Starting phenix.real_space_refine on Mon May 19 11:37:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dhs_46875/05_2025/9dhs_46875.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dhs_46875/05_2025/9dhs_46875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dhs_46875/05_2025/9dhs_46875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dhs_46875/05_2025/9dhs_46875.map" model { file = "/net/cci-nas-00/data/ceres_data/9dhs_46875/05_2025/9dhs_46875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dhs_46875/05_2025/9dhs_46875.cif" } resolution = 4.48 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= 0.001 sd= 0.011 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 128 5.16 5 C 11885 2.51 5 N 2967 2.21 5 O 3314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18294 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3236 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 401} Chain breaks: 1 Chain: "B" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3223 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3236 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 401} Chain breaks: 1 Chain: "D" Number of atoms: 3219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3219 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "F" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "G" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "H" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 12.15, per 1000 atoms: 0.66 Number of scatterers: 18294 At special positions: 0 Unit cell: (111.55, 133.86, 152.29, 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 128 16.00 O 3314 8.00 N 2967 7.00 C 11885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 67 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 39 " - pdb=" SG CYS G 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS H 39 " - pdb=" SG CYS H 67 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 76 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.09 Conformation dependent library (CDL) restraints added in 2.4 seconds 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4276 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 23 sheets defined 58.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 423 through 437 removed outlier: 4.061A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 removed outlier: 4.134A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.831A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.543A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 629 removed outlier: 3.830A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 629 " --> pdb=" O THR A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.784A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 767 removed outlier: 4.596A pdb=" N LYS A 765 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 818 removed outlier: 4.301A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.845A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 522 Proline residue: B 520 - end of helix Processing helix chain 'B' and resid 523 through 546 removed outlier: 4.003A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 595 through 624 removed outlier: 3.843A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 621 " --> pdb=" O THR B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 662 removed outlier: 3.782A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.643A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.723A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.878A pdb=" N ALA B 749 " --> pdb=" O PRO B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 768 through 771 Processing helix chain 'B' and resid 773 through 778 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 817 removed outlier: 4.447A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 811 " --> pdb=" O MET B 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.596A pdb=" N ALA C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 521 through 545 removed outlier: 4.257A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 534 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C 536 " --> pdb=" O ALA C 532 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 4.032A pdb=" N SER C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY C 582 " --> pdb=" O TRP C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 629 removed outlier: 3.734A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET C 629 " --> pdb=" O THR C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.892A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 697 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.672A pdb=" N LYS C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 818 removed outlier: 4.450A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR C 797 " --> pdb=" O ALA C 793 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 806 " --> pdb=" O GLY C 802 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.611A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 428 removed outlier: 3.928A pdb=" N LEU D 428 " --> pdb=" O TYR D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 437 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 520 Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 521 through 545 removed outlier: 4.294A pdb=" N ILE D 525 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE D 531 " --> pdb=" O MET D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 586 removed outlier: 3.634A pdb=" N GLN D 586 " --> pdb=" O GLY D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.834A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 662 removed outlier: 4.035A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.569A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.836A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 749 " --> pdb=" O PRO D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 768 removed outlier: 4.400A pdb=" N TRP D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 817 removed outlier: 4.193A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 811 " --> pdb=" O MET D 807 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 13 removed outlier: 3.674A pdb=" N LEU E 11 " --> pdb=" O VAL E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 28 removed outlier: 4.257A pdb=" N ALA E 18 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.835A pdb=" N PHE E 96 " --> pdb=" O ALA E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 96' Processing helix chain 'E' and resid 97 through 104 removed outlier: 3.974A pdb=" N ARG E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 124 removed outlier: 3.803A pdb=" N ILE E 108 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE E 121 " --> pdb=" O GLY E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 160 removed outlier: 4.004A pdb=" N LEU E 135 " --> pdb=" O HIS E 131 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER E 136 " --> pdb=" O ASN E 132 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 206 removed outlier: 4.143A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS E 204 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 28 Processing helix chain 'F' and resid 94 through 104 removed outlier: 4.718A pdb=" N ALA F 99 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL F 100 " --> pdb=" O PHE F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 4.234A pdb=" N CYS F 120 " --> pdb=" O MET F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 Processing helix chain 'F' and resid 131 through 159 removed outlier: 3.929A pdb=" N ALA F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE F 140 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY F 145 " --> pdb=" O PHE F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 206 removed outlier: 3.918A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 195 " --> pdb=" O MET F 191 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN F 206 " --> pdb=" O ASP F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'G' and resid 7 through 28 Processing helix chain 'G' and resid 94 through 104 removed outlier: 4.773A pdb=" N ALA G 99 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL G 100 " --> pdb=" O PHE G 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG G 101 " --> pdb=" O LEU G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 123 Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 131 through 159 removed outlier: 3.785A pdb=" N LEU G 135 " --> pdb=" O HIS G 131 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE G 149 " --> pdb=" O GLY G 145 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 206 removed outlier: 3.933A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL G 194 " --> pdb=" O GLU G 190 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU G 195 " --> pdb=" O MET G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 209 No H-bonds generated for 'chain 'G' and resid 207 through 209' Processing helix chain 'H' and resid 7 through 13 removed outlier: 3.595A pdb=" N LEU H 11 " --> pdb=" O VAL H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 28 removed outlier: 4.140A pdb=" N ALA H 18 " --> pdb=" O VAL H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 removed outlier: 3.882A pdb=" N PHE H 96 " --> pdb=" O ALA H 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 93 through 96' Processing helix chain 'H' and resid 97 through 104 removed outlier: 3.951A pdb=" N ARG H 101 " --> pdb=" O LEU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.806A pdb=" N ILE H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE H 121 " --> pdb=" O GLY H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 160 removed outlier: 3.948A pdb=" N LEU H 135 " --> pdb=" O HIS H 131 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA H 137 " --> pdb=" O ILE H 133 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY H 138 " --> pdb=" O ILE H 134 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 206 removed outlier: 4.205A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS H 204 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS H 205 " --> pdb=" O ILE H 201 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 209 No H-bonds generated for 'chain 'H' and resid 207 through 209' Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.404A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.114A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 682 through 683 removed outlier: 8.706A pdb=" N VAL A 683 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A 649 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU A 650 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLU A 705 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 removed outlier: 3.878A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 489 through 498 removed outlier: 5.104A pdb=" N ILE B 734 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR B 732 " --> pdb=" O PRO B 494 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET B 496 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS B 730 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 649 removed outlier: 6.658A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.086A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.921A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.582A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 394 through 395 Processing sheet with id=AB7, first strand: chain 'D' and resid 398 through 399 Processing sheet with id=AB8, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 498 removed outlier: 7.515A pdb=" N SER D 492 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N THR D 736 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE D 734 " --> pdb=" O PRO D 494 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.475A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D 702 " --> pdb=" O MET D 503 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 Processing sheet with id=AC3, first strand: chain 'F' and resid 76 through 78 removed outlier: 3.727A pdb=" N LEU F 33 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER F 174 " --> pdb=" O TYR F 34 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 76 through 78 removed outlier: 3.735A pdb=" N LEU G 33 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER G 174 " --> pdb=" O TYR G 34 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 76 through 78 954 hydrogen bonds defined for protein. 2730 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: 6.09 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5645 1.36 - 1.49: 5152 1.49 - 1.63: 7681 1.63 - 1.76: 0 1.76 - 1.90: 208 Bond restraints: 18686 Sorted by residual: bond pdb=" SD MET C 629 " pdb=" CE MET C 629 " ideal model delta sigma weight residual 1.791 1.900 -0.109 2.50e-02 1.60e+03 1.90e+01 bond pdb=" N VAL A 630 " pdb=" CA VAL A 630 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.09e+00 bond pdb=" N GLN B 586 " pdb=" CA GLN B 586 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 8.00e+00 bond pdb=" N GLN B 587 " pdb=" CA GLN B 587 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.49e+00 bond pdb=" N MET C 629 " pdb=" CA MET C 629 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.12e-02 7.97e+03 6.70e+00 ... (remaining 18681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 25157 4.18 - 8.35: 42 8.35 - 12.53: 2 12.53 - 16.70: 0 16.70 - 20.88: 1 Bond angle restraints: 25202 Sorted by residual: angle pdb=" CG MET C 629 " pdb=" SD MET C 629 " pdb=" CE MET C 629 " ideal model delta sigma weight residual 100.90 121.78 -20.88 2.20e+00 2.07e-01 9.00e+01 angle pdb=" C MET C 629 " pdb=" CA MET C 629 " pdb=" CB MET C 629 " ideal model delta sigma weight residual 111.17 103.78 7.39 1.53e+00 4.27e-01 2.33e+01 angle pdb=" C GLY B 725 " pdb=" N ASN B 726 " pdb=" CA ASN B 726 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 angle pdb=" N ALA D 522 " pdb=" CA ALA D 522 " pdb=" C ALA D 522 " ideal model delta sigma weight residual 110.80 119.16 -8.36 2.13e+00 2.20e-01 1.54e+01 angle pdb=" C MET B 629 " pdb=" N VAL B 630 " pdb=" CA VAL B 630 " ideal model delta sigma weight residual 121.97 128.55 -6.58 1.80e+00 3.09e-01 1.33e+01 ... (remaining 25197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 10195 17.62 - 35.23: 659 35.23 - 52.85: 86 52.85 - 70.47: 23 70.47 - 88.08: 13 Dihedral angle restraints: 10976 sinusoidal: 4270 harmonic: 6706 Sorted by residual: dihedral pdb=" CD ARG A 628 " pdb=" NE ARG A 628 " pdb=" CZ ARG A 628 " pdb=" NH1 ARG A 628 " ideal model delta sinusoidal sigma weight residual 0.00 -64.96 64.96 1 1.00e+01 1.00e-02 5.54e+01 dihedral pdb=" CA SER G 60 " pdb=" C SER G 60 " pdb=" N GLY G 61 " pdb=" CA GLY G 61 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA GLU B 772 " pdb=" C GLU B 772 " pdb=" N CYS B 773 " pdb=" CA CYS B 773 " ideal model delta harmonic sigma weight residual -180.00 -151.66 -28.34 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 10973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2289 0.052 - 0.105: 469 0.105 - 0.157: 63 0.157 - 0.210: 4 0.210 - 0.262: 1 Chirality restraints: 2826 Sorted by residual: chirality pdb=" CA MET C 629 " pdb=" N MET C 629 " pdb=" C MET C 629 " pdb=" CB MET C 629 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA THR A 744 " pdb=" N THR A 744 " pdb=" C THR A 744 " pdb=" CB THR A 744 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA THR C 744 " pdb=" N THR C 744 " pdb=" C THR C 744 " pdb=" CB THR C 744 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 2823 not shown) Planarity restraints: 3102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 628 " 1.008 9.50e-02 1.11e+02 4.52e-01 1.23e+02 pdb=" NE ARG A 628 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG A 628 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 628 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 628 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 684 " 0.256 9.50e-02 1.11e+02 1.15e-01 8.56e+00 pdb=" NE ARG D 684 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG D 684 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG D 684 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 684 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 684 " -0.248 9.50e-02 1.11e+02 1.11e-01 7.97e+00 pdb=" NE ARG A 684 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 684 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 684 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 684 " -0.012 2.00e-02 2.50e+03 ... (remaining 3099 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 318 2.67 - 3.23: 20104 3.23 - 3.79: 27722 3.79 - 4.34: 36040 4.34 - 4.90: 57915 Nonbonded interactions: 142099 Sorted by model distance: nonbonded pdb=" OD2 ASP D 728 " pdb=" NZ LYS D 730 " model vdw 2.118 3.120 nonbonded pdb=" O GLY B 725 " pdb=" OD1 ASN B 726 " model vdw 2.162 3.040 nonbonded pdb=" N GLU E 94 " pdb=" OE1 GLU E 94 " model vdw 2.184 3.120 nonbonded pdb=" N GLU G 94 " pdb=" OE1 GLU G 94 " model vdw 2.185 3.120 nonbonded pdb=" N GLU F 94 " pdb=" OE1 GLU F 94 " model vdw 2.188 3.120 ... (remaining 142094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 \ and (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = (chain 'B' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 819 or resid 1301)) selection = (chain 'C' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 \ and (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 4.880 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: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 44.170 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 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 : 0.003 0.109 18698 Z= 0.180 Angle : 0.714 20.876 25226 Z= 0.422 Chirality : 0.042 0.262 2826 Planarity : 0.011 0.452 3102 Dihedral : 12.439 88.082 6664 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.70 % Allowed : 5.79 % Favored : 93.52 % Rotamer: Outliers : 0.20 % Allowed : 1.23 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -1.38 (0.16), residues: 2298 helix: -0.46 (0.13), residues: 1192 sheet: -1.25 (0.42), residues: 147 loop : -1.31 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.005 TRP G 32 HIS 0.008 0.002 HIS B 435 PHE 0.041 0.002 PHE A 438 TYR 0.036 0.005 TYR B 711 ARG 0.021 0.002 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.16162 ( 954) hydrogen bonds : angle 6.57932 ( 2730) SS BOND : bond 0.00331 ( 12) SS BOND : angle 0.88279 ( 24) covalent geometry : bond 0.00330 (18686) covalent geometry : angle 0.71370 (25202) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 549 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.9293 (tp30) cc_final: 0.8818 (tt0) REVERT: A 599 ARG cc_start: 0.7628 (mtt180) cc_final: 0.7345 (mtt-85) REVERT: B 421 TYR cc_start: 0.6641 (m-80) cc_final: 0.6380 (m-80) REVERT: B 586 GLN cc_start: 0.6567 (tp40) cc_final: 0.6076 (tm-30) REVERT: B 626 VAL cc_start: 0.9099 (t) cc_final: 0.8853 (t) REVERT: B 693 VAL cc_start: 0.9113 (t) cc_final: 0.8672 (m) REVERT: B 708 MET cc_start: 0.9152 (mpp) cc_final: 0.8947 (mpp) REVERT: C 428 LEU cc_start: 0.9539 (tp) cc_final: 0.9318 (tt) REVERT: C 476 ILE cc_start: 0.8704 (mm) cc_final: 0.8428 (tp) REVERT: C 533 TYR cc_start: 0.8687 (t80) cc_final: 0.8400 (t80) REVERT: C 634 GLU cc_start: 0.8518 (tp30) cc_final: 0.8289 (mm-30) REVERT: C 638 ASP cc_start: 0.9070 (m-30) cc_final: 0.8776 (m-30) REVERT: C 816 TYR cc_start: 0.8119 (t80) cc_final: 0.7787 (t80) REVERT: D 673 TYR cc_start: 0.8552 (t80) cc_final: 0.8261 (t80) REVERT: D 693 VAL cc_start: 0.8981 (t) cc_final: 0.8337 (p) REVERT: D 708 MET cc_start: 0.9263 (mtm) cc_final: 0.8897 (mtp) REVERT: D 721 MET cc_start: 0.7220 (ptp) cc_final: 0.6970 (ptp) REVERT: E 57 MET cc_start: 0.6842 (mmm) cc_final: 0.6559 (mmt) REVERT: E 119 LEU cc_start: 0.9032 (mm) cc_final: 0.8821 (mm) REVERT: E 191 MET cc_start: 0.8298 (mmm) cc_final: 0.8027 (mmm) REVERT: F 29 THR cc_start: 0.8882 (p) cc_final: 0.8600 (t) REVERT: F 55 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7223 (tp30) REVERT: F 69 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8500 (mt-10) REVERT: F 113 LEU cc_start: 0.7892 (mt) cc_final: 0.7587 (mt) REVERT: F 148 ASN cc_start: 0.8835 (t0) cc_final: 0.8211 (m-40) REVERT: F 191 MET cc_start: 0.8412 (mtp) cc_final: 0.8014 (tpt) REVERT: G 29 THR cc_start: 0.8516 (p) cc_final: 0.8227 (t) REVERT: G 120 CYS cc_start: 0.9690 (m) cc_final: 0.9430 (t) REVERT: G 191 MET cc_start: 0.8358 (mtp) cc_final: 0.8062 (tpt) REVERT: H 57 MET cc_start: 0.6872 (mmm) cc_final: 0.6583 (mmt) REVERT: H 105 ILE cc_start: 0.9221 (tt) cc_final: 0.9019 (mt) REVERT: H 119 LEU cc_start: 0.9080 (mm) cc_final: 0.8725 (mp) REVERT: H 135 LEU cc_start: 0.8574 (tt) cc_final: 0.8278 (tt) REVERT: H 191 MET cc_start: 0.8849 (mmp) cc_final: 0.8584 (mmm) REVERT: H 202 ASP cc_start: 0.8664 (t0) cc_final: 0.8443 (t70) outliers start: 4 outliers final: 1 residues processed: 550 average time/residue: 0.2908 time to fit residues: 241.6531 Evaluate side-chains 318 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 118 optimal weight: 0.0000 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN A 791 ASN D 508 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.129950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.098966 restraints weight = 53017.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.096752 restraints weight = 58469.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097915 restraints weight = 54415.466| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18698 Z= 0.150 Angle : 0.684 9.454 25226 Z= 0.366 Chirality : 0.045 0.182 2826 Planarity : 0.004 0.056 3102 Dihedral : 5.910 58.569 2522 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.70 % Favored : 96.00 % Rotamer: Outliers : 0.15 % Allowed : 2.97 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.26 (0.18), residues: 2298 helix: 1.16 (0.15), residues: 1222 sheet: -1.11 (0.41), residues: 147 loop : -0.90 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 766 HIS 0.003 0.001 HIS A 435 PHE 0.017 0.001 PHE F 106 TYR 0.024 0.002 TYR B 405 ARG 0.006 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.05936 ( 954) hydrogen bonds : angle 4.84046 ( 2730) SS BOND : bond 0.00330 ( 12) SS BOND : angle 1.49523 ( 24) covalent geometry : bond 0.00312 (18686) covalent geometry : angle 0.68258 (25202) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 378 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.8181 (ptp) cc_final: 0.7888 (ttp) REVERT: A 533 TYR cc_start: 0.7987 (t80) cc_final: 0.7440 (t80) REVERT: A 599 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7840 (mtt-85) REVERT: A 639 LEU cc_start: 0.9038 (mt) cc_final: 0.8827 (mt) REVERT: A 650 LEU cc_start: 0.9319 (tp) cc_final: 0.8817 (tp) REVERT: A 667 PHE cc_start: 0.8734 (m-80) cc_final: 0.8531 (m-80) REVERT: B 408 MET cc_start: 0.8040 (mmp) cc_final: 0.7448 (tpt) REVERT: B 516 SER cc_start: 0.8752 (p) cc_final: 0.8385 (t) REVERT: B 586 GLN cc_start: 0.7816 (mm110) cc_final: 0.6909 (tm-30) REVERT: B 674 MET cc_start: 0.9208 (mtm) cc_final: 0.8909 (mtt) REVERT: B 708 MET cc_start: 0.9433 (mpp) cc_final: 0.9111 (mpp) REVERT: B 763 LYS cc_start: 0.7827 (tptp) cc_final: 0.7565 (tptp) REVERT: C 609 THR cc_start: 0.9443 (p) cc_final: 0.9147 (t) REVERT: C 626 VAL cc_start: 0.9122 (t) cc_final: 0.8864 (p) REVERT: D 600 ILE cc_start: 0.9032 (mm) cc_final: 0.8802 (tt) REVERT: D 673 TYR cc_start: 0.8186 (t80) cc_final: 0.7929 (t80) REVERT: D 693 VAL cc_start: 0.8825 (t) cc_final: 0.8187 (p) REVERT: E 150 ILE cc_start: 0.9191 (mm) cc_final: 0.8958 (mm) REVERT: E 190 GLU cc_start: 0.9127 (tp30) cc_final: 0.8901 (tp30) REVERT: E 202 ASP cc_start: 0.7786 (t70) cc_final: 0.7152 (t70) REVERT: F 148 ASN cc_start: 0.8592 (t0) cc_final: 0.8213 (t0) REVERT: F 191 MET cc_start: 0.8431 (mtp) cc_final: 0.7753 (tpt) REVERT: G 101 ARG cc_start: 0.8489 (tpt90) cc_final: 0.8234 (tpt90) REVERT: G 191 MET cc_start: 0.8284 (mtp) cc_final: 0.7726 (tpt) outliers start: 3 outliers final: 1 residues processed: 380 average time/residue: 0.2557 time to fit residues: 153.8124 Evaluate side-chains 276 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 121 optimal weight: 2.9990 chunk 124 optimal weight: 0.0570 chunk 86 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 chunk 187 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS C 726 ASN D 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.129739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.100363 restraints weight = 53647.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096687 restraints weight = 65577.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.097783 restraints weight = 60429.346| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18698 Z= 0.142 Angle : 0.606 6.354 25226 Z= 0.326 Chirality : 0.043 0.175 2826 Planarity : 0.004 0.055 3102 Dihedral : 5.452 67.292 2522 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.31 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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 (0.18), residues: 2298 helix: 1.56 (0.15), residues: 1222 sheet: -1.19 (0.40), residues: 148 loop : -0.82 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 766 HIS 0.004 0.001 HIS D 412 PHE 0.021 0.001 PHE G 115 TYR 0.015 0.001 TYR A 732 ARG 0.006 0.000 ARG D 420 Details of bonding type rmsd hydrogen bonds : bond 0.05223 ( 954) hydrogen bonds : angle 4.62433 ( 2730) SS BOND : bond 0.00372 ( 12) SS BOND : angle 1.21218 ( 24) covalent geometry : bond 0.00289 (18686) covalent geometry : angle 0.60523 (25202) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.8982 (tt0) cc_final: 0.8606 (tp30) REVERT: A 425 CYS cc_start: 0.9120 (m) cc_final: 0.8848 (m) REVERT: A 428 LEU cc_start: 0.9349 (pp) cc_final: 0.9084 (mm) REVERT: A 463 MET cc_start: 0.8243 (ptp) cc_final: 0.7962 (ttp) REVERT: A 587 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7737 (tp40) REVERT: A 599 ARG cc_start: 0.8098 (mtt180) cc_final: 0.7711 (mtt-85) REVERT: A 600 ILE cc_start: 0.8985 (mt) cc_final: 0.8664 (mm) REVERT: A 650 LEU cc_start: 0.9326 (tp) cc_final: 0.8885 (tp) REVERT: B 516 SER cc_start: 0.8833 (p) cc_final: 0.8540 (t) REVERT: B 534 ILE cc_start: 0.9070 (mt) cc_final: 0.8601 (tt) REVERT: B 573 ILE cc_start: 0.9158 (mp) cc_final: 0.8852 (tp) REVERT: B 645 ILE cc_start: 0.7904 (mm) cc_final: 0.7654 (mm) REVERT: B 674 MET cc_start: 0.9192 (mtm) cc_final: 0.8845 (mtt) REVERT: B 708 MET cc_start: 0.9416 (mpp) cc_final: 0.8733 (mtm) REVERT: B 763 LYS cc_start: 0.7918 (tptp) cc_final: 0.7448 (tppt) REVERT: C 479 LEU cc_start: 0.8602 (tp) cc_final: 0.8395 (tp) REVERT: C 503 MET cc_start: 0.8630 (ptp) cc_final: 0.8376 (ptp) REVERT: C 600 ILE cc_start: 0.8971 (mt) cc_final: 0.8692 (tp) REVERT: C 609 THR cc_start: 0.9409 (p) cc_final: 0.9072 (t) REVERT: C 674 MET cc_start: 0.8091 (tpp) cc_final: 0.7840 (mmp) REVERT: D 587 GLN cc_start: 0.7115 (mm110) cc_final: 0.6689 (mp10) REVERT: D 693 VAL cc_start: 0.8782 (t) cc_final: 0.8095 (p) REVERT: E 25 ILE cc_start: 0.8972 (mt) cc_final: 0.8691 (tp) REVERT: E 190 GLU cc_start: 0.8993 (tp30) cc_final: 0.8754 (tp30) REVERT: F 191 MET cc_start: 0.8493 (mtp) cc_final: 0.7973 (tpt) REVERT: G 57 MET cc_start: 0.5445 (mmm) cc_final: 0.4827 (mmm) REVERT: G 101 ARG cc_start: 0.8431 (tpt90) cc_final: 0.8105 (tpt90) REVERT: G 188 ILE cc_start: 0.9058 (mm) cc_final: 0.8824 (tp) REVERT: G 191 MET cc_start: 0.8333 (mtp) cc_final: 0.7615 (tpt) REVERT: H 9 MET cc_start: 0.8403 (tpt) cc_final: 0.7846 (tmm) REVERT: H 25 ILE cc_start: 0.9020 (mt) cc_final: 0.8718 (tp) REVERT: H 101 ARG cc_start: 0.9008 (tpt90) cc_final: 0.8772 (tpt170) REVERT: H 190 GLU cc_start: 0.9050 (tp30) cc_final: 0.8749 (tp30) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2634 time to fit residues: 144.0505 Evaluate side-chains 269 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 147 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 227 optimal weight: 0.5980 chunk 195 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS B 756 GLN D 508 GLN F 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.129928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099336 restraints weight = 53195.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.097117 restraints weight = 70255.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.098284 restraints weight = 62038.536| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18698 Z= 0.136 Angle : 0.589 7.091 25226 Z= 0.316 Chirality : 0.042 0.175 2826 Planarity : 0.004 0.058 3102 Dihedral : 5.214 63.915 2522 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.13 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.67 (0.18), residues: 2298 helix: 1.60 (0.15), residues: 1234 sheet: -1.12 (0.40), residues: 150 loop : -0.88 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 671 HIS 0.004 0.001 HIS G 59 PHE 0.019 0.001 PHE E 20 TYR 0.012 0.001 TYR A 424 ARG 0.004 0.000 ARG D 675 Details of bonding type rmsd hydrogen bonds : bond 0.04931 ( 954) hydrogen bonds : angle 4.54388 ( 2730) SS BOND : bond 0.00531 ( 12) SS BOND : angle 1.38350 ( 24) covalent geometry : bond 0.00286 (18686) covalent geometry : angle 0.58788 (25202) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 CYS cc_start: 0.9064 (m) cc_final: 0.8776 (m) REVERT: A 428 LEU cc_start: 0.9318 (pp) cc_final: 0.9101 (mm) REVERT: A 463 MET cc_start: 0.8254 (ptp) cc_final: 0.7889 (ttp) REVERT: A 587 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7676 (tp40) REVERT: A 599 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7738 (mtt-85) REVERT: A 600 ILE cc_start: 0.9090 (mt) cc_final: 0.8748 (mm) REVERT: A 639 LEU cc_start: 0.9000 (mt) cc_final: 0.8791 (mt) REVERT: A 650 LEU cc_start: 0.9275 (tp) cc_final: 0.8686 (tp) REVERT: B 408 MET cc_start: 0.8344 (mmp) cc_final: 0.6357 (mmm) REVERT: B 516 SER cc_start: 0.8790 (p) cc_final: 0.8565 (t) REVERT: B 534 ILE cc_start: 0.9068 (mt) cc_final: 0.8606 (tt) REVERT: B 573 ILE cc_start: 0.9080 (mp) cc_final: 0.8862 (mp) REVERT: B 645 ILE cc_start: 0.7812 (mm) cc_final: 0.7603 (mm) REVERT: B 670 MET cc_start: 0.8547 (mmt) cc_final: 0.8017 (mmm) REVERT: B 674 MET cc_start: 0.9138 (mtm) cc_final: 0.8853 (mtt) REVERT: B 708 MET cc_start: 0.9420 (mpp) cc_final: 0.9191 (mtm) REVERT: C 600 ILE cc_start: 0.8970 (mt) cc_final: 0.8691 (tp) REVERT: C 674 MET cc_start: 0.8093 (tpp) cc_final: 0.7691 (mmp) REVERT: C 816 TYR cc_start: 0.7131 (t80) cc_final: 0.6916 (t80) REVERT: D 585 MET cc_start: 0.7704 (mmm) cc_final: 0.6647 (mmt) REVERT: D 587 GLN cc_start: 0.7108 (mm110) cc_final: 0.6547 (mp10) REVERT: D 693 VAL cc_start: 0.8767 (t) cc_final: 0.8102 (p) REVERT: F 23 MET cc_start: 0.8656 (tpp) cc_final: 0.8430 (tpp) REVERT: F 191 MET cc_start: 0.8490 (mtp) cc_final: 0.7958 (tpt) REVERT: G 23 MET cc_start: 0.8378 (mmp) cc_final: 0.8175 (mmt) REVERT: G 101 ARG cc_start: 0.8439 (tpt90) cc_final: 0.8106 (tpt90) REVERT: G 191 MET cc_start: 0.8404 (mtp) cc_final: 0.7743 (tpt) REVERT: H 9 MET cc_start: 0.8344 (tpt) cc_final: 0.7860 (tmm) REVERT: H 25 ILE cc_start: 0.9003 (mt) cc_final: 0.8709 (tp) REVERT: H 190 GLU cc_start: 0.9019 (tp30) cc_final: 0.8756 (tp30) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2680 time to fit residues: 146.5237 Evaluate side-chains 263 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 82 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS B 756 GLN C 642 GLN D 508 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.126863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.092284 restraints weight = 53797.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.087367 restraints weight = 56033.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.085206 restraints weight = 46508.972| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18698 Z= 0.214 Angle : 0.655 7.387 25226 Z= 0.352 Chirality : 0.044 0.176 2826 Planarity : 0.004 0.057 3102 Dihedral : 5.377 66.924 2522 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.57 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.42 (0.18), residues: 2298 helix: 1.41 (0.15), residues: 1230 sheet: -1.22 (0.40), residues: 147 loop : -1.00 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 767 HIS 0.004 0.001 HIS H 131 PHE 0.024 0.002 PHE D 608 TYR 0.019 0.002 TYR G 175 ARG 0.005 0.000 ARG F 101 Details of bonding type rmsd hydrogen bonds : bond 0.05466 ( 954) hydrogen bonds : angle 4.84782 ( 2730) SS BOND : bond 0.00261 ( 12) SS BOND : angle 1.49450 ( 24) covalent geometry : bond 0.00470 (18686) covalent geometry : angle 0.65402 (25202) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 CYS cc_start: 0.9322 (m) cc_final: 0.9048 (m) REVERT: A 428 LEU cc_start: 0.9470 (pp) cc_final: 0.9179 (mm) REVERT: A 463 MET cc_start: 0.8500 (ptp) cc_final: 0.8216 (ttp) REVERT: A 587 GLN cc_start: 0.8357 (mm-40) cc_final: 0.7870 (mm110) REVERT: A 600 ILE cc_start: 0.9212 (mt) cc_final: 0.8924 (mm) REVERT: A 650 LEU cc_start: 0.9321 (tp) cc_final: 0.8789 (tp) REVERT: A 667 PHE cc_start: 0.8750 (m-80) cc_final: 0.8535 (m-80) REVERT: B 516 SER cc_start: 0.9198 (p) cc_final: 0.8906 (t) REVERT: B 573 ILE cc_start: 0.8991 (mp) cc_final: 0.8770 (mp) REVERT: B 645 ILE cc_start: 0.7873 (mm) cc_final: 0.7646 (mm) REVERT: B 667 PHE cc_start: 0.9197 (m-80) cc_final: 0.8902 (m-80) REVERT: C 600 ILE cc_start: 0.9102 (mt) cc_final: 0.8778 (tp) REVERT: C 642 GLN cc_start: 0.8748 (tp-100) cc_final: 0.8452 (tm-30) REVERT: C 674 MET cc_start: 0.8200 (tpp) cc_final: 0.7809 (mmp) REVERT: C 709 ASN cc_start: 0.8493 (t0) cc_final: 0.8276 (t0) REVERT: C 816 TYR cc_start: 0.7386 (t80) cc_final: 0.7166 (t80) REVERT: D 534 ILE cc_start: 0.9161 (mt) cc_final: 0.8735 (tt) REVERT: D 573 ILE cc_start: 0.9260 (mp) cc_final: 0.9019 (mm) REVERT: D 586 GLN cc_start: 0.4408 (tm-30) cc_final: 0.4103 (tm-30) REVERT: D 600 ILE cc_start: 0.8919 (mm) cc_final: 0.8633 (tt) REVERT: D 693 VAL cc_start: 0.8799 (t) cc_final: 0.8219 (p) REVERT: E 10 LEU cc_start: 0.8938 (mm) cc_final: 0.8507 (pp) REVERT: E 25 ILE cc_start: 0.9040 (mt) cc_final: 0.8754 (tp) REVERT: E 101 ARG cc_start: 0.9196 (tpt90) cc_final: 0.8848 (tpt170) REVERT: E 127 TYR cc_start: 0.6457 (m-80) cc_final: 0.6240 (m-10) REVERT: E 159 ASN cc_start: 0.8897 (m110) cc_final: 0.8660 (m110) REVERT: F 191 MET cc_start: 0.8620 (mtp) cc_final: 0.8071 (tpt) REVERT: G 23 MET cc_start: 0.8601 (mmp) cc_final: 0.8329 (mmt) REVERT: G 101 ARG cc_start: 0.8592 (tpt90) cc_final: 0.8157 (tpt90) REVERT: G 191 MET cc_start: 0.8549 (mtp) cc_final: 0.7963 (tpt) REVERT: H 9 MET cc_start: 0.8627 (tpt) cc_final: 0.8023 (tmm) REVERT: H 101 ARG cc_start: 0.9080 (tpt90) cc_final: 0.8638 (tpt170) REVERT: H 159 ASN cc_start: 0.8833 (m110) cc_final: 0.8545 (m110) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.2581 time to fit residues: 132.4879 Evaluate side-chains 261 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 214 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 221 optimal weight: 0.5980 chunk 147 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS B 756 GLN D 508 GLN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.129046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.100133 restraints weight = 53363.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.097051 restraints weight = 68543.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.097892 restraints weight = 66189.538| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18698 Z= 0.128 Angle : 0.593 8.302 25226 Z= 0.316 Chirality : 0.042 0.213 2826 Planarity : 0.004 0.056 3102 Dihedral : 5.061 61.713 2522 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.87 % Favored : 95.91 % Rotamer: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.59 (0.18), residues: 2298 helix: 1.60 (0.15), residues: 1223 sheet: -1.27 (0.40), residues: 150 loop : -0.96 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 767 HIS 0.013 0.001 HIS A 435 PHE 0.019 0.001 PHE E 20 TYR 0.016 0.001 TYR D 732 ARG 0.003 0.000 ARG D 675 Details of bonding type rmsd hydrogen bonds : bond 0.04914 ( 954) hydrogen bonds : angle 4.44560 ( 2730) SS BOND : bond 0.00239 ( 12) SS BOND : angle 1.39602 ( 24) covalent geometry : bond 0.00271 (18686) covalent geometry : angle 0.59160 (25202) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 CYS cc_start: 0.9150 (m) cc_final: 0.8822 (m) REVERT: A 428 LEU cc_start: 0.9344 (pp) cc_final: 0.9068 (mm) REVERT: A 463 MET cc_start: 0.8231 (ptp) cc_final: 0.7847 (ttp) REVERT: A 587 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7518 (mm110) REVERT: A 600 ILE cc_start: 0.8994 (mt) cc_final: 0.8669 (mm) REVERT: A 650 LEU cc_start: 0.9269 (tp) cc_final: 0.8663 (tp) REVERT: B 408 MET cc_start: 0.8826 (mmp) cc_final: 0.7945 (mmm) REVERT: B 421 TYR cc_start: 0.5520 (m-80) cc_final: 0.5011 (m-80) REVERT: B 534 ILE cc_start: 0.9040 (mt) cc_final: 0.8696 (tt) REVERT: B 573 ILE cc_start: 0.9081 (mp) cc_final: 0.8784 (mp) REVERT: B 645 ILE cc_start: 0.8018 (mm) cc_final: 0.7792 (mm) REVERT: B 670 MET cc_start: 0.8696 (mmt) cc_final: 0.8232 (mmm) REVERT: B 763 LYS cc_start: 0.7916 (tptp) cc_final: 0.7435 (tptm) REVERT: C 405 TYR cc_start: 0.8149 (m-80) cc_final: 0.7907 (m-80) REVERT: C 585 MET cc_start: 0.8244 (mmm) cc_final: 0.8033 (mmt) REVERT: C 600 ILE cc_start: 0.8994 (mt) cc_final: 0.8640 (tp) REVERT: C 674 MET cc_start: 0.8148 (tpp) cc_final: 0.7761 (mmp) REVERT: C 816 TYR cc_start: 0.7287 (t80) cc_final: 0.7079 (t80) REVERT: D 585 MET cc_start: 0.7762 (mmm) cc_final: 0.6685 (mmt) REVERT: D 587 GLN cc_start: 0.7242 (mm110) cc_final: 0.6462 (mp10) REVERT: D 693 VAL cc_start: 0.8804 (t) cc_final: 0.8148 (p) REVERT: E 10 LEU cc_start: 0.8587 (mm) cc_final: 0.8186 (pp) REVERT: E 101 ARG cc_start: 0.9042 (tpt90) cc_final: 0.8575 (tpt170) REVERT: E 127 TYR cc_start: 0.6538 (m-80) cc_final: 0.6289 (m-10) REVERT: F 23 MET cc_start: 0.8398 (tpp) cc_final: 0.8192 (mmt) REVERT: F 191 MET cc_start: 0.8597 (mtp) cc_final: 0.8011 (tpt) REVERT: G 101 ARG cc_start: 0.8440 (tpt90) cc_final: 0.8012 (tpt90) REVERT: G 191 MET cc_start: 0.8403 (mtp) cc_final: 0.7799 (tpt) REVERT: H 25 ILE cc_start: 0.8954 (mt) cc_final: 0.8660 (tp) REVERT: H 101 ARG cc_start: 0.8993 (tpt90) cc_final: 0.8488 (tpt170) REVERT: H 150 ILE cc_start: 0.9277 (mm) cc_final: 0.9065 (mm) outliers start: 1 outliers final: 1 residues processed: 336 average time/residue: 0.2623 time to fit residues: 139.9592 Evaluate side-chains 262 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 128 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 218 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS B 756 GLN C 412 HIS C 619 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.126214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.093932 restraints weight = 53296.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.088732 restraints weight = 63274.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.086795 restraints weight = 55225.751| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18698 Z= 0.240 Angle : 0.690 7.644 25226 Z= 0.372 Chirality : 0.045 0.214 2826 Planarity : 0.004 0.057 3102 Dihedral : 5.349 60.114 2522 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.74 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.15 (0.18), residues: 2298 helix: 1.25 (0.15), residues: 1231 sheet: -1.33 (0.42), residues: 150 loop : -1.22 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 767 HIS 0.010 0.001 HIS C 412 PHE 0.027 0.002 PHE D 608 TYR 0.021 0.002 TYR G 175 ARG 0.003 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.05667 ( 954) hydrogen bonds : angle 4.92885 ( 2730) SS BOND : bond 0.00239 ( 12) SS BOND : angle 1.29998 ( 24) covalent geometry : bond 0.00525 (18686) covalent geometry : angle 0.68894 (25202) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 CYS cc_start: 0.9277 (m) cc_final: 0.8992 (m) REVERT: A 428 LEU cc_start: 0.9425 (pp) cc_final: 0.9134 (mm) REVERT: A 463 MET cc_start: 0.8359 (ptp) cc_final: 0.8019 (ttp) REVERT: A 533 TYR cc_start: 0.8285 (t80) cc_final: 0.8009 (t80) REVERT: A 587 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7985 (mm110) REVERT: A 600 ILE cc_start: 0.9080 (mt) cc_final: 0.8751 (mm) REVERT: A 639 LEU cc_start: 0.9168 (mt) cc_final: 0.8953 (mt) REVERT: A 667 PHE cc_start: 0.8851 (m-80) cc_final: 0.8358 (m-80) REVERT: B 408 MET cc_start: 0.8861 (mmp) cc_final: 0.7731 (mmm) REVERT: B 421 TYR cc_start: 0.5743 (m-80) cc_final: 0.5248 (m-80) REVERT: B 463 MET cc_start: 0.4328 (ptp) cc_final: 0.3917 (pmm) REVERT: B 503 MET cc_start: 0.8991 (tmm) cc_final: 0.8719 (tmm) REVERT: B 667 PHE cc_start: 0.9085 (m-80) cc_final: 0.8781 (m-80) REVERT: B 763 LYS cc_start: 0.8084 (tptp) cc_final: 0.7375 (tptm) REVERT: C 405 TYR cc_start: 0.8482 (m-80) cc_final: 0.8113 (m-80) REVERT: C 463 MET cc_start: 0.8175 (ptt) cc_final: 0.7874 (pmm) REVERT: C 516 SER cc_start: 0.9521 (p) cc_final: 0.9115 (t) REVERT: D 534 ILE cc_start: 0.9149 (mt) cc_final: 0.8770 (tt) REVERT: D 573 ILE cc_start: 0.9320 (mp) cc_final: 0.9084 (mm) REVERT: D 585 MET cc_start: 0.8161 (mmm) cc_final: 0.7294 (mmt) REVERT: D 587 GLN cc_start: 0.7547 (mm110) cc_final: 0.6994 (mp10) REVERT: D 600 ILE cc_start: 0.8942 (mm) cc_final: 0.8670 (tp) REVERT: D 693 VAL cc_start: 0.8902 (t) cc_final: 0.8332 (p) REVERT: D 721 MET cc_start: 0.7297 (pmm) cc_final: 0.7069 (pmm) REVERT: E 101 ARG cc_start: 0.9265 (tpt90) cc_final: 0.8857 (tpt170) REVERT: E 127 TYR cc_start: 0.6620 (m-80) cc_final: 0.6281 (m-10) REVERT: F 191 MET cc_start: 0.8582 (mtp) cc_final: 0.8103 (tpt) REVERT: G 101 ARG cc_start: 0.8569 (tpt90) cc_final: 0.8146 (tpt90) REVERT: G 191 MET cc_start: 0.8442 (mtp) cc_final: 0.7897 (tpt) REVERT: G 199 MET cc_start: 0.8965 (mmm) cc_final: 0.8744 (mmm) REVERT: H 25 ILE cc_start: 0.8999 (mt) cc_final: 0.8761 (tp) REVERT: H 101 ARG cc_start: 0.9173 (tpt90) cc_final: 0.8555 (tpt90) REVERT: H 127 TYR cc_start: 0.6735 (m-80) cc_final: 0.6408 (m-10) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.2559 time to fit residues: 131.8690 Evaluate side-chains 249 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 193 optimal weight: 0.5980 chunk 208 optimal weight: 10.0000 chunk 179 optimal weight: 0.6980 chunk 154 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 chunk 212 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS B 586 GLN B 756 GLN D 508 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.129139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.100531 restraints weight = 53456.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.098299 restraints weight = 69308.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.099259 restraints weight = 64493.489| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18698 Z= 0.124 Angle : 0.603 9.888 25226 Z= 0.318 Chirality : 0.043 0.217 2826 Planarity : 0.004 0.056 3102 Dihedral : 4.923 51.590 2522 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.66 % Favored : 96.13 % Rotamer: Outliers : 0.05 % Allowed : 1.02 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.52 (0.18), residues: 2298 helix: 1.61 (0.16), residues: 1219 sheet: -1.31 (0.41), residues: 148 loop : -1.10 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 767 HIS 0.004 0.001 HIS A 435 PHE 0.020 0.001 PHE H 20 TYR 0.013 0.001 TYR D 732 ARG 0.003 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.04852 ( 954) hydrogen bonds : angle 4.37048 ( 2730) SS BOND : bond 0.00232 ( 12) SS BOND : angle 1.07930 ( 24) covalent geometry : bond 0.00260 (18686) covalent geometry : angle 0.60282 (25202) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 328 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 CYS cc_start: 0.9198 (m) cc_final: 0.8837 (m) REVERT: A 428 LEU cc_start: 0.9327 (pp) cc_final: 0.9052 (mm) REVERT: A 533 TYR cc_start: 0.7991 (t80) cc_final: 0.7771 (t80) REVERT: A 574 PHE cc_start: 0.8128 (t80) cc_final: 0.7124 (m-80) REVERT: A 587 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7366 (mm110) REVERT: A 600 ILE cc_start: 0.8996 (mt) cc_final: 0.8644 (mm) REVERT: A 667 PHE cc_start: 0.8701 (m-80) cc_final: 0.8307 (m-80) REVERT: B 408 MET cc_start: 0.8719 (mmp) cc_final: 0.7312 (mmp) REVERT: B 421 TYR cc_start: 0.5560 (m-80) cc_final: 0.5134 (m-80) REVERT: B 573 ILE cc_start: 0.9069 (mp) cc_final: 0.8783 (tp) REVERT: B 670 MET cc_start: 0.8573 (mmt) cc_final: 0.8203 (mmm) REVERT: C 463 MET cc_start: 0.7799 (ptt) cc_final: 0.7567 (pmm) REVERT: C 516 SER cc_start: 0.9199 (p) cc_final: 0.8628 (t) REVERT: C 538 VAL cc_start: 0.9241 (t) cc_final: 0.9033 (p) REVERT: C 585 MET cc_start: 0.7863 (mmm) cc_final: 0.7352 (mmm) REVERT: C 600 ILE cc_start: 0.8588 (tt) cc_final: 0.8172 (tp) REVERT: C 674 MET cc_start: 0.8215 (tpp) cc_final: 0.7751 (mmp) REVERT: D 585 MET cc_start: 0.7854 (mmm) cc_final: 0.7357 (mmm) REVERT: D 587 GLN cc_start: 0.7181 (mm110) cc_final: 0.6444 (mp10) REVERT: D 629 MET cc_start: 0.6199 (mmm) cc_final: 0.5999 (mmm) REVERT: D 693 VAL cc_start: 0.8843 (t) cc_final: 0.8216 (p) REVERT: E 101 ARG cc_start: 0.9118 (tpt90) cc_final: 0.8702 (tpt170) REVERT: E 127 TYR cc_start: 0.6563 (m-80) cc_final: 0.6244 (m-10) REVERT: F 191 MET cc_start: 0.8619 (mtp) cc_final: 0.8059 (tpt) REVERT: G 101 ARG cc_start: 0.8390 (tpt90) cc_final: 0.7994 (tpt90) REVERT: G 191 MET cc_start: 0.8444 (mtp) cc_final: 0.7855 (tpt) REVERT: H 101 ARG cc_start: 0.9132 (tpt90) cc_final: 0.8626 (tpt170) REVERT: H 127 TYR cc_start: 0.6692 (m-80) cc_final: 0.6390 (m-10) REVERT: H 150 ILE cc_start: 0.9295 (mm) cc_final: 0.9079 (mm) outliers start: 1 outliers final: 0 residues processed: 328 average time/residue: 0.2727 time to fit residues: 140.0887 Evaluate side-chains 263 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 84 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 70 optimal weight: 0.0770 chunk 216 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS B 586 GLN B 756 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.127356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.094488 restraints weight = 53652.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.089841 restraints weight = 63029.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.089361 restraints weight = 49623.053| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18698 Z= 0.173 Angle : 0.648 10.872 25226 Z= 0.342 Chirality : 0.044 0.198 2826 Planarity : 0.004 0.057 3102 Dihedral : 5.036 52.680 2522 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.40 % Favored : 95.39 % Rotamer: Outliers : 0.05 % Allowed : 0.87 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.38 (0.18), residues: 2298 helix: 1.49 (0.15), residues: 1232 sheet: -1.28 (0.42), residues: 147 loop : -1.20 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 767 HIS 0.005 0.001 HIS H 131 PHE 0.021 0.002 PHE E 20 TYR 0.015 0.002 TYR G 175 ARG 0.003 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.05144 ( 954) hydrogen bonds : angle 4.55178 ( 2730) SS BOND : bond 0.00213 ( 12) SS BOND : angle 1.11823 ( 24) covalent geometry : bond 0.00380 (18686) covalent geometry : angle 0.64743 (25202) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASN cc_start: 0.9217 (t0) cc_final: 0.9007 (t0) REVERT: A 425 CYS cc_start: 0.9335 (m) cc_final: 0.9045 (m) REVERT: A 428 LEU cc_start: 0.9463 (pp) cc_final: 0.9128 (mm) REVERT: A 533 TYR cc_start: 0.8237 (t80) cc_final: 0.7988 (t80) REVERT: A 574 PHE cc_start: 0.8040 (t80) cc_final: 0.7033 (m-80) REVERT: A 587 GLN cc_start: 0.8504 (mm-40) cc_final: 0.7635 (mm110) REVERT: A 600 ILE cc_start: 0.9002 (mt) cc_final: 0.8659 (mm) REVERT: B 408 MET cc_start: 0.8851 (mmp) cc_final: 0.7064 (mmp) REVERT: B 421 TYR cc_start: 0.5840 (m-80) cc_final: 0.5329 (m-80) REVERT: B 503 MET cc_start: 0.8914 (tmm) cc_final: 0.8614 (tmm) REVERT: B 573 ILE cc_start: 0.9022 (mp) cc_final: 0.8758 (tp) REVERT: B 670 MET cc_start: 0.8879 (mmm) cc_final: 0.8582 (mmm) REVERT: B 763 LYS cc_start: 0.8179 (tptp) cc_final: 0.7593 (tptm) REVERT: C 516 SER cc_start: 0.9514 (p) cc_final: 0.9081 (t) REVERT: C 586 GLN cc_start: 0.8597 (mt0) cc_final: 0.8362 (mt0) REVERT: C 600 ILE cc_start: 0.8639 (tt) cc_final: 0.8205 (tp) REVERT: D 573 ILE cc_start: 0.9311 (mp) cc_final: 0.9072 (mm) REVERT: D 585 MET cc_start: 0.7996 (mmm) cc_final: 0.6574 (mmt) REVERT: D 587 GLN cc_start: 0.7406 (mm110) cc_final: 0.6413 (mp10) REVERT: D 600 ILE cc_start: 0.8908 (mm) cc_final: 0.8594 (tp) REVERT: D 693 VAL cc_start: 0.8839 (t) cc_final: 0.8262 (p) REVERT: D 713 GLU cc_start: 0.9297 (tm-30) cc_final: 0.9077 (tm-30) REVERT: E 101 ARG cc_start: 0.9252 (tpt90) cc_final: 0.8639 (tpt90) REVERT: E 127 TYR cc_start: 0.6568 (m-80) cc_final: 0.6235 (m-10) REVERT: E 190 GLU cc_start: 0.9094 (tp30) cc_final: 0.8887 (tp30) REVERT: F 191 MET cc_start: 0.8669 (mtp) cc_final: 0.8145 (tpt) REVERT: G 101 ARG cc_start: 0.8585 (tpt90) cc_final: 0.8152 (tpt90) REVERT: G 191 MET cc_start: 0.8479 (mtp) cc_final: 0.7892 (tpt) REVERT: H 101 ARG cc_start: 0.9200 (tpt90) cc_final: 0.8685 (tpt170) REVERT: H 127 TYR cc_start: 0.6660 (m-80) cc_final: 0.6324 (m-10) outliers start: 1 outliers final: 0 residues processed: 318 average time/residue: 0.2493 time to fit residues: 125.5658 Evaluate side-chains 258 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 42 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 203 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 198 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS B 586 GLN B 756 GLN D 508 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.128687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.095982 restraints weight = 53756.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.089313 restraints weight = 62214.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.089004 restraints weight = 55696.746| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18698 Z= 0.134 Angle : 0.623 8.956 25226 Z= 0.323 Chirality : 0.043 0.177 2826 Planarity : 0.004 0.055 3102 Dihedral : 4.901 51.214 2522 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.18 % Favored : 95.60 % Rotamer: Outliers : 0.05 % Allowed : 0.36 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.48 (0.18), residues: 2298 helix: 1.57 (0.15), residues: 1232 sheet: -1.29 (0.41), residues: 148 loop : -1.15 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 671 HIS 0.004 0.001 HIS A 435 PHE 0.022 0.001 PHE H 20 TYR 0.013 0.001 TYR D 732 ARG 0.003 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.04796 ( 954) hydrogen bonds : angle 4.38737 ( 2730) SS BOND : bond 0.00219 ( 12) SS BOND : angle 1.02001 ( 24) covalent geometry : bond 0.00292 (18686) covalent geometry : angle 0.62215 (25202) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 321 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASN cc_start: 0.9297 (t0) cc_final: 0.9062 (t0) REVERT: A 425 CYS cc_start: 0.9337 (m) cc_final: 0.8975 (m) REVERT: A 428 LEU cc_start: 0.9459 (pp) cc_final: 0.9127 (mm) REVERT: A 463 MET cc_start: 0.8636 (ptt) cc_final: 0.8126 (pmm) REVERT: A 533 TYR cc_start: 0.8206 (t80) cc_final: 0.7934 (t80) REVERT: A 587 GLN cc_start: 0.8448 (mm-40) cc_final: 0.7584 (mm110) REVERT: A 600 ILE cc_start: 0.8997 (mt) cc_final: 0.8650 (mm) REVERT: B 401 LEU cc_start: 0.7440 (pt) cc_final: 0.7050 (pt) REVERT: B 408 MET cc_start: 0.8903 (mmp) cc_final: 0.7432 (mmp) REVERT: B 421 TYR cc_start: 0.5839 (m-80) cc_final: 0.5270 (m-80) REVERT: B 503 MET cc_start: 0.8865 (tmm) cc_final: 0.8534 (tmm) REVERT: B 534 ILE cc_start: 0.8938 (mt) cc_final: 0.8577 (tt) REVERT: B 573 ILE cc_start: 0.9020 (mp) cc_final: 0.8747 (tp) REVERT: B 667 PHE cc_start: 0.9218 (m-80) cc_final: 0.8991 (m-80) REVERT: B 670 MET cc_start: 0.8947 (mmm) cc_final: 0.8678 (mmm) REVERT: B 763 LYS cc_start: 0.8117 (tptp) cc_final: 0.7578 (tptm) REVERT: C 463 MET cc_start: 0.8078 (ptt) cc_final: 0.7719 (pmm) REVERT: C 600 ILE cc_start: 0.8644 (tt) cc_final: 0.8230 (tp) REVERT: D 573 ILE cc_start: 0.9258 (mp) cc_final: 0.9005 (mm) REVERT: D 585 MET cc_start: 0.8036 (mmm) cc_final: 0.6635 (mmt) REVERT: D 587 GLN cc_start: 0.7376 (mm110) cc_final: 0.6676 (mp10) REVERT: D 693 VAL cc_start: 0.8831 (t) cc_final: 0.8245 (p) REVERT: D 713 GLU cc_start: 0.9347 (tm-30) cc_final: 0.9105 (tm-30) REVERT: E 101 ARG cc_start: 0.9212 (tpt90) cc_final: 0.8796 (tpt170) REVERT: E 127 TYR cc_start: 0.6480 (m-80) cc_final: 0.6165 (m-10) REVERT: E 190 GLU cc_start: 0.9081 (tp30) cc_final: 0.8871 (tp30) REVERT: F 191 MET cc_start: 0.8682 (mtp) cc_final: 0.8154 (tpt) REVERT: G 101 ARG cc_start: 0.8581 (tpt90) cc_final: 0.8156 (tpt90) REVERT: G 191 MET cc_start: 0.8488 (mtp) cc_final: 0.7951 (tpt) REVERT: H 101 ARG cc_start: 0.9126 (tpt90) cc_final: 0.8663 (tpt170) REVERT: H 127 TYR cc_start: 0.6597 (m-80) cc_final: 0.6303 (m-10) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.2670 time to fit residues: 135.4819 Evaluate side-chains 256 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 66 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 95 optimal weight: 0.1980 chunk 172 optimal weight: 0.8980 chunk 186 optimal weight: 0.0000 chunk 174 optimal weight: 0.2980 chunk 164 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS B 586 GLN B 619 ASN B 756 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.130907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.102073 restraints weight = 53495.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099554 restraints weight = 66433.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.100439 restraints weight = 64281.714| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18698 Z= 0.114 Angle : 0.608 9.829 25226 Z= 0.314 Chirality : 0.042 0.174 2826 Planarity : 0.004 0.054 3102 Dihedral : 4.634 47.112 2522 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.13 % Favored : 95.60 % Rotamer: Outliers : 0.10 % Allowed : 0.31 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.54 (0.18), residues: 2298 helix: 1.60 (0.15), residues: 1236 sheet: -1.26 (0.41), residues: 148 loop : -1.10 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 767 HIS 0.005 0.001 HIS G 198 PHE 0.026 0.001 PHE E 20 TYR 0.012 0.001 TYR C 424 ARG 0.004 0.000 ARG F 101 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 954) hydrogen bonds : angle 4.16675 ( 2730) SS BOND : bond 0.00202 ( 12) SS BOND : angle 0.95536 ( 24) covalent geometry : bond 0.00232 (18686) covalent geometry : angle 0.60765 (25202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5838.67 seconds wall clock time: 103 minutes 14.79 seconds (6194.79 seconds total)