Starting phenix.real_space_refine on Wed Mar 4 16:46:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l2n_23134/03_2026/7l2n_23134.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2n_23134/03_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_23134/03_2026/7l2n_23134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2n_23134/03_2026/7l2n_23134.map" model { file = "/net/cci-nas-00/data/ceres_data/7l2n_23134/03_2026/7l2n_23134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2n_23134/03_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-5986/lib/python3.9/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: 1.05 Conformation dependent library (CDL) restraints added in 531.5 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: 0.35 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: 2.06 Time building geometry restraints manager: 1.39 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: 8537 16.19 - 32.37: 483 32.37 - 48.56: 100 48.56 - 64.74: 22 64.74 - 80.93: 14 Dihedral angle restraints: 9156 sinusoidal: 3892 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 9153 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: 2.100 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.300 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 11.270 80.929 5772 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 covalent geometry : bond 0.01124 (15092) covalent geometry : angle 0.85771 (20460) hydrogen bonds : bond 0.13189 ( 911) hydrogen bonds : angle 5.54423 ( 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 : 0.395 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: 0.1263 time to fit residues: 136.2841 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 : 0.502 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.161643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118632 restraints weight = 20258.534| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.47 r_work: 0.3256 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2332 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= 0.153 Angle : 0.596 10.639 20460 Z= 0.314 Chirality : 0.039 0.169 2304 Planarity : 0.003 0.046 2500 Dihedral : 7.641 59.662 2352 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.75 % Allowed : 12.69 % Favored : 84.56 % 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: 0.49 (0.20), residues: 1764 helix: 1.42 (0.15), residues: 1180 sheet: -2.50 (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 0.019 0.001 TYR C 463 PHE 0.023 0.001 PHE D 304 TRP 0.014 0.002 TRP A 697 HIS 0.008 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00322 (15092) covalent geometry : angle 0.59617 (20460) hydrogen bonds : bond 0.04961 ( 911) hydrogen bonds : angle 4.49802 ( 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 679 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 635 time to evaluate : 0.519 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: 0.8016 (mmm) cc_final: 0.7502 (mmm) REVERT: A 313 LEU cc_start: 0.9011 (mt) cc_final: 0.8716 (mt) REVERT: A 356 GLU cc_start: 0.6557 (tt0) cc_final: 0.6263 (tt0) REVERT: A 379 SER cc_start: 0.7425 (m) cc_final: 0.7215 (t) REVERT: A 409 ARG cc_start: 0.8341 (ttp-170) cc_final: 0.8121 (ttp-110) REVERT: A 425 LYS cc_start: 0.8282 (tptt) cc_final: 0.7971 (tptt) REVERT: A 427 ASP cc_start: 0.8728 (m-30) cc_final: 0.8476 (m-30) REVERT: A 432 ARG cc_start: 0.8346 (mtt90) cc_final: 0.8091 (mmt180) REVERT: A 472 TYR cc_start: 0.8151 (m-80) cc_final: 0.7472 (m-10) REVERT: A 491 ARG cc_start: 0.8178 (mmm160) cc_final: 0.7867 (mtp180) REVERT: A 533 GLN cc_start: 0.8765 (mt0) cc_final: 0.8529 (mt0) REVERT: A 560 GLN cc_start: 0.8642 (tt0) cc_final: 0.8354 (tp40) REVERT: A 571 LYS cc_start: 0.8951 (mttt) cc_final: 0.8498 (mmtt) REVERT: A 627 TYR cc_start: 0.6870 (m-80) cc_final: 0.6514 (m-80) REVERT: A 644 MET cc_start: 0.9127 (mmm) cc_final: 0.8854 (mmm) REVERT: A 653 TYR cc_start: 0.8550 (p90) cc_final: 0.8204 (p90) REVERT: A 688 LYS cc_start: 0.8597 (mtpt) cc_final: 0.7964 (tptt) REVERT: A 696 ILE cc_start: 0.8452 (tt) cc_final: 0.8178 (mm) REVERT: C 358 HIS cc_start: 0.6642 (p90) cc_final: 0.5800 (t-90) REVERT: C 371 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7656 (mm-30) REVERT: C 379 SER cc_start: 0.8159 (m) cc_final: 0.7919 (t) REVERT: C 393 ASN cc_start: 0.8261 (m-40) cc_final: 0.7736 (m-40) REVERT: C 397 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7215 (tt0) REVERT: C 420 ARG cc_start: 0.8419 (tpp80) cc_final: 0.7586 (tpp80) REVERT: C 427 ASP cc_start: 0.8802 (m-30) cc_final: 0.8563 (m-30) REVERT: C 432 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7978 (mmt180) REVERT: C 472 TYR cc_start: 0.7733 (m-80) cc_final: 0.7439 (m-80) REVERT: C 491 ARG cc_start: 0.8277 (mmm160) cc_final: 0.7940 (mtp180) REVERT: C 560 GLN cc_start: 0.8396 (tt0) cc_final: 0.7977 (tp40) REVERT: C 561 GLN cc_start: 0.7275 (mt0) cc_final: 0.6616 (tt0) REVERT: C 564 ILE cc_start: 0.8751 (tt) cc_final: 0.8495 (tp) REVERT: C 571 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8433 (mtpp) REVERT: C 653 TYR cc_start: 0.8654 (p90) cc_final: 0.8254 (p90) REVERT: C 743 ARG cc_start: 0.8024 (ttm110) cc_final: 0.7433 (ttm170) REVERT: C 746 GLU cc_start: 0.5742 (tt0) cc_final: 0.4685 (tt0) REVERT: D 308 MET cc_start: 0.8056 (mmm) cc_final: 0.7535 (mmm) REVERT: D 313 LEU cc_start: 0.8961 (mt) cc_final: 0.8522 (mt) REVERT: D 397 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7660 (tt0) REVERT: D 420 ARG cc_start: 0.8559 (tpp80) cc_final: 0.7833 (tpp80) REVERT: D 432 ARG cc_start: 0.8340 (mtt90) cc_final: 0.7933 (mmt90) REVERT: D 465 LEU cc_start: 0.8205 (tp) cc_final: 0.7780 (tp) REVERT: D 471 ASP cc_start: 0.8117 (m-30) cc_final: 0.7821 (t0) REVERT: D 472 TYR cc_start: 0.7569 (m-80) cc_final: 0.7219 (m-80) REVERT: D 504 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.6704 (ptpt) REVERT: D 560 GLN cc_start: 0.8349 (tt0) cc_final: 0.8095 (tt0) REVERT: D 561 GLN cc_start: 0.7541 (mt0) cc_final: 0.6966 (tt0) REVERT: D 571 LYS cc_start: 0.8912 (mttt) cc_final: 0.8511 (mmtt) REVERT: D 572 MET cc_start: 0.7985 (mtt) cc_final: 0.7313 (mtt) REVERT: D 644 MET cc_start: 0.9170 (mmm) cc_final: 0.8828 (mmm) REVERT: D 658 VAL cc_start: 0.9334 (t) cc_final: 0.9117 (p) REVERT: D 684 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7361 (tm-30) REVERT: D 696 ILE cc_start: 0.8466 (tt) cc_final: 0.8069 (mm) REVERT: D 746 GLU cc_start: 0.5919 (tt0) cc_final: 0.4983 (tt0) REVERT: B 288 LEU cc_start: 0.8916 (mt) cc_final: 0.8709 (mt) REVERT: B 308 MET cc_start: 0.8453 (mmm) cc_final: 0.7937 (mmm) REVERT: B 324 LYS cc_start: 0.8054 (mttt) cc_final: 0.7420 (ptpp) REVERT: B 363 ARG cc_start: 0.7223 (ttt90) cc_final: 0.6641 (mtt90) REVERT: B 379 SER cc_start: 0.7656 (m) cc_final: 0.7307 (t) REVERT: B 381 LEU cc_start: 0.7493 (mp) cc_final: 0.7008 (mp) REVERT: B 420 ARG cc_start: 0.8722 (tpp80) cc_final: 0.8347 (tpp80) REVERT: B 432 ARG cc_start: 0.8332 (mtt90) cc_final: 0.7986 (mmt180) REVERT: B 472 TYR cc_start: 0.7690 (m-80) cc_final: 0.7224 (m-80) REVERT: B 491 ARG cc_start: 0.8186 (mmm160) cc_final: 0.7916 (mtp180) REVERT: B 627 TYR cc_start: 0.7002 (m-80) cc_final: 0.6572 (m-80) REVERT: B 644 MET cc_start: 0.9081 (mmm) cc_final: 0.8779 (mmm) REVERT: B 658 VAL cc_start: 0.9336 (t) cc_final: 0.9089 (p) REVERT: B 695 ASN cc_start: 0.7978 (m-40) cc_final: 0.7200 (t0) REVERT: B 743 ARG cc_start: 0.8077 (ttm110) cc_final: 0.7417 (ttm170) outliers start: 44 outliers final: 26 residues processed: 646 average time/residue: 0.1161 time to fit residues: 110.0576 Evaluate side-chains 585 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 558 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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: 2.9990 chunk 143 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN C 354 GLN ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN D 364 HIS D 687 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 = 0.3931 r_free = 0.3931 target = 0.161259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117004 restraints weight = 20620.060| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.55 r_work: 0.3216 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15092 Z= 0.157 Angle : 0.579 6.378 20460 Z= 0.307 Chirality : 0.039 0.191 2304 Planarity : 0.003 0.032 2500 Dihedral : 7.443 59.120 2352 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.94 % Allowed : 15.50 % Favored : 81.56 % 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: 0.46 (0.20), residues: 1764 helix: 1.44 (0.15), residues: 1180 sheet: -2.62 (0.53), residues: 72 loop : -1.96 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 721 TYR 0.012 0.001 TYR C 463 PHE 0.025 0.001 PHE D 304 TRP 0.018 0.002 TRP A 740 HIS 0.006 0.001 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00343 (15092) covalent geometry : angle 0.57906 (20460) hydrogen bonds : bond 0.04558 ( 911) hydrogen bonds : angle 4.38930 ( 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 630 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 583 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8042 (mmm) cc_final: 0.7766 (mmt) REVERT: A 313 LEU cc_start: 0.9008 (mt) cc_final: 0.8656 (mt) REVERT: A 356 GLU cc_start: 0.6535 (tt0) cc_final: 0.6214 (tt0) REVERT: A 379 SER cc_start: 0.7419 (m) cc_final: 0.7154 (t) REVERT: A 397 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7714 (tt0) REVERT: A 409 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.7613 (ttp-170) REVERT: A 427 ASP cc_start: 0.8776 (m-30) cc_final: 0.8551 (m-30) REVERT: A 432 ARG cc_start: 0.8356 (mtt90) cc_final: 0.8006 (mmt90) REVERT: A 472 TYR cc_start: 0.8157 (m-80) cc_final: 0.7435 (m-10) REVERT: A 491 ARG cc_start: 0.8216 (mmm160) cc_final: 0.7902 (mtp180) REVERT: A 559 PHE cc_start: 0.5810 (t80) cc_final: 0.5127 (m-10) REVERT: A 571 LYS cc_start: 0.8991 (mttt) cc_final: 0.8521 (mmtt) REVERT: A 627 TYR cc_start: 0.6977 (m-80) cc_final: 0.6606 (m-80) REVERT: A 653 TYR cc_start: 0.8495 (p90) cc_final: 0.8124 (p90) REVERT: A 696 ILE cc_start: 0.8505 (tt) cc_final: 0.8278 (mm) REVERT: A 698 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8838 (mmtt) REVERT: C 304 PHE cc_start: 0.7743 (t80) cc_final: 0.7531 (t80) REVERT: C 358 HIS cc_start: 0.6671 (p90) cc_final: 0.5820 (t-90) REVERT: C 393 ASN cc_start: 0.8289 (m-40) cc_final: 0.7774 (m-40) REVERT: C 397 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7251 (tt0) REVERT: C 409 ARG cc_start: 0.8278 (ttp-170) cc_final: 0.7775 (ttp-170) REVERT: C 420 ARG cc_start: 0.8454 (tpp80) cc_final: 0.7646 (tpp80) REVERT: C 432 ARG cc_start: 0.8331 (mtt90) cc_final: 0.7841 (mmt90) REVERT: C 471 ASP cc_start: 0.8071 (m-30) cc_final: 0.7738 (t0) REVERT: C 472 TYR cc_start: 0.7734 (m-80) cc_final: 0.7351 (m-80) REVERT: C 491 ARG cc_start: 0.8313 (mmm160) cc_final: 0.7933 (mtp180) REVERT: C 560 GLN cc_start: 0.8469 (tt0) cc_final: 0.8155 (tp40) REVERT: C 571 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8486 (mtpp) REVERT: C 653 TYR cc_start: 0.8540 (p90) cc_final: 0.8223 (p90) REVERT: C 743 ARG cc_start: 0.7930 (ttm110) cc_final: 0.7349 (ttm170) REVERT: D 308 MET cc_start: 0.8051 (mmm) cc_final: 0.7708 (mmt) REVERT: D 397 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7562 (tt0) REVERT: D 420 ARG cc_start: 0.8495 (tpp80) cc_final: 0.7809 (tpp80) REVERT: D 429 PHE cc_start: 0.8393 (p90) cc_final: 0.8128 (p90) REVERT: D 432 ARG cc_start: 0.8371 (mtt90) cc_final: 0.8036 (mmt180) REVERT: D 472 TYR cc_start: 0.7737 (m-80) cc_final: 0.7279 (m-80) REVERT: D 560 GLN cc_start: 0.8467 (tt0) cc_final: 0.8118 (tt0) REVERT: D 561 GLN cc_start: 0.7621 (mt0) cc_final: 0.6949 (tt0) REVERT: D 644 MET cc_start: 0.9220 (mmm) cc_final: 0.8225 (mmm) REVERT: D 658 VAL cc_start: 0.9338 (t) cc_final: 0.9120 (p) REVERT: D 709 GLU cc_start: 0.8396 (tt0) cc_final: 0.8062 (tt0) REVERT: D 746 GLU cc_start: 0.5803 (tt0) cc_final: 0.4914 (tt0) REVERT: B 288 LEU cc_start: 0.9018 (mt) cc_final: 0.8742 (mt) REVERT: B 293 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7660 (mt-10) REVERT: B 308 MET cc_start: 0.8507 (mmm) cc_final: 0.8014 (mmm) REVERT: B 324 LYS cc_start: 0.8075 (mttt) cc_final: 0.7796 (mmpt) REVERT: B 363 ARG cc_start: 0.7333 (ttt90) cc_final: 0.6566 (mtt90) REVERT: B 379 SER cc_start: 0.7550 (m) cc_final: 0.7261 (t) REVERT: B 381 LEU cc_start: 0.7666 (mp) cc_final: 0.7165 (mp) REVERT: B 397 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7831 (tt0) REVERT: B 409 ARG cc_start: 0.7525 (ptt-90) cc_final: 0.7214 (ptt-90) REVERT: B 420 ARG cc_start: 0.8713 (tpp80) cc_final: 0.8255 (tpp80) REVERT: B 432 ARG cc_start: 0.8384 (mtt90) cc_final: 0.7889 (mmt90) REVERT: B 471 ASP cc_start: 0.8146 (m-30) cc_final: 0.7752 (t0) REVERT: B 472 TYR cc_start: 0.7718 (m-80) cc_final: 0.7245 (m-80) REVERT: B 491 ARG cc_start: 0.8262 (mmm160) cc_final: 0.7923 (mtp180) REVERT: B 533 GLN cc_start: 0.8745 (mt0) cc_final: 0.8518 (mt0) REVERT: B 560 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7826 (tp40) REVERT: B 627 TYR cc_start: 0.7033 (m-80) cc_final: 0.6573 (m-80) REVERT: B 644 MET cc_start: 0.9111 (mmm) cc_final: 0.8819 (mmm) REVERT: B 658 VAL cc_start: 0.9331 (t) cc_final: 0.9092 (p) REVERT: B 681 LEU cc_start: 0.8675 (mm) cc_final: 0.8387 (mm) REVERT: B 695 ASN cc_start: 0.7789 (m-40) cc_final: 0.7291 (m-40) REVERT: B 743 ARG cc_start: 0.8103 (ttm110) cc_final: 0.7437 (ttm170) outliers start: 47 outliers final: 31 residues processed: 602 average time/residue: 0.1153 time to fit residues: 102.1169 Evaluate side-chains 595 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 563 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 560 GLN 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: 6.9990 chunk 20 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN C 354 GLN ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 687 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 = 0.3853 r_free = 0.3853 target = 0.154534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109936 restraints weight = 20863.929| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.52 r_work: 0.3133 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 15092 Z= 0.309 Angle : 0.668 6.608 20460 Z= 0.350 Chirality : 0.043 0.180 2304 Planarity : 0.004 0.085 2500 Dihedral : 7.502 58.585 2352 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.56 % Allowed : 16.88 % Favored : 78.56 % 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: 0.21 (0.20), residues: 1764 helix: 1.25 (0.15), residues: 1180 sheet: -3.06 (0.49), residues: 72 loop : -2.01 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 409 TYR 0.013 0.002 TYR D 351 PHE 0.026 0.002 PHE A 582 TRP 0.032 0.002 TRP B 697 HIS 0.005 0.001 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00698 (15092) covalent geometry : angle 0.66833 (20460) hydrogen bonds : bond 0.04862 ( 911) hydrogen bonds : angle 4.52561 ( 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 637 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 564 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8062 (mmm) cc_final: 0.7790 (mmt) REVERT: A 313 LEU cc_start: 0.9067 (mt) cc_final: 0.8664 (mt) REVERT: A 356 GLU cc_start: 0.6812 (tt0) cc_final: 0.6529 (tt0) REVERT: A 363 ARG cc_start: 0.7310 (ttt90) cc_final: 0.6606 (mtt90) REVERT: A 379 SER cc_start: 0.7521 (m) cc_final: 0.7315 (t) REVERT: A 397 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7699 (tt0) REVERT: A 409 ARG cc_start: 0.8406 (ttp-170) cc_final: 0.8031 (ttp-170) REVERT: A 422 LEU cc_start: 0.8941 (mt) cc_final: 0.8701 (mt) REVERT: A 432 ARG cc_start: 0.8474 (mtt90) cc_final: 0.8076 (mmt90) REVERT: A 472 TYR cc_start: 0.8217 (m-80) cc_final: 0.7460 (m-10) REVERT: A 559 PHE cc_start: 0.6180 (t80) cc_final: 0.4941 (m-10) REVERT: A 571 LYS cc_start: 0.8972 (mttt) cc_final: 0.8579 (mmtt) REVERT: A 627 TYR cc_start: 0.7226 (m-80) cc_final: 0.6722 (m-80) REVERT: A 653 TYR cc_start: 0.8621 (p90) cc_final: 0.8208 (p90) REVERT: A 673 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8534 (tp) REVERT: A 698 LYS cc_start: 0.9248 (mmmt) cc_final: 0.8868 (mtpp) REVERT: C 409 ARG cc_start: 0.8345 (ttp-170) cc_final: 0.7982 (ttp-170) REVERT: C 420 ARG cc_start: 0.8450 (tpp80) cc_final: 0.7691 (tpp80) REVERT: C 422 LEU cc_start: 0.8899 (mt) cc_final: 0.8651 (mt) REVERT: C 432 ARG cc_start: 0.8474 (mtt90) cc_final: 0.8059 (mmt180) REVERT: C 471 ASP cc_start: 0.8091 (m-30) cc_final: 0.7794 (t0) REVERT: C 472 TYR cc_start: 0.7829 (m-80) cc_final: 0.7505 (m-80) REVERT: C 571 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8650 (mtpp) REVERT: C 627 TYR cc_start: 0.7255 (m-80) cc_final: 0.6727 (m-80) REVERT: C 653 TYR cc_start: 0.8663 (p90) cc_final: 0.8317 (p90) REVERT: C 673 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8621 (tt) REVERT: C 709 GLU cc_start: 0.8621 (tt0) cc_final: 0.8373 (tt0) REVERT: C 743 ARG cc_start: 0.7957 (ttm110) cc_final: 0.7376 (ttm170) REVERT: D 308 MET cc_start: 0.8078 (mmm) cc_final: 0.7496 (mmm) REVERT: D 397 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7672 (tt0) REVERT: D 420 ARG cc_start: 0.8515 (tpp80) cc_final: 0.7867 (tpp80) REVERT: D 432 ARG cc_start: 0.8444 (mtt90) cc_final: 0.7996 (mmt90) REVERT: D 471 ASP cc_start: 0.8366 (t0) cc_final: 0.7730 (t0) REVERT: D 504 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.6832 (ptpt) REVERT: D 560 GLN cc_start: 0.8645 (tt0) cc_final: 0.8379 (tp40) REVERT: D 627 TYR cc_start: 0.7124 (m-80) cc_final: 0.6646 (m-80) REVERT: D 636 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8921 (tp30) REVERT: D 684 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7565 (tm-30) REVERT: D 698 LYS cc_start: 0.9229 (mmmt) cc_final: 0.9010 (mttp) REVERT: B 288 LEU cc_start: 0.9068 (mt) cc_final: 0.8809 (mt) REVERT: B 293 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7603 (mt-10) REVERT: B 308 MET cc_start: 0.8514 (mmm) cc_final: 0.7981 (mmm) REVERT: B 363 ARG cc_start: 0.7370 (ttt90) cc_final: 0.6586 (mtt90) REVERT: B 397 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7796 (tt0) REVERT: B 420 ARG cc_start: 0.8724 (tpp80) cc_final: 0.8310 (tpp80) REVERT: B 432 ARG cc_start: 0.8435 (mtt90) cc_final: 0.8029 (mmt180) REVERT: B 471 ASP cc_start: 0.8164 (m-30) cc_final: 0.7791 (t0) REVERT: B 491 ARG cc_start: 0.8365 (mmm160) cc_final: 0.8144 (mmm160) REVERT: B 627 TYR cc_start: 0.7261 (m-80) cc_final: 0.6669 (m-80) REVERT: B 695 ASN cc_start: 0.8121 (m-40) cc_final: 0.7388 (m-40) REVERT: B 697 TRP cc_start: 0.8616 (t60) cc_final: 0.8160 (t60) REVERT: B 698 LYS cc_start: 0.9170 (mmmt) cc_final: 0.8909 (mttp) outliers start: 73 outliers final: 44 residues processed: 596 average time/residue: 0.1166 time to fit residues: 101.9564 Evaluate side-chains 583 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 536 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 293 GLU 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 673 LEU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain C residue 414 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 673 LEU 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 328 ILE Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 425 LYS 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 283 VAL 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 687 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 110 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 393 ASN ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN D 354 GLN B 354 GLN B 393 ASN B 628 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.159241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115096 restraints weight = 20626.047| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.54 r_work: 0.3197 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15092 Z= 0.146 Angle : 0.600 8.345 20460 Z= 0.312 Chirality : 0.039 0.163 2304 Planarity : 0.003 0.071 2500 Dihedral : 7.142 57.995 2352 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.69 % Allowed : 18.75 % Favored : 77.56 % 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: 0.22 (0.20), residues: 1764 helix: 1.27 (0.15), residues: 1180 sheet: -2.36 (0.50), residues: 68 loop : -2.17 (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 0.023 0.001 PHE D 304 TRP 0.016 0.002 TRP B 697 HIS 0.003 0.001 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00325 (15092) covalent geometry : angle 0.59978 (20460) hydrogen bonds : bond 0.04281 ( 911) hydrogen bonds : angle 4.44004 ( 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 633 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 574 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8137 (mmm) cc_final: 0.7553 (mmm) REVERT: A 313 LEU cc_start: 0.9027 (mt) cc_final: 0.8651 (mt) REVERT: A 326 GLU cc_start: 0.9025 (mp0) cc_final: 0.8790 (mp0) REVERT: A 356 GLU cc_start: 0.6780 (tt0) cc_final: 0.6529 (tt0) REVERT: A 397 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7642 (tt0) REVERT: A 409 ARG cc_start: 0.8359 (ttp-170) cc_final: 0.8024 (ttp-170) REVERT: A 432 ARG cc_start: 0.8380 (mtt90) cc_final: 0.8080 (mmt180) REVERT: A 472 TYR cc_start: 0.8299 (m-80) cc_final: 0.7457 (m-10) REVERT: A 559 PHE cc_start: 0.6112 (t80) cc_final: 0.4915 (m-10) REVERT: A 562 MET cc_start: 0.8356 (mmt) cc_final: 0.8045 (mmt) REVERT: A 571 LYS cc_start: 0.8948 (mttt) cc_final: 0.8544 (mmtt) REVERT: A 572 MET cc_start: 0.8385 (ttm) cc_final: 0.7743 (ttm) REVERT: A 627 TYR cc_start: 0.7220 (m-80) cc_final: 0.6705 (m-80) REVERT: A 644 MET cc_start: 0.9146 (mmm) cc_final: 0.8888 (mmm) REVERT: A 653 TYR cc_start: 0.8332 (p90) cc_final: 0.8118 (p90) REVERT: A 696 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8304 (mm) REVERT: A 698 LYS cc_start: 0.9243 (mmmt) cc_final: 0.8974 (mmtt) REVERT: C 393 ASN cc_start: 0.8338 (m110) cc_final: 0.7934 (m-40) REVERT: C 409 ARG cc_start: 0.8258 (ttp-170) cc_final: 0.7787 (ttp-170) REVERT: C 420 ARG cc_start: 0.8425 (tpp80) cc_final: 0.7642 (tpp80) REVERT: C 432 ARG cc_start: 0.8386 (mtt90) cc_final: 0.7883 (mmt90) REVERT: C 471 ASP cc_start: 0.8108 (m-30) cc_final: 0.7820 (t0) REVERT: C 472 TYR cc_start: 0.7817 (m-80) cc_final: 0.7431 (m-80) REVERT: C 559 PHE cc_start: 0.5117 (t80) cc_final: 0.4513 (m-10) REVERT: C 571 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8442 (mmtt) REVERT: C 627 TYR cc_start: 0.7176 (m-80) cc_final: 0.6663 (m-80) REVERT: C 644 MET cc_start: 0.9180 (mmm) cc_final: 0.8840 (mmm) REVERT: C 698 LYS cc_start: 0.9255 (ttmm) cc_final: 0.9022 (mmmt) REVERT: C 709 GLU cc_start: 0.8635 (tt0) cc_final: 0.8396 (tt0) REVERT: C 738 TYR cc_start: 0.3800 (OUTLIER) cc_final: 0.2086 (p90) REVERT: C 743 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7333 (ttm170) REVERT: D 308 MET cc_start: 0.8053 (mmm) cc_final: 0.7457 (mmm) REVERT: D 356 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6940 (tp30) REVERT: D 397 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7579 (tt0) REVERT: D 420 ARG cc_start: 0.8484 (tpp80) cc_final: 0.7783 (tpp80) REVERT: D 429 PHE cc_start: 0.8297 (p90) cc_final: 0.8054 (p90) REVERT: D 432 ARG cc_start: 0.8404 (mtt90) cc_final: 0.7987 (mmt90) REVERT: D 471 ASP cc_start: 0.8426 (t0) cc_final: 0.7661 (t0) REVERT: D 560 GLN cc_start: 0.8523 (tt0) cc_final: 0.8195 (tp40) REVERT: D 636 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8895 (tp30) REVERT: D 644 MET cc_start: 0.9180 (mmm) cc_final: 0.8867 (mmm) REVERT: B 288 LEU cc_start: 0.9049 (mt) cc_final: 0.8772 (mt) REVERT: B 293 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7606 (mt-10) REVERT: B 308 MET cc_start: 0.8349 (mmm) cc_final: 0.8000 (mmt) REVERT: B 363 ARG cc_start: 0.7302 (ttt90) cc_final: 0.6534 (mtt90) REVERT: B 397 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7781 (tt0) REVERT: B 420 ARG cc_start: 0.8684 (tpp80) cc_final: 0.8268 (tpp80) REVERT: B 432 ARG cc_start: 0.8374 (mtt90) cc_final: 0.7938 (mmt90) REVERT: B 471 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7861 (t0) REVERT: B 491 ARG cc_start: 0.8331 (mmm160) cc_final: 0.7887 (mtp180) REVERT: B 533 GLN cc_start: 0.8816 (mt0) cc_final: 0.8588 (mt0) REVERT: B 560 GLN cc_start: 0.8351 (tp40) cc_final: 0.8049 (tp40) REVERT: B 627 TYR cc_start: 0.7293 (m-80) cc_final: 0.6716 (m-80) REVERT: B 644 MET cc_start: 0.9143 (mmm) cc_final: 0.8842 (mmm) REVERT: B 695 ASN cc_start: 0.7931 (m-40) cc_final: 0.7338 (m-40) REVERT: B 698 LYS cc_start: 0.9118 (mmmt) cc_final: 0.8894 (mttp) REVERT: B 746 GLU cc_start: 0.6300 (tt0) cc_final: 0.5697 (tt0) outliers start: 59 outliers final: 43 residues processed: 597 average time/residue: 0.1102 time to fit residues: 98.8421 Evaluate side-chains 597 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 550 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 473 PHE 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 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 421 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 C residue 703 ILE 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 334 LEU Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 422 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 656 LYS Chi-restraints excluded: chain D residue 687 ASN Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 471 ASP 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 681 LEU 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: 0.7980 chunk 173 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 150 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3914 r_free = 0.3914 target = 0.160002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.115791 restraints weight = 20696.985| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.55 r_work: 0.3204 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3664 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= 0.149 Angle : 0.588 8.281 20460 Z= 0.307 Chirality : 0.039 0.179 2304 Planarity : 0.003 0.057 2500 Dihedral : 6.988 57.295 2352 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.12 % Allowed : 19.38 % Favored : 76.50 % 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: 0.19 (0.20), residues: 1764 helix: 1.25 (0.15), residues: 1180 sheet: -2.32 (0.51), residues: 68 loop : -2.20 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 409 TYR 0.015 0.001 TYR C 653 PHE 0.029 0.001 PHE D 304 TRP 0.013 0.002 TRP A 740 HIS 0.002 0.001 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00336 (15092) covalent geometry : angle 0.58799 (20460) hydrogen bonds : bond 0.04152 ( 911) hydrogen bonds : angle 4.45224 ( 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 627 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 561 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8154 (mmm) cc_final: 0.7573 (mmm) REVERT: A 313 LEU cc_start: 0.9067 (mt) cc_final: 0.8718 (mt) REVERT: A 356 GLU cc_start: 0.6782 (tt0) cc_final: 0.6533 (tt0) REVERT: A 397 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7612 (tt0) REVERT: A 409 ARG cc_start: 0.8417 (ttp-170) cc_final: 0.8137 (ttp-170) REVERT: A 432 ARG cc_start: 0.8449 (mtt90) cc_final: 0.8104 (mmt180) REVERT: A 472 TYR cc_start: 0.8222 (m-80) cc_final: 0.7751 (m-80) REVERT: A 532 SER cc_start: 0.9313 (m) cc_final: 0.9016 (t) REVERT: A 559 PHE cc_start: 0.6110 (t80) cc_final: 0.4945 (m-10) REVERT: A 562 MET cc_start: 0.8274 (mmt) cc_final: 0.7958 (mmt) REVERT: A 571 LYS cc_start: 0.8919 (mttt) cc_final: 0.8498 (mmtt) REVERT: A 627 TYR cc_start: 0.7262 (m-80) cc_final: 0.6771 (m-80) REVERT: A 644 MET cc_start: 0.9144 (mmm) cc_final: 0.8908 (mmm) REVERT: A 653 TYR cc_start: 0.8267 (p90) cc_final: 0.8011 (p90) REVERT: A 696 ILE cc_start: 0.8531 (tt) cc_final: 0.8305 (mm) REVERT: A 698 LYS cc_start: 0.9209 (mmmt) cc_final: 0.8878 (mttp) REVERT: C 393 ASN cc_start: 0.8366 (m110) cc_final: 0.8091 (m110) REVERT: C 409 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.7933 (ttp-170) REVERT: C 420 ARG cc_start: 0.8414 (tpp80) cc_final: 0.7619 (tpp80) REVERT: C 432 ARG cc_start: 0.8426 (mtt90) cc_final: 0.7961 (mmt90) REVERT: C 471 ASP cc_start: 0.8109 (m-30) cc_final: 0.7828 (t0) REVERT: C 472 TYR cc_start: 0.7853 (m-80) cc_final: 0.7469 (m-80) REVERT: C 559 PHE cc_start: 0.5161 (t80) cc_final: 0.4608 (m-10) REVERT: C 571 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8561 (mtpp) REVERT: C 627 TYR cc_start: 0.7249 (m-80) cc_final: 0.6753 (m-80) REVERT: C 716 MET cc_start: 0.2196 (ttp) cc_final: 0.1384 (ptt) REVERT: C 738 TYR cc_start: 0.3765 (OUTLIER) cc_final: 0.2110 (p90) REVERT: C 743 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7379 (ttm170) REVERT: D 308 MET cc_start: 0.8048 (mmm) cc_final: 0.7800 (mmt) REVERT: D 356 GLU cc_start: 0.7098 (tt0) cc_final: 0.6850 (tp30) REVERT: D 397 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7573 (tt0) REVERT: D 409 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7852 (ttp-170) REVERT: D 420 ARG cc_start: 0.8462 (tpp80) cc_final: 0.7771 (tpp80) REVERT: D 429 PHE cc_start: 0.8301 (p90) cc_final: 0.8035 (p90) REVERT: D 432 ARG cc_start: 0.8406 (mtt90) cc_final: 0.7974 (mmt90) REVERT: D 471 ASP cc_start: 0.8310 (t0) cc_final: 0.7678 (t0) REVERT: D 636 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8969 (tp30) REVERT: D 709 GLU cc_start: 0.8399 (tt0) cc_final: 0.8172 (tt0) REVERT: D 738 TYR cc_start: 0.3564 (OUTLIER) cc_final: 0.1975 (p90) REVERT: B 293 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7597 (mt-10) REVERT: B 308 MET cc_start: 0.8350 (mmm) cc_final: 0.8099 (mmt) REVERT: B 363 ARG cc_start: 0.7310 (ttt90) cc_final: 0.6559 (mtt90) REVERT: B 397 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7763 (tt0) REVERT: B 420 ARG cc_start: 0.8659 (tpp80) cc_final: 0.8265 (tpp80) REVERT: B 422 LEU cc_start: 0.8847 (mt) cc_final: 0.8472 (mt) REVERT: B 432 ARG cc_start: 0.8390 (mtt90) cc_final: 0.7940 (mmt90) REVERT: B 471 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7776 (t0) REVERT: B 532 SER cc_start: 0.9309 (m) cc_final: 0.9048 (t) REVERT: B 560 GLN cc_start: 0.8338 (tp40) cc_final: 0.8028 (tp40) REVERT: B 627 TYR cc_start: 0.7323 (m-80) cc_final: 0.6756 (m-80) REVERT: B 695 ASN cc_start: 0.7821 (m-40) cc_final: 0.7210 (m-40) REVERT: B 698 LYS cc_start: 0.9140 (mmmt) cc_final: 0.8919 (mttp) REVERT: B 746 GLU cc_start: 0.6356 (tt0) cc_final: 0.5773 (tt0) outliers start: 66 outliers final: 48 residues processed: 590 average time/residue: 0.1101 time to fit residues: 97.2072 Evaluate side-chains 598 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 547 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 473 PHE 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 648 GLU Chi-restraints excluded: chain A residue 687 ASN 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 414 LEU Chi-restraints excluded: chain C residue 421 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 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 334 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 422 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 561 GLN Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 656 LYS 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 471 ASP 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 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: 0.7980 chunk 98 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 137 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 393 ASN A 560 GLN C 354 GLN C 393 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 = 0.3900 r_free = 0.3900 target = 0.158987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116517 restraints weight = 20618.743| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.46 r_work: 0.3216 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15092 Z= 0.154 Angle : 0.600 10.089 20460 Z= 0.313 Chirality : 0.039 0.223 2304 Planarity : 0.003 0.056 2500 Dihedral : 6.954 56.890 2352 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.94 % Allowed : 19.94 % Favored : 76.12 % 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: 0.17 (0.20), residues: 1764 helix: 1.22 (0.15), residues: 1180 sheet: -2.24 (0.51), residues: 68 loop : -2.19 (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 A 351 PHE 0.028 0.001 PHE D 304 TRP 0.012 0.001 TRP A 426 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00348 (15092) covalent geometry : angle 0.60017 (20460) hydrogen bonds : bond 0.04116 ( 911) hydrogen bonds : angle 4.47527 ( 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 621 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 558 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 308 MET cc_start: 0.8120 (mmm) cc_final: 0.7519 (mmm) REVERT: A 313 LEU cc_start: 0.9070 (mt) cc_final: 0.8737 (mt) REVERT: A 397 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7620 (tt0) REVERT: A 409 ARG cc_start: 0.8388 (ttp-170) cc_final: 0.8086 (ttp-170) REVERT: A 432 ARG cc_start: 0.8394 (mtt90) cc_final: 0.8090 (mmt180) REVERT: A 472 TYR cc_start: 0.8191 (m-80) cc_final: 0.7681 (m-80) REVERT: A 532 SER cc_start: 0.9306 (m) cc_final: 0.9016 (t) REVERT: A 559 PHE cc_start: 0.6011 (t80) cc_final: 0.4840 (m-10) REVERT: A 571 LYS cc_start: 0.8916 (mttt) cc_final: 0.8481 (mmtt) REVERT: A 627 TYR cc_start: 0.7263 (m-80) cc_final: 0.6787 (m-80) REVERT: A 644 MET cc_start: 0.9150 (mmm) cc_final: 0.8918 (mmm) REVERT: A 696 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8262 (mm) REVERT: A 698 LYS cc_start: 0.9192 (mmmt) cc_final: 0.8895 (mttp) REVERT: C 393 ASN cc_start: 0.8407 (m-40) cc_final: 0.7994 (m-40) REVERT: C 409 ARG cc_start: 0.8279 (ttp-170) cc_final: 0.7927 (ttp-170) REVERT: C 420 ARG cc_start: 0.8405 (tpp80) cc_final: 0.7605 (tpp80) REVERT: C 432 ARG cc_start: 0.8421 (mtt90) cc_final: 0.7963 (mmt90) REVERT: C 471 ASP cc_start: 0.8099 (m-30) cc_final: 0.7836 (t0) REVERT: C 472 TYR cc_start: 0.7865 (m-80) cc_final: 0.7466 (m-80) REVERT: C 559 PHE cc_start: 0.5250 (t80) cc_final: 0.4655 (m-10) REVERT: C 571 LYS cc_start: 0.8804 (mtpp) cc_final: 0.8597 (mtpp) REVERT: C 627 TYR cc_start: 0.7245 (m-80) cc_final: 0.6718 (m-80) REVERT: C 738 TYR cc_start: 0.3709 (OUTLIER) cc_final: 0.2218 (p90) REVERT: C 743 ARG cc_start: 0.7957 (ttm110) cc_final: 0.7400 (ttm170) REVERT: D 308 MET cc_start: 0.8048 (mmm) cc_final: 0.7810 (mmt) REVERT: D 356 GLU cc_start: 0.6985 (tt0) cc_final: 0.6655 (tp30) REVERT: D 363 ARG cc_start: 0.7359 (ttt90) cc_final: 0.6569 (mtt90) REVERT: D 397 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7592 (tt0) REVERT: D 409 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7703 (ttp-170) REVERT: D 420 ARG cc_start: 0.8452 (tpp80) cc_final: 0.7778 (tpp80) REVERT: D 432 ARG cc_start: 0.8435 (mtt90) cc_final: 0.8010 (mmt90) REVERT: D 471 ASP cc_start: 0.8292 (t0) cc_final: 0.7624 (t0) REVERT: D 504 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.6788 (ptpt) REVERT: D 709 GLU cc_start: 0.8377 (tt0) cc_final: 0.8168 (tt0) REVERT: D 738 TYR cc_start: 0.3677 (OUTLIER) cc_final: 0.2083 (p90) REVERT: B 293 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7563 (mt-10) REVERT: B 308 MET cc_start: 0.8294 (mmm) cc_final: 0.8041 (mmt) REVERT: B 363 ARG cc_start: 0.7252 (ttt90) cc_final: 0.6479 (mtt90) REVERT: B 397 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7787 (tt0) REVERT: B 420 ARG cc_start: 0.8651 (tpp80) cc_final: 0.8225 (tpp80) REVERT: B 432 ARG cc_start: 0.8372 (mtt90) cc_final: 0.7932 (mmt90) REVERT: B 471 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7816 (t0) REVERT: B 532 SER cc_start: 0.9283 (m) cc_final: 0.9032 (t) REVERT: B 560 GLN cc_start: 0.8338 (tp40) cc_final: 0.8136 (tp40) REVERT: B 627 TYR cc_start: 0.7365 (m-80) cc_final: 0.6772 (m-80) REVERT: B 697 TRP cc_start: 0.8526 (t60) cc_final: 0.7979 (t60) REVERT: B 698 LYS cc_start: 0.9140 (mmmt) cc_final: 0.8914 (mttp) outliers start: 63 outliers final: 48 residues processed: 588 average time/residue: 0.1109 time to fit residues: 97.3498 Evaluate side-chains 582 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 529 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 464 LYS Chi-restraints excluded: chain A residue 473 PHE 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 648 GLU 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 414 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 586 VAL 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 422 LEU 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 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 283 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 471 ASP 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 687 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 54 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 393 ASN D 354 GLN D 393 ASN D 560 GLN 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 = 0.3872 r_free = 0.3872 target = 0.156626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.113141 restraints weight = 20864.503| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.50 r_work: 0.3182 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15092 Z= 0.222 Angle : 0.658 14.638 20460 Z= 0.343 Chirality : 0.042 0.278 2304 Planarity : 0.004 0.075 2500 Dihedral : 7.102 58.839 2352 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.06 % Allowed : 20.19 % Favored : 75.75 % 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: 1.30 (0.15), residues: 1156 sheet: -2.15 (0.54), residues: 68 loop : -1.97 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 409 TYR 0.014 0.001 TYR D 351 PHE 0.026 0.002 PHE D 429 TRP 0.033 0.002 TRP C 697 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00513 (15092) covalent geometry : angle 0.65839 (20460) hydrogen bonds : bond 0.04338 ( 911) hydrogen bonds : angle 4.60472 ( 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 607 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 542 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8099 (mmm) cc_final: 0.7509 (mmm) REVERT: A 313 LEU cc_start: 0.9087 (mt) cc_final: 0.8727 (mt) REVERT: A 363 ARG cc_start: 0.7343 (ttt90) cc_final: 0.6600 (mtt90) REVERT: A 397 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7632 (tt0) REVERT: A 422 LEU cc_start: 0.8926 (mt) cc_final: 0.8682 (mt) REVERT: A 432 ARG cc_start: 0.8447 (mtt90) cc_final: 0.8114 (mmt180) REVERT: A 472 TYR cc_start: 0.8267 (m-80) cc_final: 0.7751 (m-80) REVERT: A 532 SER cc_start: 0.9275 (m) cc_final: 0.8993 (t) REVERT: A 559 PHE cc_start: 0.5952 (t80) cc_final: 0.4808 (m-10) REVERT: A 562 MET cc_start: 0.8156 (mmp) cc_final: 0.7751 (mmt) REVERT: A 627 TYR cc_start: 0.7354 (m-80) cc_final: 0.6859 (m-80) REVERT: A 696 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8316 (mm) REVERT: A 698 LYS cc_start: 0.9174 (mmmt) cc_final: 0.8969 (mttp) REVERT: C 393 ASN cc_start: 0.8462 (m-40) cc_final: 0.7958 (m-40) REVERT: C 409 ARG cc_start: 0.8266 (ttp-170) cc_final: 0.7977 (ttp-170) REVERT: C 420 ARG cc_start: 0.8399 (tpp80) cc_final: 0.7634 (tpp80) REVERT: C 432 ARG cc_start: 0.8469 (mtt90) cc_final: 0.7988 (mmt90) REVERT: C 471 ASP cc_start: 0.8105 (m-30) cc_final: 0.7834 (t0) REVERT: C 472 TYR cc_start: 0.7886 (m-80) cc_final: 0.7506 (m-80) REVERT: C 559 PHE cc_start: 0.5363 (t80) cc_final: 0.4635 (m-10) REVERT: C 627 TYR cc_start: 0.7320 (m-80) cc_final: 0.6756 (m-80) REVERT: C 644 MET cc_start: 0.9174 (mmm) cc_final: 0.8249 (mmm) REVERT: C 696 ILE cc_start: 0.8604 (mm) cc_final: 0.8385 (mm) REVERT: C 716 MET cc_start: 0.2028 (ttp) cc_final: 0.1193 (ptp) REVERT: C 743 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7321 (ttm170) REVERT: D 308 MET cc_start: 0.8042 (mmm) cc_final: 0.7809 (mmt) REVERT: D 356 GLU cc_start: 0.7119 (tt0) cc_final: 0.6821 (tp30) REVERT: D 363 ARG cc_start: 0.7427 (ttt90) cc_final: 0.6670 (mtt90) REVERT: D 397 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7596 (tt0) REVERT: D 409 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7908 (ttp-110) REVERT: D 420 ARG cc_start: 0.8446 (tpp80) cc_final: 0.7901 (tpp80) REVERT: D 432 ARG cc_start: 0.8473 (mtt90) cc_final: 0.8030 (mmt90) REVERT: D 471 ASP cc_start: 0.8292 (t0) cc_final: 0.7752 (t0) REVERT: D 504 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.6820 (ptpt) REVERT: D 698 LYS cc_start: 0.9249 (mmmt) cc_final: 0.9031 (mmtt) REVERT: D 709 GLU cc_start: 0.8346 (tt0) cc_final: 0.8142 (tt0) REVERT: B 293 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7543 (mt-10) REVERT: B 308 MET cc_start: 0.8334 (mmm) cc_final: 0.8079 (mmt) REVERT: B 363 ARG cc_start: 0.7263 (ttt90) cc_final: 0.6536 (mtt90) REVERT: B 397 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7681 (tt0) REVERT: B 420 ARG cc_start: 0.8519 (tpp80) cc_final: 0.8289 (tpp80) REVERT: B 422 LEU cc_start: 0.8919 (mt) cc_final: 0.8668 (mt) REVERT: B 432 ARG cc_start: 0.8424 (mtt90) cc_final: 0.7959 (mmt90) REVERT: B 471 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7814 (t0) REVERT: B 532 SER cc_start: 0.9297 (m) cc_final: 0.9039 (t) REVERT: B 560 GLN cc_start: 0.8459 (tp40) cc_final: 0.8122 (tp40) REVERT: B 627 TYR cc_start: 0.7424 (m-80) cc_final: 0.6772 (m-80) REVERT: B 746 GLU cc_start: 0.5093 (tp30) cc_final: 0.4742 (tp30) outliers start: 65 outliers final: 53 residues processed: 575 average time/residue: 0.1114 time to fit residues: 95.3825 Evaluate side-chains 594 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 538 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 648 GLU 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 414 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 586 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 687 ASN Chi-restraints excluded: chain C residue 711 SER 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 422 LEU 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 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 B residue 287 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 471 ASP 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 656 LYS 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: 0.7980 chunk 68 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.0060 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 393 ASN A 628 ASN 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 = 0.3906 r_free = 0.3906 target = 0.159814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116843 restraints weight = 20757.217| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.52 r_work: 0.3225 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15092 Z= 0.151 Angle : 0.645 12.277 20460 Z= 0.334 Chirality : 0.041 0.304 2304 Planarity : 0.003 0.067 2500 Dihedral : 6.913 55.994 2352 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.31 % Allowed : 21.25 % Favored : 75.44 % 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: 0.09 (0.20), residues: 1764 helix: 1.19 (0.15), residues: 1176 sheet: -2.04 (0.56), residues: 68 loop : -2.31 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 409 TYR 0.010 0.001 TYR D 351 PHE 0.026 0.001 PHE D 304 TRP 0.015 0.002 TRP C 740 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00346 (15092) covalent geometry : angle 0.64507 (20460) hydrogen bonds : bond 0.04124 ( 911) hydrogen bonds : angle 4.61831 ( 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 608 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 555 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8123 (mmm) cc_final: 0.7528 (mmm) REVERT: A 313 LEU cc_start: 0.9033 (mt) cc_final: 0.8705 (mt) REVERT: A 397 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7526 (tt0) REVERT: A 422 LEU cc_start: 0.8925 (mt) cc_final: 0.8664 (mt) REVERT: A 432 ARG cc_start: 0.8388 (mtt90) cc_final: 0.8081 (mmt180) REVERT: A 472 TYR cc_start: 0.8286 (m-80) cc_final: 0.7769 (m-80) REVERT: A 532 SER cc_start: 0.9315 (m) cc_final: 0.9031 (t) REVERT: A 559 PHE cc_start: 0.5924 (t80) cc_final: 0.4850 (m-10) REVERT: A 562 MET cc_start: 0.7994 (mmp) cc_final: 0.7623 (mmt) REVERT: A 627 TYR cc_start: 0.7340 (m-80) cc_final: 0.6786 (m-80) REVERT: A 644 MET cc_start: 0.9139 (mmm) cc_final: 0.8897 (mmm) REVERT: C 393 ASN cc_start: 0.8444 (m-40) cc_final: 0.7946 (m-40) REVERT: C 409 ARG cc_start: 0.8246 (ttp-170) cc_final: 0.7899 (ttp-170) REVERT: C 420 ARG cc_start: 0.8378 (tpp80) cc_final: 0.7608 (tpp80) REVERT: C 432 ARG cc_start: 0.8428 (mtt90) cc_final: 0.7971 (mmt90) REVERT: C 471 ASP cc_start: 0.8053 (m-30) cc_final: 0.7733 (t0) REVERT: C 472 TYR cc_start: 0.7903 (m-80) cc_final: 0.7487 (m-80) REVERT: C 559 PHE cc_start: 0.5206 (t80) cc_final: 0.4658 (m-10) REVERT: C 627 TYR cc_start: 0.7298 (m-80) cc_final: 0.6742 (m-80) REVERT: C 696 ILE cc_start: 0.8535 (mm) cc_final: 0.8319 (mm) REVERT: C 716 MET cc_start: 0.1971 (ttp) cc_final: 0.1494 (ptp) REVERT: C 743 ARG cc_start: 0.7899 (ttm110) cc_final: 0.7310 (ttm170) REVERT: D 308 MET cc_start: 0.8028 (mmm) cc_final: 0.7447 (mmm) REVERT: D 356 GLU cc_start: 0.7050 (tt0) cc_final: 0.6761 (tp30) REVERT: D 363 ARG cc_start: 0.7458 (ttt90) cc_final: 0.6670 (mtt90) REVERT: D 409 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7690 (ttp-170) REVERT: D 420 ARG cc_start: 0.8476 (tpp80) cc_final: 0.7869 (tpp80) REVERT: D 432 ARG cc_start: 0.8458 (mtt90) cc_final: 0.8024 (mmt90) REVERT: D 471 ASP cc_start: 0.8338 (t0) cc_final: 0.7744 (t0) REVERT: D 644 MET cc_start: 0.9205 (mmm) cc_final: 0.8919 (mmm) REVERT: D 738 TYR cc_start: 0.3329 (OUTLIER) cc_final: 0.1786 (p90) REVERT: B 293 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7490 (mt-10) REVERT: B 308 MET cc_start: 0.8231 (mmm) cc_final: 0.7926 (mmt) REVERT: B 363 ARG cc_start: 0.7213 (ttt90) cc_final: 0.6504 (mtt90) REVERT: B 397 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7661 (tt0) REVERT: B 420 ARG cc_start: 0.8521 (tpp80) cc_final: 0.8243 (tpp80) REVERT: B 432 ARG cc_start: 0.8327 (mtt90) cc_final: 0.7923 (mmt90) REVERT: B 532 SER cc_start: 0.9306 (m) cc_final: 0.9058 (t) REVERT: B 627 TYR cc_start: 0.7393 (m-80) cc_final: 0.6746 (m-80) REVERT: B 697 TRP cc_start: 0.8342 (t60) cc_final: 0.7978 (t60) outliers start: 53 outliers final: 43 residues processed: 580 average time/residue: 0.1113 time to fit residues: 96.6227 Evaluate side-chains 587 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 543 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 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 648 GLU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 315 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 384 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 422 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 738 TYR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 369 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 656 LYS Chi-restraints excluded: chain B residue 660 ILE 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: 0.9980 chunk 9 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.159321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115885 restraints weight = 20785.471| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.53 r_work: 0.3228 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 15092 Z= 0.166 Angle : 0.663 13.558 20460 Z= 0.343 Chirality : 0.042 0.388 2304 Planarity : 0.004 0.062 2500 Dihedral : 6.922 56.887 2352 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.25 % Allowed : 22.44 % Favored : 74.31 % 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: 0.13 (0.20), residues: 1764 helix: 1.22 (0.15), residues: 1176 sheet: -1.96 (0.57), residues: 68 loop : -2.31 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 409 TYR 0.011 0.001 TYR A 351 PHE 0.026 0.001 PHE D 304 TRP 0.018 0.002 TRP A 697 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00390 (15092) covalent geometry : angle 0.66326 (20460) hydrogen bonds : bond 0.04125 ( 911) hydrogen bonds : angle 4.64788 ( 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 598 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 546 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8125 (mmm) cc_final: 0.7853 (mmt) REVERT: A 313 LEU cc_start: 0.9088 (mt) cc_final: 0.8746 (mt) REVERT: A 356 GLU cc_start: 0.7145 (tt0) cc_final: 0.6685 (tp30) REVERT: A 363 ARG cc_start: 0.7305 (ttt90) cc_final: 0.6588 (mtt90) REVERT: A 422 LEU cc_start: 0.8903 (mt) cc_final: 0.8683 (mt) REVERT: A 432 ARG cc_start: 0.8395 (mtt90) cc_final: 0.8084 (mmt180) REVERT: A 472 TYR cc_start: 0.8345 (m-80) cc_final: 0.7789 (m-80) REVERT: A 532 SER cc_start: 0.9262 (m) cc_final: 0.8989 (t) REVERT: A 559 PHE cc_start: 0.5877 (t80) cc_final: 0.4824 (m-10) REVERT: A 627 TYR cc_start: 0.7349 (m-80) cc_final: 0.6805 (m-80) REVERT: A 644 MET cc_start: 0.9177 (mmm) cc_final: 0.8918 (mmm) REVERT: C 393 ASN cc_start: 0.8447 (m-40) cc_final: 0.8153 (m-40) REVERT: C 409 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.7899 (ttp-170) REVERT: C 420 ARG cc_start: 0.8398 (tpp80) cc_final: 0.7638 (tpp80) REVERT: C 423 GLN cc_start: 0.8887 (tp40) cc_final: 0.8507 (tp-100) REVERT: C 432 ARG cc_start: 0.8450 (mtt90) cc_final: 0.7978 (mmt90) REVERT: C 471 ASP cc_start: 0.8053 (m-30) cc_final: 0.7771 (t0) REVERT: C 472 TYR cc_start: 0.7902 (m-80) cc_final: 0.7489 (m-80) REVERT: C 559 PHE cc_start: 0.5285 (t80) cc_final: 0.4635 (m-10) REVERT: C 627 TYR cc_start: 0.7316 (m-80) cc_final: 0.6755 (m-80) REVERT: C 696 ILE cc_start: 0.8535 (mm) cc_final: 0.8294 (mm) REVERT: C 716 MET cc_start: 0.1993 (ttp) cc_final: 0.1530 (ptp) REVERT: C 743 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7301 (ttm170) REVERT: D 308 MET cc_start: 0.8041 (mmm) cc_final: 0.7815 (mmt) REVERT: D 356 GLU cc_start: 0.7057 (tt0) cc_final: 0.6774 (tp30) REVERT: D 363 ARG cc_start: 0.7476 (ttt90) cc_final: 0.6664 (mtt90) REVERT: D 409 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7706 (ttp-170) REVERT: D 420 ARG cc_start: 0.8441 (tpp80) cc_final: 0.7892 (tpp80) REVERT: D 471 ASP cc_start: 0.8350 (t0) cc_final: 0.7915 (t0) REVERT: B 293 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7540 (mt-10) REVERT: B 308 MET cc_start: 0.8203 (mmm) cc_final: 0.7905 (mmt) REVERT: B 363 ARG cc_start: 0.7202 (ttt90) cc_final: 0.6510 (mtt90) REVERT: B 397 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7680 (tt0) REVERT: B 409 ARG cc_start: 0.7537 (ptt-90) cc_final: 0.7128 (ptt-90) REVERT: B 432 ARG cc_start: 0.8347 (mtt90) cc_final: 0.7984 (mmt180) REVERT: B 471 ASP cc_start: 0.8391 (t0) cc_final: 0.7789 (t0) REVERT: B 532 SER cc_start: 0.9299 (m) cc_final: 0.9056 (t) REVERT: B 627 TYR cc_start: 0.7396 (m-80) cc_final: 0.6787 (m-80) REVERT: B 644 MET cc_start: 0.9162 (mmm) cc_final: 0.8892 (mmm) REVERT: B 673 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8364 (tt) outliers start: 52 outliers final: 48 residues processed: 572 average time/residue: 0.1086 time to fit residues: 92.5787 Evaluate side-chains 582 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 533 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 648 GLU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 351 TYR 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 576 ASP 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 422 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 B residue 287 VAL Chi-restraints excluded: chain B residue 369 PHE 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 586 VAL Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 673 LEU 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: 0.0370 chunk 48 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 158 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN B 354 GLN B 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.159312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115779 restraints weight = 20672.385| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.52 r_work: 0.3211 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.161 15092 Z= 0.276 Angle : 1.051 59.189 20460 Z= 0.610 Chirality : 0.050 0.994 2304 Planarity : 0.005 0.167 2500 Dihedral : 6.924 56.881 2352 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.19 % Allowed : 22.38 % Favored : 74.44 % Cbeta Deviations : 0.18 % 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: 0.13 (0.20), residues: 1764 helix: 1.22 (0.15), residues: 1176 sheet: -1.95 (0.57), residues: 68 loop : -2.31 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 409 TYR 0.010 0.001 TYR D 351 PHE 0.021 0.001 PHE D 304 TRP 0.090 0.005 TRP B 697 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00553 (15092) covalent geometry : angle 1.05123 (20460) hydrogen bonds : bond 0.04125 ( 911) hydrogen bonds : angle 4.64947 ( 2673) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3809.70 seconds wall clock time: 65 minutes 54.25 seconds (3954.25 seconds total)