Starting phenix.real_space_refine on Fri Apr 12 03:55:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5z_20659/04_2024/6u5z_20659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5z_20659/04_2024/6u5z_20659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5z_20659/04_2024/6u5z_20659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5z_20659/04_2024/6u5z_20659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5z_20659/04_2024/6u5z_20659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5z_20659/04_2024/6u5z_20659.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 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 126 5.16 5 C 15462 2.51 5 N 4380 2.21 5 O 4638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 545": "OE1" <-> "OE2" Residue "B GLU 545": "OE1" <-> "OE2" Residue "C GLU 545": "OE1" <-> "OE2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "E GLU 545": "OE1" <-> "OE2" Residue "F GLU 545": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24606 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "B" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "C" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "D" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "E" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "F" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Time building chain proxies: 13.02, per 1000 atoms: 0.53 Number of scatterers: 24606 At special positions: 0 Unit cell: (143.312, 133.136, 166.208, 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 126 16.00 O 4638 8.00 N 4380 7.00 C 15462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 691 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 691 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 691 " distance=2.04 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 691 " distance=2.04 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 691 " distance=2.04 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 691 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 9.78 Conformation dependent library (CDL) restraints added in 4.5 seconds 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 30 sheets defined 48.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.733A pdb=" N GLU A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 374 Processing helix chain 'A' and resid 387 through 392 removed outlier: 4.263A pdb=" N ILE A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 Processing helix chain 'A' and resid 436 through 445 Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.532A pdb=" N PHE A 452 " --> pdb=" O ASN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 4.062A pdb=" N ASP A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 514 Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.762A pdb=" N ILE A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 561 Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 631 through 653 removed outlier: 5.274A pdb=" N GLU A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'A' and resid 680 through 694 Processing helix chain 'A' and resid 718 through 729 Processing helix chain 'A' and resid 739 through 747 removed outlier: 4.141A pdb=" N ARG A 742 " --> pdb=" O GLU A 739 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A 745 " --> pdb=" O ARG A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE A 752 " --> pdb=" O PRO A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL A 766 " --> pdb=" O ARG A 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.734A pdb=" N GLU B 252 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 321 Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 374 Processing helix chain 'B' and resid 387 through 392 removed outlier: 4.263A pdb=" N ILE B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 413 Processing helix chain 'B' and resid 436 through 445 Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.532A pdb=" N PHE B 452 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 4.061A pdb=" N ASP B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 505 through 514 Processing helix chain 'B' and resid 524 through 535 removed outlier: 3.762A pdb=" N ILE B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 561 Processing helix chain 'B' and resid 575 through 580 Processing helix chain 'B' and resid 631 through 653 removed outlier: 5.274A pdb=" N GLU B 650 " --> pdb=" O ARG B 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 661 Processing helix chain 'B' and resid 680 through 694 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 739 through 747 removed outlier: 4.140A pdb=" N ARG B 742 " --> pdb=" O GLU B 739 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B 745 " --> pdb=" O ARG B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE B 752 " --> pdb=" O PRO B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 260 removed outlier: 3.733A pdb=" N GLU C 252 " --> pdb=" O PRO C 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 321 Processing helix chain 'C' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 374 Processing helix chain 'C' and resid 387 through 392 removed outlier: 4.263A pdb=" N ILE C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 413 Processing helix chain 'C' and resid 436 through 445 Processing helix chain 'C' and resid 448 through 452 removed outlier: 3.533A pdb=" N PHE C 452 " --> pdb=" O ASN C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 4.062A pdb=" N ASP C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 514 Processing helix chain 'C' and resid 524 through 535 removed outlier: 3.762A pdb=" N ILE C 528 " --> pdb=" O ASP C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 561 Processing helix chain 'C' and resid 575 through 580 Processing helix chain 'C' and resid 631 through 653 removed outlier: 5.274A pdb=" N GLU C 650 " --> pdb=" O ARG C 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS C 651 " --> pdb=" O ALA C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 661 Processing helix chain 'C' and resid 680 through 694 Processing helix chain 'C' and resid 718 through 729 Processing helix chain 'C' and resid 739 through 747 removed outlier: 4.141A pdb=" N ARG C 742 " --> pdb=" O GLU C 739 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU C 745 " --> pdb=" O ARG C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE C 752 " --> pdb=" O PRO C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL C 766 " --> pdb=" O ARG C 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 260 removed outlier: 3.733A pdb=" N GLU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP D 259 " --> pdb=" O LYS D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 287 through 301 removed outlier: 3.558A pdb=" N VAL D 291 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 321 Processing helix chain 'D' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG D 333 " --> pdb=" O ARG D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 374 Processing helix chain 'D' and resid 387 through 392 removed outlier: 4.263A pdb=" N ILE D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 413 Processing helix chain 'D' and resid 436 through 445 Processing helix chain 'D' and resid 448 through 452 removed outlier: 3.533A pdb=" N PHE D 452 " --> pdb=" O ASN D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 removed outlier: 4.062A pdb=" N ASP D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 524 through 535 removed outlier: 3.761A pdb=" N ILE D 528 " --> pdb=" O ASP D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 561 Processing helix chain 'D' and resid 575 through 580 Processing helix chain 'D' and resid 631 through 653 removed outlier: 5.275A pdb=" N GLU D 650 " --> pdb=" O ARG D 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS D 651 " --> pdb=" O ALA D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'D' and resid 680 through 694 Processing helix chain 'D' and resid 718 through 729 Processing helix chain 'D' and resid 739 through 747 removed outlier: 4.140A pdb=" N ARG D 742 " --> pdb=" O GLU D 739 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU D 745 " --> pdb=" O ARG D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE D 752 " --> pdb=" O PRO D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL D 766 " --> pdb=" O ARG D 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 260 removed outlier: 3.733A pdb=" N GLU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP E 259 " --> pdb=" O LYS E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 321 Processing helix chain 'E' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 374 Processing helix chain 'E' and resid 387 through 392 removed outlier: 4.262A pdb=" N ILE E 391 " --> pdb=" O ASP E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 413 Processing helix chain 'E' and resid 436 through 445 Processing helix chain 'E' and resid 448 through 452 removed outlier: 3.531A pdb=" N PHE E 452 " --> pdb=" O ASN E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 483 removed outlier: 4.061A pdb=" N ASP E 483 " --> pdb=" O ALA E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 505 through 514 Processing helix chain 'E' and resid 524 through 535 removed outlier: 3.762A pdb=" N ILE E 528 " --> pdb=" O ASP E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 561 Processing helix chain 'E' and resid 575 through 580 Processing helix chain 'E' and resid 631 through 653 removed outlier: 5.274A pdb=" N GLU E 650 " --> pdb=" O ARG E 646 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LYS E 651 " --> pdb=" O ALA E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 661 Processing helix chain 'E' and resid 680 through 694 Processing helix chain 'E' and resid 718 through 729 Processing helix chain 'E' and resid 739 through 747 removed outlier: 4.140A pdb=" N ARG E 742 " --> pdb=" O GLU E 739 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU E 745 " --> pdb=" O ARG E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE E 752 " --> pdb=" O PRO E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL E 766 " --> pdb=" O ARG E 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 260 removed outlier: 3.734A pdb=" N GLU F 252 " --> pdb=" O PRO F 248 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP F 259 " --> pdb=" O LYS F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 278 Processing helix chain 'F' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 329 through 341 removed outlier: 3.970A pdb=" N ARG F 333 " --> pdb=" O ARG F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 374 Processing helix chain 'F' and resid 387 through 392 removed outlier: 4.262A pdb=" N ILE F 391 " --> pdb=" O ASP F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 413 Processing helix chain 'F' and resid 436 through 445 Processing helix chain 'F' and resid 448 through 452 removed outlier: 3.532A pdb=" N PHE F 452 " --> pdb=" O ASN F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 483 removed outlier: 4.062A pdb=" N ASP F 483 " --> pdb=" O ALA F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 505 Processing helix chain 'F' and resid 505 through 514 Processing helix chain 'F' and resid 524 through 535 removed outlier: 3.761A pdb=" N ILE F 528 " --> pdb=" O ASP F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 561 Processing helix chain 'F' and resid 575 through 580 Processing helix chain 'F' and resid 631 through 653 removed outlier: 5.275A pdb=" N GLU F 650 " --> pdb=" O ARG F 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS F 651 " --> pdb=" O ALA F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 661 Processing helix chain 'F' and resid 680 through 694 Processing helix chain 'F' and resid 718 through 729 Processing helix chain 'F' and resid 739 through 747 removed outlier: 4.141A pdb=" N ARG F 742 " --> pdb=" O GLU F 739 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU F 745 " --> pdb=" O ARG F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE F 752 " --> pdb=" O PRO F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 762 through 771 removed outlier: 3.592A pdb=" N VAL F 766 " --> pdb=" O ARG F 762 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 381 removed outlier: 7.363A pdb=" N VAL A 378 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASP A 423 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET A 380 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AA3, first strand: chain 'A' and resid 597 through 602 removed outlier: 6.559A pdb=" N THR A 625 " --> pdb=" O VAL A 666 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.651A pdb=" N ALA A 702 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 734 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL A 760 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A 736 " --> pdb=" O VAL A 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 706 through 707 removed outlier: 3.608A pdb=" N GLU A 706 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 377 through 381 removed outlier: 7.362A pdb=" N VAL B 378 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASP B 423 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET B 380 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 521 through 523 removed outlier: 6.611A pdb=" N THR B 522 " --> pdb=" O ILE B 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 597 through 602 removed outlier: 6.559A pdb=" N THR B 625 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.650A pdb=" N ALA B 702 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 734 " --> pdb=" O HIS B 758 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL B 760 " --> pdb=" O VAL B 734 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE B 736 " --> pdb=" O VAL B 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 706 through 707 removed outlier: 3.607A pdb=" N GLU B 706 " --> pdb=" O LEU B 714 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 377 through 381 removed outlier: 7.363A pdb=" N VAL C 378 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASP C 423 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET C 380 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 521 through 523 Processing sheet with id=AB4, first strand: chain 'C' and resid 597 through 602 removed outlier: 6.559A pdb=" N THR C 625 " --> pdb=" O VAL C 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 701 through 703 removed outlier: 6.651A pdb=" N ALA C 702 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 734 " --> pdb=" O HIS C 758 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL C 760 " --> pdb=" O VAL C 734 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE C 736 " --> pdb=" O VAL C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 706 through 707 removed outlier: 3.608A pdb=" N GLU C 706 " --> pdb=" O LEU C 714 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 377 through 381 removed outlier: 7.363A pdb=" N VAL D 378 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ASP D 423 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET D 380 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 521 through 523 Processing sheet with id=AB9, first strand: chain 'D' and resid 597 through 602 removed outlier: 6.559A pdb=" N THR D 625 " --> pdb=" O VAL D 666 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 701 through 703 removed outlier: 6.651A pdb=" N ALA D 702 " --> pdb=" O LEU D 735 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL D 734 " --> pdb=" O HIS D 758 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL D 760 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE D 736 " --> pdb=" O VAL D 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 706 through 707 removed outlier: 3.607A pdb=" N GLU D 706 " --> pdb=" O LEU D 714 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 377 through 381 removed outlier: 7.363A pdb=" N VAL E 378 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASP E 423 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET E 380 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 521 through 523 Processing sheet with id=AC5, first strand: chain 'E' and resid 597 through 602 removed outlier: 6.558A pdb=" N THR E 625 " --> pdb=" O VAL E 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 701 through 703 removed outlier: 6.650A pdb=" N ALA E 702 " --> pdb=" O LEU E 735 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL E 734 " --> pdb=" O HIS E 758 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL E 760 " --> pdb=" O VAL E 734 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE E 736 " --> pdb=" O VAL E 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 706 through 707 removed outlier: 3.607A pdb=" N GLU E 706 " --> pdb=" O LEU E 714 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 377 through 381 removed outlier: 7.362A pdb=" N VAL F 378 " --> pdb=" O LEU F 421 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASP F 423 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET F 380 " --> pdb=" O ASP F 423 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 521 through 523 Processing sheet with id=AD1, first strand: chain 'F' and resid 597 through 602 removed outlier: 6.558A pdb=" N THR F 625 " --> pdb=" O VAL F 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 701 through 703 removed outlier: 6.651A pdb=" N ALA F 702 " --> pdb=" O LEU F 735 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL F 734 " --> pdb=" O HIS F 758 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL F 760 " --> pdb=" O VAL F 734 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE F 736 " --> pdb=" O VAL F 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 706 through 707 removed outlier: 3.608A pdb=" N GLU F 706 " --> pdb=" O LEU F 714 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 3036 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: 7.83 Time building geometry restraints manager: 10.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8376 1.35 - 1.47: 4717 1.47 - 1.59: 11651 1.59 - 1.71: 0 1.71 - 1.83: 222 Bond restraints: 24966 Sorted by residual: bond pdb=" N ASP A 585 " pdb=" CA ASP A 585 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.21e-02 6.83e+03 7.17e+00 bond pdb=" N ASP D 585 " pdb=" CA ASP D 585 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.90e+00 bond pdb=" N ASP B 585 " pdb=" CA ASP B 585 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.90e+00 bond pdb=" N ASP F 585 " pdb=" CA ASP F 585 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.87e+00 bond pdb=" N LYS B 416 " pdb=" CA LYS B 416 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.31e-02 5.83e+03 6.86e+00 ... (remaining 24961 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.21: 867 107.21 - 113.91: 14383 113.91 - 120.62: 9835 120.62 - 127.32: 8376 127.32 - 134.02: 223 Bond angle restraints: 33684 Sorted by residual: angle pdb=" C GLY D 326 " pdb=" N LEU D 327 " pdb=" CA LEU D 327 " ideal model delta sigma weight residual 121.54 126.22 -4.68 1.91e+00 2.74e-01 6.01e+00 angle pdb=" C GLY C 326 " pdb=" N LEU C 327 " pdb=" CA LEU C 327 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.96e+00 angle pdb=" C GLY B 326 " pdb=" N LEU B 327 " pdb=" CA LEU B 327 " ideal model delta sigma weight residual 121.54 126.18 -4.64 1.91e+00 2.74e-01 5.90e+00 angle pdb=" C GLY F 326 " pdb=" N LEU F 327 " pdb=" CA LEU F 327 " ideal model delta sigma weight residual 121.54 126.16 -4.62 1.91e+00 2.74e-01 5.86e+00 angle pdb=" C GLY E 326 " pdb=" N LEU E 327 " pdb=" CA LEU E 327 " ideal model delta sigma weight residual 121.54 126.16 -4.62 1.91e+00 2.74e-01 5.86e+00 ... (remaining 33679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.43: 14647 13.43 - 26.86: 650 26.86 - 40.29: 207 40.29 - 53.72: 54 53.72 - 67.15: 24 Dihedral angle restraints: 15582 sinusoidal: 6486 harmonic: 9096 Sorted by residual: dihedral pdb=" CA ASP F 454 " pdb=" CB ASP F 454 " pdb=" CG ASP F 454 " pdb=" OD1 ASP F 454 " ideal model delta sinusoidal sigma weight residual -30.00 -86.95 56.95 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP D 454 " pdb=" CB ASP D 454 " pdb=" CG ASP D 454 " pdb=" OD1 ASP D 454 " ideal model delta sinusoidal sigma weight residual -30.00 -86.93 56.93 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP A 454 " pdb=" CB ASP A 454 " pdb=" CG ASP A 454 " pdb=" OD1 ASP A 454 " ideal model delta sinusoidal sigma weight residual -30.00 -86.92 56.92 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 15579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2258 0.029 - 0.057: 1028 0.057 - 0.086: 348 0.086 - 0.114: 187 0.114 - 0.143: 37 Chirality restraints: 3858 Sorted by residual: chirality pdb=" CA ILE F 747 " pdb=" N ILE F 747 " pdb=" C ILE F 747 " pdb=" CB ILE F 747 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE D 747 " pdb=" N ILE D 747 " pdb=" C ILE D 747 " pdb=" CB ILE D 747 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE E 747 " pdb=" N ILE E 747 " pdb=" C ILE E 747 " pdb=" CB ILE E 747 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 3855 not shown) Planarity restraints: 4380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET F 263 " -0.027 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO F 264 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 264 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 264 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 263 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO E 264 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 264 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 264 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 263 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 264 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 264 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 264 " -0.023 5.00e-02 4.00e+02 ... (remaining 4377 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1473 2.73 - 3.28: 25104 3.28 - 3.82: 38760 3.82 - 4.36: 48541 4.36 - 4.90: 80775 Nonbonded interactions: 194653 Sorted by model distance: nonbonded pdb=" OG SER C 453 " pdb=" OD1 ASP C 460 " model vdw 2.194 2.440 nonbonded pdb=" OG SER E 453 " pdb=" OD1 ASP E 460 " model vdw 2.194 2.440 nonbonded pdb=" OG SER A 453 " pdb=" OD1 ASP A 460 " model vdw 2.194 2.440 nonbonded pdb=" OG SER D 453 " pdb=" OD1 ASP D 460 " model vdw 2.195 2.440 nonbonded pdb=" OG SER F 453 " pdb=" OD1 ASP F 460 " model vdw 2.195 2.440 ... (remaining 194648 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.020 Extract box with map and model: 8.470 Check model and map are aligned: 0.380 Set scattering table: 0.260 Process input model: 64.240 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.130 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5511 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 : 0.002 0.034 24966 Z= 0.133 Angle : 0.540 5.790 33684 Z= 0.319 Chirality : 0.041 0.143 3858 Planarity : 0.004 0.042 4380 Dihedral : 9.077 67.151 9720 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 3162 helix: -0.07 (0.14), residues: 1242 sheet: -1.03 (0.19), residues: 474 loop : -1.91 (0.14), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 303 HIS 0.001 0.000 HIS E 324 PHE 0.003 0.001 PHE F 420 TYR 0.006 0.001 TYR C 377 ARG 0.002 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 MET cc_start: 0.1416 (mtm) cc_final: 0.1196 (ttt) REVERT: A 312 ASP cc_start: 0.1662 (t0) cc_final: 0.0953 (m-30) REVERT: A 546 ARG cc_start: 0.4885 (mtm-85) cc_final: 0.4526 (tpt170) REVERT: A 573 ASP cc_start: 0.6622 (m-30) cc_final: 0.6171 (t0) REVERT: A 611 LEU cc_start: 0.5635 (mt) cc_final: 0.5261 (tp) REVERT: A 703 MET cc_start: 0.3628 (ptp) cc_final: 0.3381 (ptp) REVERT: A 704 THR cc_start: 0.3181 (t) cc_final: 0.2594 (t) REVERT: B 284 MET cc_start: -0.0143 (ttt) cc_final: -0.0763 (tpp) REVERT: B 410 MET cc_start: 0.4054 (mmm) cc_final: 0.2852 (tmm) REVERT: B 475 MET cc_start: 0.4453 (mtt) cc_final: 0.3851 (tpp) REVERT: C 432 MET cc_start: 0.4808 (ttm) cc_final: 0.4494 (ttt) REVERT: C 570 ILE cc_start: 0.6421 (mt) cc_final: 0.6143 (mt) REVERT: C 584 PHE cc_start: 0.5832 (m-80) cc_final: 0.4639 (m-10) REVERT: C 588 ARG cc_start: 0.7763 (mmt90) cc_final: 0.7167 (mtt90) REVERT: C 651 LYS cc_start: 0.5636 (mttt) cc_final: 0.5399 (tptm) REVERT: C 659 TYR cc_start: 0.5708 (p90) cc_final: 0.5257 (p90) REVERT: D 735 LEU cc_start: 0.6078 (mt) cc_final: 0.4872 (mm) REVERT: E 284 MET cc_start: 0.4784 (ttt) cc_final: 0.4273 (ttt) REVERT: E 321 ASP cc_start: 0.7207 (m-30) cc_final: 0.6826 (m-30) REVERT: E 614 GLU cc_start: 0.5303 (mt-10) cc_final: 0.4867 (mt-10) REVERT: E 743 ASP cc_start: 0.4407 (m-30) cc_final: 0.4143 (t0) REVERT: F 432 MET cc_start: 0.3679 (ttm) cc_final: 0.3218 (mmt) REVERT: F 481 LEU cc_start: 0.2479 (mt) cc_final: 0.2143 (mt) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.4196 time to fit residues: 329.2917 Evaluate side-chains 272 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 94 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 0.0470 overall best weight: 1.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS A 510 GLN A 597 GLN C 510 GLN C 667 HIS C 712 GLN D 635 GLN E 251 ASN E 473 ASN F 455 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6032 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24966 Z= 0.245 Angle : 0.612 8.496 33684 Z= 0.309 Chirality : 0.044 0.261 3858 Planarity : 0.005 0.058 4380 Dihedral : 3.003 17.848 3456 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.53 % Allowed : 9.62 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3162 helix: 1.02 (0.14), residues: 1248 sheet: -0.63 (0.20), residues: 474 loop : -1.32 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 303 HIS 0.005 0.001 HIS A 505 PHE 0.017 0.001 PHE E 658 TYR 0.025 0.001 TYR B 337 ARG 0.006 0.001 ARG E 728 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 322 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 ARG cc_start: 0.4908 (mtm-85) cc_final: 0.4501 (tpt170) REVERT: A 573 ASP cc_start: 0.6373 (m-30) cc_final: 0.6037 (t0) REVERT: A 625 THR cc_start: 0.4072 (m) cc_final: 0.3798 (t) REVERT: A 636 GLU cc_start: 0.5817 (tm-30) cc_final: 0.5329 (tt0) REVERT: A 661 LYS cc_start: 0.5124 (mttt) cc_final: 0.4866 (pttp) REVERT: A 749 ASP cc_start: 0.5957 (p0) cc_final: 0.5510 (t0) REVERT: B 263 MET cc_start: 0.3087 (mtt) cc_final: 0.2686 (mtt) REVERT: B 329 ARG cc_start: 0.5757 (mpt180) cc_final: 0.5269 (mtp85) REVERT: B 390 GLU cc_start: 0.4469 (OUTLIER) cc_final: 0.4049 (pt0) REVERT: B 410 MET cc_start: 0.3924 (mmm) cc_final: 0.2772 (tmm) REVERT: B 475 MET cc_start: 0.4407 (mtt) cc_final: 0.4058 (tpp) REVERT: B 569 GLU cc_start: 0.7829 (tt0) cc_final: 0.6941 (pm20) REVERT: C 263 MET cc_start: 0.4931 (OUTLIER) cc_final: 0.4410 (ttm) REVERT: C 280 MET cc_start: 0.0237 (mtt) cc_final: -0.0255 (ppp) REVERT: C 380 MET cc_start: 0.7044 (tmm) cc_final: 0.6810 (tmm) REVERT: C 465 ASP cc_start: 0.6773 (m-30) cc_final: 0.6515 (m-30) REVERT: C 588 ARG cc_start: 0.7909 (mmt90) cc_final: 0.7227 (mtt90) REVERT: C 591 ASN cc_start: 0.7644 (t0) cc_final: 0.7183 (m110) REVERT: C 627 THR cc_start: 0.7923 (OUTLIER) cc_final: 0.7624 (p) REVERT: C 651 LYS cc_start: 0.6089 (mttt) cc_final: 0.5625 (tptm) REVERT: C 661 LYS cc_start: 0.7660 (mttt) cc_final: 0.7302 (tmtt) REVERT: C 664 ILE cc_start: 0.8360 (mt) cc_final: 0.7871 (mm) REVERT: D 524 ASP cc_start: 0.7339 (p0) cc_final: 0.7071 (p0) REVERT: D 588 ARG cc_start: 0.6704 (mmt90) cc_final: 0.5585 (mmm-85) REVERT: D 627 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7941 (p) REVERT: D 727 HIS cc_start: 0.6548 (t70) cc_final: 0.6324 (t70) REVERT: E 280 MET cc_start: 0.2320 (pmm) cc_final: 0.2014 (mmm) REVERT: E 379 ARG cc_start: 0.5630 (OUTLIER) cc_final: 0.4893 (ttm110) REVERT: E 419 LEU cc_start: 0.5026 (tp) cc_final: 0.4806 (mm) REVERT: E 421 LEU cc_start: 0.6065 (tt) cc_final: 0.5682 (tt) REVERT: E 467 MET cc_start: 0.1573 (ttm) cc_final: 0.1349 (ttm) REVERT: E 614 GLU cc_start: 0.5514 (mt-10) cc_final: 0.5082 (pt0) REVERT: F 281 MET cc_start: 0.1113 (mmm) cc_final: 0.0753 (pmm) REVERT: F 432 MET cc_start: 0.3553 (ttm) cc_final: 0.3086 (mmt) outliers start: 67 outliers final: 26 residues processed: 372 average time/residue: 0.3851 time to fit residues: 223.1597 Evaluate side-chains 292 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 261 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain D residue 303 TRP Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 652 LEU Chi-restraints excluded: chain F residue 410 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 235 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 283 optimal weight: 30.0000 chunk 306 optimal weight: 0.0980 chunk 252 optimal weight: 0.9990 chunk 281 optimal weight: 5.9990 chunk 96 optimal weight: 0.0270 chunk 227 optimal weight: 0.9990 overall best weight: 0.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 GLN F 635 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 24966 Z= 0.159 Angle : 0.524 7.243 33684 Z= 0.262 Chirality : 0.041 0.170 3858 Planarity : 0.004 0.054 4380 Dihedral : 3.111 23.959 3456 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.85 % Allowed : 11.76 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3162 helix: 1.51 (0.15), residues: 1248 sheet: -0.30 (0.20), residues: 516 loop : -1.12 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 303 HIS 0.003 0.000 HIS C 727 PHE 0.014 0.001 PHE E 658 TYR 0.014 0.001 TYR D 535 ARG 0.006 0.000 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 289 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.2352 (ptm) cc_final: 0.1664 (ptm) REVERT: A 402 MET cc_start: -0.0074 (mmp) cc_final: -0.0374 (ptp) REVERT: A 405 LYS cc_start: 0.3205 (pttp) cc_final: 0.2590 (tmtt) REVERT: A 546 ARG cc_start: 0.4836 (mtm-85) cc_final: 0.4386 (tpt170) REVERT: A 573 ASP cc_start: 0.6394 (m-30) cc_final: 0.6082 (t0) REVERT: A 625 THR cc_start: 0.4309 (m) cc_final: 0.4009 (t) REVERT: A 661 LYS cc_start: 0.5133 (mttt) cc_final: 0.4883 (pttt) REVERT: A 749 ASP cc_start: 0.5981 (p0) cc_final: 0.5537 (t0) REVERT: B 263 MET cc_start: 0.2950 (mtt) cc_final: 0.2735 (mtt) REVERT: B 428 MET cc_start: 0.1250 (ptm) cc_final: 0.0470 (mmt) REVERT: B 475 MET cc_start: 0.4533 (mtt) cc_final: 0.4084 (tpp) REVERT: B 569 GLU cc_start: 0.7838 (tt0) cc_final: 0.6955 (pm20) REVERT: C 263 MET cc_start: 0.4972 (OUTLIER) cc_final: 0.4388 (ttm) REVERT: C 280 MET cc_start: 0.0276 (mtt) cc_final: -0.0230 (ppp) REVERT: C 380 MET cc_start: 0.7024 (tmm) cc_final: 0.6805 (tmm) REVERT: C 422 LEU cc_start: 0.7242 (mt) cc_final: 0.6934 (mt) REVERT: C 456 TYR cc_start: 0.5143 (t80) cc_final: 0.4690 (t80) REVERT: C 553 ARG cc_start: 0.6551 (mtt-85) cc_final: 0.5734 (mtp-110) REVERT: C 588 ARG cc_start: 0.7918 (mmt90) cc_final: 0.7188 (mtt90) REVERT: C 591 ASN cc_start: 0.7762 (t0) cc_final: 0.7230 (m110) REVERT: C 651 LYS cc_start: 0.6067 (mttt) cc_final: 0.5706 (tptm) REVERT: C 661 LYS cc_start: 0.7703 (mttt) cc_final: 0.7427 (tmtt) REVERT: C 664 ILE cc_start: 0.8376 (mt) cc_final: 0.7982 (mm) REVERT: C 745 GLU cc_start: 0.7443 (mp0) cc_final: 0.6949 (mp0) REVERT: D 524 ASP cc_start: 0.7485 (p0) cc_final: 0.7142 (p0) REVERT: D 559 LEU cc_start: 0.6084 (mt) cc_final: 0.5695 (pp) REVERT: D 588 ARG cc_start: 0.6756 (mmt90) cc_final: 0.5521 (mmm-85) REVERT: D 627 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8138 (p) REVERT: E 379 ARG cc_start: 0.5518 (OUTLIER) cc_final: 0.4822 (ttm110) REVERT: E 421 LEU cc_start: 0.5999 (tt) cc_final: 0.5602 (tt) REVERT: E 467 MET cc_start: 0.1519 (ttm) cc_final: 0.1306 (ttm) REVERT: E 614 GLU cc_start: 0.5420 (mt-10) cc_final: 0.5072 (pt0) REVERT: F 281 MET cc_start: 0.1194 (mmm) cc_final: 0.0831 (pmm) REVERT: F 432 MET cc_start: 0.3460 (ttm) cc_final: 0.3038 (mmt) REVERT: F 467 MET cc_start: -0.5188 (tpp) cc_final: -0.5388 (tpp) outliers start: 49 outliers final: 27 residues processed: 323 average time/residue: 0.3729 time to fit residues: 190.1595 Evaluate side-chains 281 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 251 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain D residue 303 TRP Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 697 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 0.8980 chunk 213 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 284 optimal weight: 5.9990 chunk 301 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 269 optimal weight: 3.9990 chunk 81 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN A 597 GLN B 667 HIS C 576 HIS D 727 HIS F 635 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 24966 Z= 0.158 Angle : 0.517 7.850 33684 Z= 0.256 Chirality : 0.041 0.184 3858 Planarity : 0.004 0.057 4380 Dihedral : 3.230 25.378 3456 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.38 % Allowed : 12.33 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3162 helix: 1.76 (0.15), residues: 1242 sheet: -0.10 (0.21), residues: 516 loop : -1.03 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 303 HIS 0.009 0.001 HIS C 576 PHE 0.011 0.001 PHE E 658 TYR 0.012 0.001 TYR B 337 ARG 0.004 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 261 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: -0.0063 (mmp) cc_final: -0.0302 (ptp) REVERT: A 546 ARG cc_start: 0.4920 (mtm-85) cc_final: 0.4500 (tpt170) REVERT: A 573 ASP cc_start: 0.6375 (m-30) cc_final: 0.6060 (t0) REVERT: A 625 THR cc_start: 0.4358 (m) cc_final: 0.4052 (t) REVERT: A 749 ASP cc_start: 0.5986 (p0) cc_final: 0.5533 (t0) REVERT: B 263 MET cc_start: 0.3066 (mtt) cc_final: 0.2862 (mtt) REVERT: B 405 LYS cc_start: 0.6711 (tppt) cc_final: 0.6410 (mtmt) REVERT: B 475 MET cc_start: 0.4575 (mtt) cc_final: 0.4128 (tpp) REVERT: B 569 GLU cc_start: 0.7868 (tt0) cc_final: 0.6998 (pm20) REVERT: C 280 MET cc_start: 0.0212 (mtt) cc_final: -0.0305 (ppp) REVERT: C 380 MET cc_start: 0.7104 (tmm) cc_final: 0.6656 (tmm) REVERT: C 421 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7707 (tt) REVERT: C 422 LEU cc_start: 0.7329 (mt) cc_final: 0.7077 (mt) REVERT: C 456 TYR cc_start: 0.4991 (t80) cc_final: 0.4678 (t80) REVERT: C 553 ARG cc_start: 0.6652 (mtt-85) cc_final: 0.5851 (mtp-110) REVERT: C 588 ARG cc_start: 0.8044 (mmt90) cc_final: 0.7217 (mtt90) REVERT: C 591 ASN cc_start: 0.7681 (t0) cc_final: 0.7202 (m110) REVERT: C 661 LYS cc_start: 0.7733 (mttt) cc_final: 0.7481 (tmtt) REVERT: C 664 ILE cc_start: 0.8407 (mt) cc_final: 0.8016 (mm) REVERT: D 473 ASN cc_start: 0.7024 (m-40) cc_final: 0.6746 (t0) REVERT: D 524 ASP cc_start: 0.7420 (p0) cc_final: 0.7081 (p0) REVERT: D 559 LEU cc_start: 0.6119 (mt) cc_final: 0.5765 (pp) REVERT: D 588 ARG cc_start: 0.6786 (mmt90) cc_final: 0.5565 (mmm-85) REVERT: D 627 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8116 (p) REVERT: E 280 MET cc_start: 0.3081 (pmm) cc_final: 0.1390 (mmt) REVERT: E 379 ARG cc_start: 0.5528 (OUTLIER) cc_final: 0.4910 (ttm110) REVERT: E 421 LEU cc_start: 0.5811 (tt) cc_final: 0.5517 (tt) REVERT: E 614 GLU cc_start: 0.5517 (mt-10) cc_final: 0.5141 (pt0) REVERT: F 281 MET cc_start: 0.1185 (mmm) cc_final: 0.0810 (pmm) REVERT: F 432 MET cc_start: 0.3437 (ttm) cc_final: 0.3011 (mmt) outliers start: 63 outliers final: 36 residues processed: 305 average time/residue: 0.3498 time to fit residues: 170.6344 Evaluate side-chains 281 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 242 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 695 ASN Chi-restraints excluded: chain D residue 303 TRP Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 546 ARG Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain F residue 637 SER Chi-restraints excluded: chain F residue 703 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.0170 chunk 171 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 257 optimal weight: 4.9990 chunk 208 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 153 optimal weight: 5.9990 chunk 270 optimal weight: 10.0000 chunk 76 optimal weight: 0.2980 overall best weight: 2.6624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN A 597 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN C 455 HIS D 341 GLN D 455 HIS ** D 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 727 HIS E 758 HIS ** E 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 635 GLN ** F 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 24966 Z= 0.335 Angle : 0.706 10.329 33684 Z= 0.361 Chirality : 0.046 0.212 3858 Planarity : 0.005 0.058 4380 Dihedral : 4.332 30.994 3456 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 3.43 % Allowed : 12.37 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3162 helix: 0.84 (0.14), residues: 1320 sheet: -0.09 (0.25), residues: 378 loop : -1.76 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 303 HIS 0.007 0.001 HIS D 727 PHE 0.034 0.002 PHE A 738 TYR 0.021 0.002 TYR C 626 ARG 0.007 0.001 ARG C 728 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 316 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.1779 (ptm) cc_final: 0.0862 (ptm) REVERT: A 402 MET cc_start: -0.0230 (mmp) cc_final: -0.0473 (ptp) REVERT: A 405 LYS cc_start: 0.3211 (pttp) cc_final: 0.2480 (tmtt) REVERT: A 546 ARG cc_start: 0.5377 (mtm-85) cc_final: 0.4841 (tpt170) REVERT: A 573 ASP cc_start: 0.6287 (m-30) cc_final: 0.5966 (t0) REVERT: A 625 THR cc_start: 0.4338 (m) cc_final: 0.4034 (t) REVERT: A 658 PHE cc_start: 0.4118 (p90) cc_final: 0.3915 (p90) REVERT: A 728 ARG cc_start: 0.4521 (mtm-85) cc_final: 0.3514 (ppt170) REVERT: A 741 LYS cc_start: 0.3891 (mtpt) cc_final: 0.3180 (tptt) REVERT: A 749 ASP cc_start: 0.6056 (p0) cc_final: 0.5549 (t0) REVERT: B 394 HIS cc_start: 0.3283 (OUTLIER) cc_final: 0.2977 (t-90) REVERT: B 405 LYS cc_start: 0.6757 (tppt) cc_final: 0.6455 (mmtt) REVERT: B 432 MET cc_start: 0.2357 (ptp) cc_final: 0.0736 (ttp) REVERT: B 475 MET cc_start: 0.4866 (mtt) cc_final: 0.4166 (tpp) REVERT: B 569 GLU cc_start: 0.7792 (tt0) cc_final: 0.6962 (pm20) REVERT: B 651 LYS cc_start: 0.7376 (mttt) cc_final: 0.6833 (tptp) REVERT: B 657 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7204 (t70) REVERT: B 721 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6828 (mm-30) REVERT: C 303 TRP cc_start: 0.2597 (p90) cc_final: 0.2375 (p90) REVERT: C 512 GLU cc_start: 0.7666 (tp30) cc_final: 0.7381 (tp30) REVERT: C 588 ARG cc_start: 0.8102 (mmt90) cc_final: 0.7542 (mtt90) REVERT: C 623 LYS cc_start: 0.8354 (mttt) cc_final: 0.8047 (tttm) REVERT: C 661 LYS cc_start: 0.7957 (mttt) cc_final: 0.7712 (mmtp) REVERT: C 772 GLN cc_start: 0.7550 (tt0) cc_final: 0.7260 (tt0) REVERT: D 298 MET cc_start: 0.4885 (mmm) cc_final: 0.4508 (mmp) REVERT: D 424 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7036 (mm-30) REVERT: D 526 SER cc_start: 0.8262 (m) cc_final: 0.8023 (t) REVERT: D 588 ARG cc_start: 0.7359 (mmt90) cc_final: 0.6293 (mmm-85) REVERT: E 280 MET cc_start: 0.2451 (pmm) cc_final: 0.2198 (pmm) REVERT: E 379 ARG cc_start: 0.5175 (OUTLIER) cc_final: 0.4825 (ttm110) REVERT: E 421 LEU cc_start: 0.6029 (tt) cc_final: 0.5790 (tt) REVERT: F 415 VAL cc_start: 0.1383 (m) cc_final: 0.1168 (t) REVERT: F 432 MET cc_start: 0.3476 (ttm) cc_final: 0.3106 (mmt) outliers start: 91 outliers final: 49 residues processed: 380 average time/residue: 0.3778 time to fit residues: 223.3027 Evaluate side-chains 304 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 252 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 303 TRP Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 633 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 546 ARG Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 664 ILE Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 603 TRP Chi-restraints excluded: chain F residue 703 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 2.9990 chunk 271 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 301 optimal weight: 8.9990 chunk 250 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN D 558 GLN D 635 GLN E 473 ASN E 758 HIS ** F 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24966 Z= 0.239 Angle : 0.607 11.879 33684 Z= 0.303 Chirality : 0.043 0.223 3858 Planarity : 0.004 0.067 4380 Dihedral : 4.035 32.623 3456 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.19 % Rotamer: Outliers : 2.87 % Allowed : 14.48 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3162 helix: 1.12 (0.14), residues: 1320 sheet: -0.48 (0.23), residues: 480 loop : -1.84 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 303 HIS 0.004 0.001 HIS B 505 PHE 0.010 0.001 PHE B 468 TYR 0.031 0.001 TYR C 377 ARG 0.007 0.000 ARG E 762 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 274 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: -0.0297 (mmp) cc_final: -0.0595 (ptp) REVERT: A 546 ARG cc_start: 0.5431 (mtm-85) cc_final: 0.4872 (tpt170) REVERT: A 573 ASP cc_start: 0.6356 (m-30) cc_final: 0.6045 (t0) REVERT: A 625 THR cc_start: 0.4447 (m) cc_final: 0.4128 (t) REVERT: A 728 ARG cc_start: 0.4465 (mtm-85) cc_final: 0.3389 (ppt170) REVERT: A 749 ASP cc_start: 0.5995 (p0) cc_final: 0.5462 (t0) REVERT: B 394 HIS cc_start: 0.3180 (OUTLIER) cc_final: 0.2892 (t-90) REVERT: B 405 LYS cc_start: 0.6723 (tppt) cc_final: 0.6444 (mmtt) REVERT: B 475 MET cc_start: 0.4831 (mtt) cc_final: 0.4392 (tpp) REVERT: B 586 TYR cc_start: 0.6647 (t80) cc_final: 0.6429 (t80) REVERT: B 651 LYS cc_start: 0.7402 (mttt) cc_final: 0.6911 (tptp) REVERT: C 456 TYR cc_start: 0.4523 (t80) cc_final: 0.4034 (t80) REVERT: C 512 GLU cc_start: 0.7712 (tp30) cc_final: 0.7430 (tp30) REVERT: C 553 ARG cc_start: 0.7006 (mtt-85) cc_final: 0.6190 (mtp-110) REVERT: C 588 ARG cc_start: 0.8095 (mmt90) cc_final: 0.7275 (mtt90) REVERT: C 591 ASN cc_start: 0.7505 (OUTLIER) cc_final: 0.6979 (m110) REVERT: C 623 LYS cc_start: 0.8297 (mttt) cc_final: 0.7942 (tttm) REVERT: C 634 MET cc_start: 0.8325 (mmm) cc_final: 0.8119 (tpp) REVERT: C 661 LYS cc_start: 0.8045 (mttt) cc_final: 0.7692 (tmtt) REVERT: C 684 MET cc_start: 0.7340 (mtm) cc_final: 0.7015 (mtt) REVERT: D 298 MET cc_start: 0.5005 (mmm) cc_final: 0.4744 (mmp) REVERT: D 424 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6766 (mm-30) REVERT: D 526 SER cc_start: 0.8269 (m) cc_final: 0.8022 (t) REVERT: D 588 ARG cc_start: 0.7361 (mmt90) cc_final: 0.6222 (mmm-85) REVERT: E 257 LYS cc_start: 0.3429 (tppt) cc_final: 0.2931 (mtpt) REVERT: E 379 ARG cc_start: 0.5250 (OUTLIER) cc_final: 0.5037 (ttm110) REVERT: E 421 LEU cc_start: 0.6017 (tt) cc_final: 0.5730 (tt) REVERT: E 579 LEU cc_start: 0.6096 (mt) cc_final: 0.5426 (mp) REVERT: E 623 LYS cc_start: 0.6895 (mttt) cc_final: 0.6513 (mmtt) REVERT: F 432 MET cc_start: 0.3428 (ttm) cc_final: 0.3084 (mmt) outliers start: 76 outliers final: 52 residues processed: 327 average time/residue: 0.3629 time to fit residues: 187.6352 Evaluate side-chains 310 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 255 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain D residue 303 TRP Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 546 ARG Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 664 ILE Chi-restraints excluded: chain F residue 603 TRP Chi-restraints excluded: chain F residue 703 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 220 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 183 optimal weight: 0.3980 chunk 138 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN B 591 ASN E 758 HIS ** F 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24966 Z= 0.256 Angle : 0.626 15.103 33684 Z= 0.313 Chirality : 0.044 0.196 3858 Planarity : 0.005 0.059 4380 Dihedral : 4.134 33.248 3456 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.90 % Allowed : 15.05 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3162 helix: 0.92 (0.14), residues: 1356 sheet: -0.11 (0.25), residues: 450 loop : -1.91 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 303 HIS 0.004 0.001 HIS B 505 PHE 0.025 0.001 PHE A 658 TYR 0.029 0.002 TYR C 377 ARG 0.005 0.000 ARG E 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 278 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 ARG cc_start: 0.5456 (mtm-85) cc_final: 0.4895 (tpt170) REVERT: A 573 ASP cc_start: 0.6415 (m-30) cc_final: 0.6114 (t0) REVERT: A 625 THR cc_start: 0.4438 (m) cc_final: 0.4136 (t) REVERT: A 728 ARG cc_start: 0.4511 (mtm-85) cc_final: 0.3451 (ppt170) REVERT: A 749 ASP cc_start: 0.6125 (p0) cc_final: 0.5588 (t0) REVERT: B 394 HIS cc_start: 0.3091 (OUTLIER) cc_final: 0.2801 (t-90) REVERT: B 405 LYS cc_start: 0.6817 (tppt) cc_final: 0.6519 (mmtt) REVERT: B 475 MET cc_start: 0.4890 (mtt) cc_final: 0.4341 (tpp) REVERT: B 547 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7304 (mp0) REVERT: B 588 ARG cc_start: 0.7269 (mmt90) cc_final: 0.7068 (mmt90) REVERT: B 651 LYS cc_start: 0.7372 (mttt) cc_final: 0.6844 (tptp) REVERT: B 657 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7154 (t70) REVERT: C 348 LYS cc_start: 0.6116 (mmtt) cc_final: 0.5004 (pttt) REVERT: C 512 GLU cc_start: 0.7743 (tp30) cc_final: 0.7477 (tp30) REVERT: C 553 ARG cc_start: 0.7052 (mtt-85) cc_final: 0.6158 (mtp-110) REVERT: C 588 ARG cc_start: 0.8038 (mmt90) cc_final: 0.7393 (mtt90) REVERT: C 623 LYS cc_start: 0.8348 (mttt) cc_final: 0.8015 (tttm) REVERT: C 634 MET cc_start: 0.8474 (mmm) cc_final: 0.8168 (mmt) REVERT: C 661 LYS cc_start: 0.8045 (mttt) cc_final: 0.7755 (tmtt) REVERT: C 684 MET cc_start: 0.7341 (mtm) cc_final: 0.7074 (mtt) REVERT: C 765 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6077 (mp0) REVERT: D 298 MET cc_start: 0.5130 (mmm) cc_final: 0.4525 (mmp) REVERT: D 424 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6998 (mm-30) REVERT: D 526 SER cc_start: 0.8305 (m) cc_final: 0.8047 (t) REVERT: D 588 ARG cc_start: 0.7363 (mmt90) cc_final: 0.6329 (mmm-85) REVERT: D 591 ASN cc_start: 0.6007 (t0) cc_final: 0.4874 (t0) REVERT: E 284 MET cc_start: 0.4453 (ptt) cc_final: 0.3902 (pmm) REVERT: E 335 LEU cc_start: 0.7982 (mt) cc_final: 0.7734 (mm) REVERT: E 379 ARG cc_start: 0.5379 (OUTLIER) cc_final: 0.5023 (ttm110) REVERT: E 421 LEU cc_start: 0.6021 (tt) cc_final: 0.5764 (tt) REVERT: E 623 LYS cc_start: 0.6985 (mttt) cc_final: 0.6564 (mmtt) REVERT: F 432 MET cc_start: 0.3521 (ttm) cc_final: 0.3154 (mmt) outliers start: 77 outliers final: 55 residues processed: 332 average time/residue: 0.3602 time to fit residues: 190.3078 Evaluate side-chains 315 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 256 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 765 GLU Chi-restraints excluded: chain D residue 303 TRP Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 633 VAL Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain E residue 303 TRP Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 546 ARG Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain F residue 603 TRP Chi-restraints excluded: chain F residue 637 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 191 optimal weight: 0.5980 chunk 204 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 236 optimal weight: 0.7980 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 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 HIS D 635 GLN ** F 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24966 Z= 0.174 Angle : 0.578 12.604 33684 Z= 0.286 Chirality : 0.042 0.159 3858 Planarity : 0.004 0.052 4380 Dihedral : 3.965 29.357 3456 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.34 % Allowed : 16.10 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3162 helix: 1.30 (0.14), residues: 1320 sheet: -0.01 (0.25), residues: 444 loop : -1.86 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 303 HIS 0.003 0.001 HIS B 505 PHE 0.015 0.001 PHE A 658 TYR 0.025 0.001 TYR C 377 ARG 0.005 0.000 ARG E 762 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 264 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 ARG cc_start: 0.5471 (mtm-85) cc_final: 0.4970 (tpt170) REVERT: A 573 ASP cc_start: 0.6448 (m-30) cc_final: 0.6115 (t0) REVERT: A 625 THR cc_start: 0.4266 (m) cc_final: 0.3972 (t) REVERT: A 749 ASP cc_start: 0.6142 (p0) cc_final: 0.5587 (t0) REVERT: B 263 MET cc_start: 0.3359 (mtt) cc_final: 0.2551 (mtt) REVERT: B 394 HIS cc_start: 0.3129 (OUTLIER) cc_final: 0.2849 (t-90) REVERT: B 405 LYS cc_start: 0.6772 (tppt) cc_final: 0.6439 (mmtt) REVERT: B 475 MET cc_start: 0.4946 (mtt) cc_final: 0.4393 (tpp) REVERT: B 547 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7193 (mp0) REVERT: B 588 ARG cc_start: 0.7246 (mmt90) cc_final: 0.7022 (mmt90) REVERT: B 651 LYS cc_start: 0.7333 (mttt) cc_final: 0.6870 (tptp) REVERT: B 657 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7108 (t0) REVERT: C 348 LYS cc_start: 0.6101 (mmtt) cc_final: 0.5011 (pttt) REVERT: C 405 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6819 (mtmt) REVERT: C 512 GLU cc_start: 0.7729 (tp30) cc_final: 0.7481 (tp30) REVERT: C 553 ARG cc_start: 0.6958 (mtt-85) cc_final: 0.6145 (mtp-110) REVERT: C 588 ARG cc_start: 0.8065 (mmt90) cc_final: 0.7404 (mtt90) REVERT: C 623 LYS cc_start: 0.8347 (mttt) cc_final: 0.7932 (tttm) REVERT: C 634 MET cc_start: 0.8351 (mmm) cc_final: 0.8115 (mmt) REVERT: C 661 LYS cc_start: 0.8096 (mttt) cc_final: 0.7820 (tmtt) REVERT: D 424 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6974 (mm-30) REVERT: D 526 SER cc_start: 0.8278 (m) cc_final: 0.8010 (t) REVERT: D 588 ARG cc_start: 0.7391 (mmt90) cc_final: 0.6292 (mmm-85) REVERT: D 591 ASN cc_start: 0.6047 (t0) cc_final: 0.4909 (t0) REVERT: E 257 LYS cc_start: 0.3205 (tppt) cc_final: 0.2598 (tttt) REVERT: E 284 MET cc_start: 0.4539 (ptt) cc_final: 0.4013 (pmm) REVERT: E 321 ASP cc_start: 0.7387 (m-30) cc_final: 0.7102 (p0) REVERT: E 379 ARG cc_start: 0.5363 (OUTLIER) cc_final: 0.4964 (ttm110) REVERT: E 421 LEU cc_start: 0.5970 (tt) cc_final: 0.5679 (tt) REVERT: E 623 LYS cc_start: 0.6930 (mttt) cc_final: 0.6519 (mmtt) REVERT: F 432 MET cc_start: 0.3492 (ttm) cc_final: 0.3113 (mmt) outliers start: 62 outliers final: 44 residues processed: 307 average time/residue: 0.3622 time to fit residues: 177.2257 Evaluate side-chains 296 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 248 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 633 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 546 ARG Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 719 LEU Chi-restraints excluded: chain E residue 739 GLU Chi-restraints excluded: chain F residue 703 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 3.9990 chunk 288 optimal weight: 30.0000 chunk 262 optimal weight: 3.9990 chunk 280 optimal weight: 9.9990 chunk 168 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 220 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 265 optimal weight: 8.9990 chunk 279 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 HIS D 635 GLN F 665 HIS ** F 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.6971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24966 Z= 0.291 Angle : 0.659 10.273 33684 Z= 0.330 Chirality : 0.045 0.270 3858 Planarity : 0.005 0.059 4380 Dihedral : 4.303 29.765 3456 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.45 % Allowed : 15.91 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3162 helix: 0.87 (0.14), residues: 1356 sheet: -0.12 (0.26), residues: 444 loop : -1.91 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 303 HIS 0.005 0.001 HIS B 505 PHE 0.013 0.002 PHE A 658 TYR 0.029 0.002 TYR C 377 ARG 0.008 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 265 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 ARG cc_start: 0.5465 (mtm-85) cc_final: 0.4983 (tpt170) REVERT: A 573 ASP cc_start: 0.6429 (m-30) cc_final: 0.6122 (t0) REVERT: A 625 THR cc_start: 0.4392 (m) cc_final: 0.4102 (t) REVERT: A 728 ARG cc_start: 0.4579 (mtm-85) cc_final: 0.3470 (ppt170) REVERT: A 749 ASP cc_start: 0.6285 (p0) cc_final: 0.5621 (t0) REVERT: B 375 ARG cc_start: 0.4600 (mmt-90) cc_final: 0.4283 (mmt-90) REVERT: B 394 HIS cc_start: 0.3103 (OUTLIER) cc_final: 0.2832 (t-90) REVERT: B 405 LYS cc_start: 0.6762 (tppt) cc_final: 0.6406 (mmtt) REVERT: B 475 MET cc_start: 0.4787 (mtt) cc_final: 0.4197 (tpp) REVERT: B 588 ARG cc_start: 0.7323 (mmt90) cc_final: 0.7062 (mmt90) REVERT: B 651 LYS cc_start: 0.7432 (mttt) cc_final: 0.7035 (tptp) REVERT: B 657 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7144 (t0) REVERT: C 303 TRP cc_start: 0.2768 (p90) cc_final: 0.2541 (p90) REVERT: C 405 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6740 (mtmt) REVERT: C 485 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7290 (ttp) REVERT: C 512 GLU cc_start: 0.7765 (tp30) cc_final: 0.7490 (tp30) REVERT: C 553 ARG cc_start: 0.7053 (mtt-85) cc_final: 0.6155 (mtp-110) REVERT: C 588 ARG cc_start: 0.7983 (mmt90) cc_final: 0.7350 (mtt90) REVERT: C 623 LYS cc_start: 0.8407 (mttt) cc_final: 0.8066 (tttt) REVERT: C 684 MET cc_start: 0.7325 (mtm) cc_final: 0.7120 (mtt) REVERT: C 744 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6444 (mp) REVERT: D 588 ARG cc_start: 0.7345 (mmt90) cc_final: 0.6327 (mmm-85) REVERT: D 591 ASN cc_start: 0.6137 (t0) cc_final: 0.5397 (t0) REVERT: D 623 LYS cc_start: 0.8506 (tttm) cc_final: 0.7735 (ptpp) REVERT: E 284 MET cc_start: 0.4374 (ptt) cc_final: 0.3854 (pmm) REVERT: E 421 LEU cc_start: 0.5989 (tt) cc_final: 0.5723 (tt) REVERT: E 623 LYS cc_start: 0.7085 (mttt) cc_final: 0.6454 (tppt) REVERT: E 745 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7046 (tp30) REVERT: F 281 MET cc_start: 0.1709 (mmm) cc_final: 0.1277 (pmm) REVERT: F 432 MET cc_start: 0.3485 (ttm) cc_final: 0.3113 (mmt) outliers start: 65 outliers final: 48 residues processed: 311 average time/residue: 0.3676 time to fit residues: 180.9425 Evaluate side-chains 304 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 251 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 633 VAL Chi-restraints excluded: chain E residue 303 TRP Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 546 ARG Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 719 LEU Chi-restraints excluded: chain E residue 739 GLU Chi-restraints excluded: chain F residue 603 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 2.9990 chunk 296 optimal weight: 20.0000 chunk 180 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 310 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 247 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 191 optimal weight: 0.0270 chunk 151 optimal weight: 0.9980 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN B 758 HIS ** F 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.7052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24966 Z= 0.195 Angle : 0.589 10.131 33684 Z= 0.293 Chirality : 0.043 0.164 3858 Planarity : 0.004 0.053 4380 Dihedral : 4.109 31.555 3456 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.15 % Allowed : 16.40 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3162 helix: 1.35 (0.15), residues: 1290 sheet: 0.21 (0.27), residues: 390 loop : -1.34 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 303 HIS 0.004 0.001 HIS B 505 PHE 0.013 0.001 PHE A 658 TYR 0.026 0.001 TYR C 377 ARG 0.008 0.000 ARG C 489 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 263 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 ARG cc_start: 0.5431 (mtm-85) cc_final: 0.4959 (tpt170) REVERT: A 573 ASP cc_start: 0.6472 (m-30) cc_final: 0.6171 (t0) REVERT: A 625 THR cc_start: 0.4338 (m) cc_final: 0.4089 (t) REVERT: A 749 ASP cc_start: 0.6246 (p0) cc_final: 0.5576 (t0) REVERT: B 394 HIS cc_start: 0.2976 (OUTLIER) cc_final: 0.2707 (t-90) REVERT: B 405 LYS cc_start: 0.6744 (tppt) cc_final: 0.6408 (mmtt) REVERT: B 475 MET cc_start: 0.4643 (mtt) cc_final: 0.4029 (tpp) REVERT: B 517 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7505 (mttt) REVERT: B 588 ARG cc_start: 0.7321 (mmt90) cc_final: 0.7035 (mmt90) REVERT: B 651 LYS cc_start: 0.7378 (mttt) cc_final: 0.7061 (tptp) REVERT: B 657 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7093 (t0) REVERT: C 303 TRP cc_start: 0.2836 (p90) cc_final: 0.2497 (p90) REVERT: C 348 LYS cc_start: 0.6365 (mmtt) cc_final: 0.5266 (pttt) REVERT: C 405 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6776 (mtmt) REVERT: C 485 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7148 (ttm) REVERT: C 512 GLU cc_start: 0.7727 (tp30) cc_final: 0.7472 (tp30) REVERT: C 553 ARG cc_start: 0.6991 (mtt-85) cc_final: 0.6137 (mtp-110) REVERT: C 588 ARG cc_start: 0.8010 (mmt90) cc_final: 0.7371 (mtt90) REVERT: C 623 LYS cc_start: 0.8311 (mttt) cc_final: 0.7977 (tttm) REVERT: C 744 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6464 (mp) REVERT: D 380 MET cc_start: 0.7729 (ptt) cc_final: 0.7045 (ptt) REVERT: D 588 ARG cc_start: 0.7299 (mmt90) cc_final: 0.6288 (mmm-85) REVERT: D 591 ASN cc_start: 0.6122 (t0) cc_final: 0.5372 (t0) REVERT: E 257 LYS cc_start: 0.3865 (tttm) cc_final: 0.3626 (ptmt) REVERT: E 284 MET cc_start: 0.4440 (ptt) cc_final: 0.3842 (pmm) REVERT: E 321 ASP cc_start: 0.7423 (m-30) cc_final: 0.7111 (p0) REVERT: E 623 LYS cc_start: 0.7058 (mttt) cc_final: 0.6351 (tppt) REVERT: E 745 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7034 (tp30) REVERT: F 432 MET cc_start: 0.3531 (ttm) cc_final: 0.3148 (mmt) REVERT: F 433 ARG cc_start: -0.1652 (ttt180) cc_final: -0.1986 (tpt170) outliers start: 57 outliers final: 46 residues processed: 301 average time/residue: 0.3639 time to fit residues: 175.1114 Evaluate side-chains 308 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 257 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 633 VAL Chi-restraints excluded: chain E residue 303 TRP Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 546 ARG Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 739 GLU Chi-restraints excluded: chain F residue 603 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 228 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 247 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 254 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 HIS ** F 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.273283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.241752 restraints weight = 31883.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.238533 restraints weight = 47142.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.237028 restraints weight = 35303.407| |-----------------------------------------------------------------------------| r_work (final): 0.4635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.7389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24966 Z= 0.266 Angle : 0.649 10.399 33684 Z= 0.324 Chirality : 0.045 0.191 3858 Planarity : 0.005 0.059 4380 Dihedral : 4.364 33.519 3456 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.93 % Rotamer: Outliers : 2.30 % Allowed : 16.59 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3162 helix: 0.98 (0.14), residues: 1344 sheet: -0.20 (0.26), residues: 450 loop : -1.82 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 303 HIS 0.005 0.001 HIS B 505 PHE 0.012 0.001 PHE E 658 TYR 0.026 0.002 TYR C 377 ARG 0.008 0.000 ARG C 489 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4957.53 seconds wall clock time: 91 minutes 42.96 seconds (5502.96 seconds total)