0.20), residues: 1764 helix: 1.33 (0.15), residues: 1176 sheet: -1.98 (0.56), residues: 68 loop : -2.23 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 409 TYR 0.009 0.001 TYR C 309 PHE 0.031 0.001 PHE C 304 TRP 0.015 0.002 TRP A 697 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (15092) covalent geometry : angle 0.64116 / 0.33 (20460) hydrogen bonds : bond 0.03989 / 2.65 ( 911) hydrogen bonds : angle 4.54058 / 3.34 ( 2673) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 541 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8090 (mmm) cc_final: 0.7509 (mmm) REVERT: A 313 LEU cc_start: 0.9008 (mt) cc_final: 0.8743 (mt) REVERT: A 356 GLU cc_start: 0.6937 (tt0) cc_final: 0.6547 (tp30) REVERT: A 379 SER cc_start: 0.7431 (m) cc_final: 0.7204 (t) REVERT: A 397 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7554 (tt0) REVERT: A 409 ARG cc_start: 0.8391 (ttp-170) cc_final: 0.8156 (ttp-170) REVERT: A 432 ARG cc_start: 0.8400 (mtt90) cc_final: 0.8113 (mmt180) REVERT: A 472 TYR cc_start: 0.8265 (m-80) cc_final: 0.7708 (m-80) REVERT: A 532 SER cc_start: 0.9282 (m) cc_final: 0.9001 (t) REVERT: A 559 PHE cc_start: 0.5974 (t80) cc_final: 0.4860 (m-10) REVERT: A 627 TYR cc_start: 0.7300 (m-80) cc_final: 0.6808 (m-80) REVERT: A 644 MET cc_start: 0.9135 (mmm) cc_final: 0.8860 (mmm) REVERT: A 653 TYR cc_start: 0.8426 (p90) cc_final: 0.8198 (p90) REVERT: A 696 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8246 (mm) REVERT: C 393 ASN cc_start: 0.8336 (m-40) cc_final: 0.7996 (m-40) REVERT: C 409 ARG cc_start: 0.8161 (ttp-170) cc_final: 0.7784 (ttp-170) REVERT: C 420 ARG cc_start: 0.8385 (tpp80) cc_final: 0.7642 (tpp80) REVERT: C 423 GLN cc_start: 0.8847 (tp40) cc_final: 0.8466 (tp-100) REVERT: C 432 ARG cc_start: 0.8403 (mtt90) cc_final: 0.7961 (mmt90) REVERT: C 471 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8135 (t0) REVERT: C 472 TYR cc_start: 0.7861 (m-80) cc_final: 0.7450 (m-80) REVERT: C 562 MET cc_start: 0.8937 (mmm) cc_final: 0.8557 (mmt) REVERT: C 627 TYR cc_start: 0.7245 (m-80) cc_final: 0.6747 (m-80) REVERT: C 716 MET cc_start: 0.2016 (ttp) cc_final: 0.1553 (ptp) REVERT: C 743 ARG cc_start: 0.7954 (ttm110) cc_final: 0.7418 (ttm170) REVERT: D 308 MET cc_start: 0.8046 (mmm) cc_final: 0.7737 (mmt) REVERT: D 397 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7503 (tt0) REVERT: D 409 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7749 (ttp-170) REVERT: D 420 ARG cc_start: 0.8541 (tpp80) cc_final: 0.8012 (tpp80) REVERT: D 422 LEU cc_start: 0.8767 (mt) cc_final: 0.8405 (mt) REVERT: D 432 ARG cc_start: 0.8365 (mtt90) cc_final: 0.8119 (mmt180) REVERT: D 471 ASP cc_start: 0.8349 (t0) cc_final: 0.7803 (t0) REVERT: D 561 GLN cc_start: 0.7534 (mt0) cc_final: 0.6709 (pm20) REVERT: D 562 MET cc_start: 0.8384 (mtt) cc_final: 0.8069 (mtt) REVERT: D 738 TYR cc_start: 0.3426 (OUTLIER) cc_final: 0.2030 (p90) REVERT: B 293 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7583 (mt-10) REVERT: B 308 MET cc_start: 0.8261 (mmm) cc_final: 0.7943 (mmt) REVERT: B 363 ARG cc_start: 0.7265 (ttt90) cc_final: 0.6477 (mtt90) REVERT: B 397 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7722 (tt0) REVERT: B 409 ARG cc_start: 0.7623 (ptt-90) cc_final: 0.7396 (ptt-90) REVERT: B 420 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8284 (tpp80) REVERT: B 423 GLN cc_start: 0.8976 (tp40) cc_final: 0.8627 (tp-100) REVERT: B 432 ARG cc_start: 0.8290 (mtt90) cc_final: 0.7983 (mmt180) REVERT: B 471 ASP cc_start: 0.8396 (t0) cc_final: 0.7947 (t0) REVERT: B 532 SER cc_start: 0.9289 (m) cc_final: 0.9044 (t) REVERT: B 627 TYR cc_start: 0.7299 (m-80) cc_final: 0.6747 (m-80) REVERT: B 644 MET cc_start: 0.9117 (mmm) cc_final: 0.8823 (mmm) REVERT: B 746 GLU cc_start: 0.6117 (tt0) cc_final: 0.5518 (tt0) outliers start: 56 outliers final: 48 residues processed: 568 average time/residue: 0.1046 time to fit residues: 89.4789 Evaluate side-chains 592 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 541 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 309 TYR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 738 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 2 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 129 optimal weight: 20.0000 chunk 172 optimal weight: 0.8980 chunk 158 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 393 ASN C 354 GLN D 354 GLN D 393 ASN D 494 GLN B 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.160914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117104 restraints weight = 20568.387| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.56 r_work: 0.3233 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 15092 Z= 0.155 Angle : 0.645 13.278 20460 Z= 0.334 Chirality : 0.041 0.279 2304 Planarity : 0.003 0.057 2500 Dihedral : 5.303 48.223 2008 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.44 % Allowed : 20.69 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.31 (0.20), residues: 1764 helix: 1.38 (0.15), residues: 1172 sheet: -1.87 (0.57), residues: 68 loop : -2.28 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 409 TYR 0.010 0.001 TYR A 537 PHE 0.031 0.001 PHE C 304 TRP 0.019 0.002 TRP A 697 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (15092) covalent geometry : angle 0.64501 / 0.33 (20460) hydrogen bonds : bond 0.03993 / 2.67 ( 911) hydrogen bonds : angle 4.55358 / 3.35 ( 2673) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3664.05 seconds wall clock time: 63 minutes 33.32 seconds (3813.32 seconds total)