Starting phenix.real_space_refine on Thu Sep 18 16:45:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dhs_46875/09_2025/9dhs_46875.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dhs_46875/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dhs_46875/09_2025/9dhs_46875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dhs_46875/09_2025/9dhs_46875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dhs_46875/09_2025/9dhs_46875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dhs_46875/09_2025/9dhs_46875.map" } resolution = 4.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.60, per 1000 atoms: 0.25 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: 1.65 Conformation dependent library (CDL) restraints added in 785.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.67 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: 3.26 Time building geometry restraints manager: 2.17 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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.480 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.021 0.002 ARG B 453 TYR 0.036 0.005 TYR B 711 PHE 0.041 0.002 PHE A 438 TRP 0.027 0.005 TRP G 32 HIS 0.008 0.002 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00330 (18686) covalent geometry : angle 0.71370 (25202) SS BOND : bond 0.00331 ( 12) SS BOND : angle 0.88279 ( 24) hydrogen bonds : bond 0.16162 ( 954) hydrogen bonds : angle 6.57932 ( 2730) *********************** 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 : 0.704 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: 0.1366 time to fit residues: 114.4399 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 : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 586 GLN 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 = 0.3908 r_free = 0.3908 target = 0.127265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.097764 restraints weight = 53020.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.094797 restraints weight = 68013.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.095842 restraints weight = 62452.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096504 restraints weight = 42721.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.096974 restraints weight = 41379.554| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18698 Z= 0.204 Angle : 0.721 8.917 25226 Z= 0.392 Chirality : 0.046 0.178 2826 Planarity : 0.005 0.057 3102 Dihedral : 6.251 62.693 2522 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.13 % Favored : 95.47 % Rotamer: Outliers : 0.15 % Allowed : 3.07 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.17), residues: 2298 helix: 0.86 (0.15), residues: 1215 sheet: -1.31 (0.40), residues: 151 loop : -1.05 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 485 TYR 0.021 0.002 TYR B 405 PHE 0.017 0.002 PHE F 106 TRP 0.017 0.002 TRP B 671 HIS 0.004 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00447 (18686) covalent geometry : angle 0.71910 (25202) SS BOND : bond 0.01283 ( 12) SS BOND : angle 1.99381 ( 24) hydrogen bonds : bond 0.06642 ( 954) hydrogen bonds : angle 5.24727 ( 2730) *********************** 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 366 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 363 time to evaluate : 0.723 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: A 463 MET cc_start: 0.8084 (ptp) cc_final: 0.7838 (ttp) REVERT: A 599 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7907 (mtt-85) REVERT: A 650 LEU cc_start: 0.9332 (tp) cc_final: 0.8835 (tp) REVERT: A 667 PHE cc_start: 0.8836 (m-80) cc_final: 0.8621 (m-80) REVERT: B 408 MET cc_start: 0.7992 (mmp) cc_final: 0.7395 (tpt) REVERT: B 516 SER cc_start: 0.8972 (p) cc_final: 0.8740 (t) REVERT: B 586 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7223 (tm-30) REVERT: B 674 MET cc_start: 0.9192 (mtm) cc_final: 0.8905 (mtt) REVERT: B 693 VAL cc_start: 0.8983 (t) cc_final: 0.8607 (m) REVERT: B 708 MET cc_start: 0.9435 (mpp) cc_final: 0.9091 (mpp) REVERT: C 479 LEU cc_start: 0.8854 (tp) cc_final: 0.8591 (tp) REVERT: C 626 VAL cc_start: 0.9226 (t) cc_final: 0.8950 (p) REVERT: C 674 MET cc_start: 0.8181 (mmm) cc_final: 0.7852 (mmp) REVERT: D 673 TYR cc_start: 0.8118 (t80) cc_final: 0.7902 (t80) REVERT: D 693 VAL cc_start: 0.8868 (t) cc_final: 0.8258 (p) REVERT: E 150 ILE cc_start: 0.9243 (mm) cc_final: 0.8979 (mm) REVERT: E 190 GLU cc_start: 0.9012 (tp30) cc_final: 0.8746 (tp30) REVERT: F 148 ASN cc_start: 0.8621 (t0) cc_final: 0.8406 (t0) REVERT: F 191 MET cc_start: 0.8340 (mtp) cc_final: 0.7677 (tpt) REVERT: G 101 ARG cc_start: 0.8496 (tpt90) cc_final: 0.8133 (tpt90) REVERT: G 188 ILE cc_start: 0.8959 (mm) cc_final: 0.8752 (tp) REVERT: G 191 MET cc_start: 0.8285 (mtp) cc_final: 0.7725 (tpt) REVERT: H 150 ILE cc_start: 0.9356 (mm) cc_final: 0.9136 (mm) outliers start: 3 outliers final: 1 residues processed: 366 average time/residue: 0.1161 time to fit residues: 68.3298 Evaluate side-chains 269 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 79 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 51 optimal weight: 0.0670 chunk 211 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS D 508 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 HIS 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 = 0.129726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.098161 restraints weight = 53539.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.096613 restraints weight = 59914.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.097497 restraints weight = 55080.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.098652 restraints weight = 37477.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.098796 restraints weight = 36280.676| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18698 Z= 0.133 Angle : 0.615 7.169 25226 Z= 0.331 Chirality : 0.043 0.176 2826 Planarity : 0.004 0.058 3102 Dihedral : 5.523 67.605 2522 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.35 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.18), residues: 2298 helix: 1.51 (0.15), residues: 1215 sheet: -1.19 (0.41), residues: 146 loop : -0.89 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 684 TYR 0.020 0.001 TYR D 732 PHE 0.022 0.001 PHE G 115 TRP 0.012 0.001 TRP B 671 HIS 0.003 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00271 (18686) covalent geometry : angle 0.61361 (25202) SS BOND : bond 0.00273 ( 12) SS BOND : angle 1.35688 ( 24) hydrogen bonds : bond 0.05323 ( 954) hydrogen bonds : angle 4.66764 ( 2730) *********************** 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 357 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.464 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: 0.9125 (m) cc_final: 0.8867 (m) REVERT: A 428 LEU cc_start: 0.9378 (pp) cc_final: 0.9083 (mm) REVERT: A 463 MET cc_start: 0.8161 (ptp) cc_final: 0.7956 (ttp) REVERT: A 587 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7747 (tp40) REVERT: A 599 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7620 (mtt-85) REVERT: A 600 ILE cc_start: 0.9050 (mt) cc_final: 0.8747 (mm) REVERT: A 639 LEU cc_start: 0.9083 (mt) cc_final: 0.8878 (mt) REVERT: A 650 LEU cc_start: 0.9316 (tp) cc_final: 0.8845 (tp) REVERT: A 667 PHE cc_start: 0.8676 (m-80) cc_final: 0.8437 (m-80) REVERT: B 408 MET cc_start: 0.8234 (mmp) cc_final: 0.7513 (mmt) REVERT: B 516 SER cc_start: 0.8920 (p) cc_final: 0.8572 (t) REVERT: B 534 ILE cc_start: 0.9053 (mt) cc_final: 0.8575 (tt) REVERT: B 573 ILE cc_start: 0.9130 (mp) cc_final: 0.8841 (tp) REVERT: B 667 PHE cc_start: 0.8931 (m-80) cc_final: 0.8645 (m-80) REVERT: B 708 MET cc_start: 0.9432 (mpp) cc_final: 0.9206 (mpp) REVERT: C 402 GLU cc_start: 0.8690 (tt0) cc_final: 0.8489 (tp30) REVERT: C 463 MET cc_start: 0.8403 (ttt) cc_final: 0.8092 (ptm) REVERT: C 503 MET cc_start: 0.8640 (ptp) cc_final: 0.8304 (ptp) REVERT: C 600 ILE cc_start: 0.9025 (mt) cc_final: 0.8786 (tp) REVERT: C 626 VAL cc_start: 0.9088 (t) cc_final: 0.8863 (p) REVERT: C 674 MET cc_start: 0.8169 (mmm) cc_final: 0.7754 (mmp) REVERT: C 705 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7308 (mt-10) REVERT: C 708 MET cc_start: 0.8938 (mtm) cc_final: 0.8676 (mtt) REVERT: D 587 GLN cc_start: 0.7148 (mm110) cc_final: 0.6513 (mp10) REVERT: D 693 VAL cc_start: 0.8749 (t) cc_final: 0.8071 (p) REVERT: E 25 ILE cc_start: 0.8979 (mt) cc_final: 0.8673 (tp) REVERT: E 190 GLU cc_start: 0.9044 (tp30) cc_final: 0.8804 (tp30) REVERT: F 191 MET cc_start: 0.8437 (mtp) cc_final: 0.7928 (tpt) REVERT: G 23 MET cc_start: 0.8612 (tpp) cc_final: 0.8107 (mmt) REVERT: G 57 MET cc_start: 0.5657 (mmm) cc_final: 0.5136 (mmm) REVERT: G 101 ARG cc_start: 0.8539 (tpt90) cc_final: 0.8213 (tpt90) REVERT: G 191 MET cc_start: 0.8363 (mtp) cc_final: 0.7690 (tpt) REVERT: H 9 MET cc_start: 0.8367 (tpt) cc_final: 0.7813 (tmm) REVERT: H 25 ILE cc_start: 0.8993 (mt) cc_final: 0.8711 (tp) REVERT: H 101 ARG cc_start: 0.9090 (tpt90) cc_final: 0.8669 (tpt170) REVERT: H 114 LEU cc_start: 0.8832 (mm) cc_final: 0.8631 (mm) REVERT: H 190 GLU cc_start: 0.9039 (tp30) cc_final: 0.8801 (tp30) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.1113 time to fit residues: 63.1248 Evaluate side-chains 275 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 114 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 187 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 586 GLN C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN 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 = 0.3848 r_free = 0.3848 target = 0.123845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.089370 restraints weight = 54129.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.085991 restraints weight = 57114.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.083079 restraints weight = 44335.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.083570 restraints weight = 42664.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.083594 restraints weight = 39952.927| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 18698 Z= 0.304 Angle : 0.777 9.542 25226 Z= 0.420 Chirality : 0.048 0.176 2826 Planarity : 0.005 0.063 3102 Dihedral : 5.991 69.342 2522 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.31 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.18), residues: 2298 helix: 0.85 (0.15), residues: 1232 sheet: -1.30 (0.42), residues: 138 loop : -1.18 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 660 TYR 0.028 0.002 TYR A 616 PHE 0.033 0.002 PHE D 608 TRP 0.019 0.002 TRP B 605 HIS 0.006 0.001 HIS H 131 Details of bonding type rmsd covalent geometry : bond 0.00666 (18686) covalent geometry : angle 0.77542 (25202) SS BOND : bond 0.00372 ( 12) SS BOND : angle 1.70761 ( 24) hydrogen bonds : bond 0.06537 ( 954) hydrogen bonds : angle 5.47896 ( 2730) *********************** 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 324 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.621 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: 0.9343 (m) cc_final: 0.9030 (m) REVERT: A 428 LEU cc_start: 0.9457 (pp) cc_final: 0.9171 (mm) REVERT: A 438 PHE cc_start: 0.7967 (p90) cc_final: 0.7034 (p90) REVERT: A 533 TYR cc_start: 0.8356 (t80) cc_final: 0.8054 (t80) REVERT: A 587 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7915 (mm110) REVERT: A 629 MET cc_start: 0.8992 (ptp) cc_final: 0.8773 (ptp) REVERT: A 650 LEU cc_start: 0.9338 (tp) cc_final: 0.8766 (tp) REVERT: A 667 PHE cc_start: 0.8914 (m-80) cc_final: 0.8692 (m-80) REVERT: B 401 LEU cc_start: 0.7300 (pt) cc_final: 0.7053 (pt) REVERT: B 408 MET cc_start: 0.8838 (mmp) cc_final: 0.7597 (mmp) REVERT: B 421 TYR cc_start: 0.6300 (m-80) cc_final: 0.5653 (m-80) REVERT: B 503 MET cc_start: 0.9005 (tmm) cc_final: 0.8803 (tmm) REVERT: B 516 SER cc_start: 0.9220 (p) cc_final: 0.8920 (t) REVERT: B 573 ILE cc_start: 0.9152 (mp) cc_final: 0.8945 (mp) REVERT: B 629 MET cc_start: 0.5543 (mtp) cc_final: 0.4988 (mtp) REVERT: B 667 PHE cc_start: 0.9265 (m-80) cc_final: 0.8961 (m-80) REVERT: B 708 MET cc_start: 0.9522 (mpp) cc_final: 0.9005 (mpp) REVERT: C 463 MET cc_start: 0.8911 (ttt) cc_final: 0.8365 (ptm) REVERT: C 516 SER cc_start: 0.9503 (p) cc_final: 0.9293 (t) REVERT: C 626 VAL cc_start: 0.9331 (t) cc_final: 0.9101 (p) REVERT: C 674 MET cc_start: 0.8314 (mmm) cc_final: 0.8035 (mmp) REVERT: D 408 MET cc_start: 0.8087 (tpt) cc_final: 0.7397 (tpt) REVERT: D 573 ILE cc_start: 0.9341 (mp) cc_final: 0.9112 (mm) REVERT: D 721 MET cc_start: 0.7931 (ptp) cc_final: 0.7696 (pmm) REVERT: E 150 ILE cc_start: 0.9322 (mm) cc_final: 0.9088 (mm) REVERT: E 190 GLU cc_start: 0.9097 (tp30) cc_final: 0.8873 (tp30) REVERT: F 188 ILE cc_start: 0.9087 (tp) cc_final: 0.8818 (tp) REVERT: F 191 MET cc_start: 0.8612 (mtp) cc_final: 0.8032 (tpt) REVERT: G 23 MET cc_start: 0.8813 (tpp) cc_final: 0.8589 (mmp) REVERT: G 57 MET cc_start: 0.6273 (mmm) cc_final: 0.6064 (mmm) REVERT: G 101 ARG cc_start: 0.8578 (tpt90) cc_final: 0.8167 (tpt90) REVERT: G 191 MET cc_start: 0.8496 (mtp) cc_final: 0.7978 (tpt) REVERT: H 105 ILE cc_start: 0.8509 (mm) cc_final: 0.8309 (mm) REVERT: H 127 TYR cc_start: 0.6558 (m-80) cc_final: 0.6295 (m-10) REVERT: H 150 ILE cc_start: 0.9395 (mm) cc_final: 0.9158 (mm) REVERT: H 190 GLU cc_start: 0.9121 (tp30) cc_final: 0.8881 (tp30) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.1114 time to fit residues: 57.5021 Evaluate side-chains 243 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 88 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 215 optimal weight: 0.5980 chunk 212 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 135 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 C 642 GLN D 508 GLN E 131 HIS ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.128493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098887 restraints weight = 53762.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.098313 restraints weight = 74695.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.099649 restraints weight = 60159.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.099785 restraints weight = 39667.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.101836 restraints weight = 38188.120| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18698 Z= 0.129 Angle : 0.605 7.821 25226 Z= 0.324 Chirality : 0.043 0.203 2826 Planarity : 0.004 0.061 3102 Dihedral : 5.314 63.994 2522 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.00 % Favored : 95.78 % Rotamer: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.18), residues: 2298 helix: 1.47 (0.15), residues: 1217 sheet: -1.40 (0.40), residues: 149 loop : -1.07 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 675 TYR 0.013 0.001 TYR C 424 PHE 0.022 0.001 PHE H 20 TRP 0.025 0.001 TRP C 767 HIS 0.004 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00269 (18686) covalent geometry : angle 0.60420 (25202) SS BOND : bond 0.00225 ( 12) SS BOND : angle 1.37488 ( 24) hydrogen bonds : bond 0.05288 ( 954) hydrogen bonds : angle 4.57655 ( 2730) *********************** 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 345 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 344 time to evaluate : 0.636 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: A 425 CYS cc_start: 0.9233 (m) cc_final: 0.8880 (m) REVERT: A 428 LEU cc_start: 0.9364 (pp) cc_final: 0.9083 (mm) REVERT: A 587 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7532 (mm110) REVERT: A 600 ILE cc_start: 0.9031 (mt) cc_final: 0.8717 (mm) REVERT: A 650 LEU cc_start: 0.9277 (tp) cc_final: 0.8666 (tp) REVERT: A 667 PHE cc_start: 0.8628 (m-80) cc_final: 0.8423 (m-80) REVERT: B 408 MET cc_start: 0.8600 (mmp) cc_final: 0.7398 (mmp) REVERT: B 421 TYR cc_start: 0.5993 (m-80) cc_final: 0.5430 (m-80) REVERT: B 503 MET cc_start: 0.8935 (tmm) cc_final: 0.8635 (tmm) REVERT: B 573 ILE cc_start: 0.9044 (mp) cc_final: 0.8766 (mp) REVERT: B 574 PHE cc_start: 0.8206 (t80) cc_final: 0.7767 (t80) REVERT: B 645 ILE cc_start: 0.7972 (mm) cc_final: 0.7749 (mm) REVERT: B 670 MET cc_start: 0.8718 (mmt) cc_final: 0.8071 (mmm) REVERT: C 463 MET cc_start: 0.8456 (ttt) cc_final: 0.8171 (ptm) REVERT: C 516 SER cc_start: 0.9507 (p) cc_final: 0.9163 (t) REVERT: C 674 MET cc_start: 0.8174 (mmm) cc_final: 0.7872 (tpp) REVERT: D 534 ILE cc_start: 0.9086 (mt) cc_final: 0.8704 (tt) REVERT: D 587 GLN cc_start: 0.7207 (mm110) cc_final: 0.6698 (mp10) REVERT: D 693 VAL cc_start: 0.8777 (t) cc_final: 0.8142 (p) REVERT: E 25 ILE cc_start: 0.8986 (mt) cc_final: 0.8675 (tp) REVERT: E 127 TYR cc_start: 0.6453 (m-80) cc_final: 0.6215 (m-10) REVERT: E 150 ILE cc_start: 0.9263 (mm) cc_final: 0.9038 (mm) REVERT: E 190 GLU cc_start: 0.8945 (tp30) cc_final: 0.8732 (tp30) REVERT: F 191 MET cc_start: 0.8488 (mtp) cc_final: 0.7889 (tpt) REVERT: G 101 ARG cc_start: 0.8489 (tpt90) cc_final: 0.8058 (tpt90) REVERT: G 191 MET cc_start: 0.8360 (mtp) cc_final: 0.7811 (tpt) REVERT: H 10 LEU cc_start: 0.8767 (mm) cc_final: 0.8461 (pp) REVERT: H 25 ILE cc_start: 0.8910 (mt) cc_final: 0.8638 (tp) REVERT: H 127 TYR cc_start: 0.6450 (m-80) cc_final: 0.6213 (m-10) REVERT: H 150 ILE cc_start: 0.9338 (mm) cc_final: 0.9134 (mm) REVERT: H 190 GLU cc_start: 0.8905 (tp30) cc_final: 0.8698 (tp30) outliers start: 1 outliers final: 0 residues processed: 345 average time/residue: 0.1116 time to fit residues: 61.9875 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 : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 22 optimal weight: 0.0770 chunk 179 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 overall best weight: 1.1540 ------------------------------------------------------------------------------- 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 756 GLN D 508 GLN E 131 HIS ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.127757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.099218 restraints weight = 53068.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.096532 restraints weight = 75476.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.097684 restraints weight = 67208.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.097850 restraints weight = 43411.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.099996 restraints weight = 41687.316| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18698 Z= 0.155 Angle : 0.608 7.342 25226 Z= 0.328 Chirality : 0.043 0.174 2826 Planarity : 0.004 0.060 3102 Dihedral : 5.236 61.250 2522 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.31 % Favored : 95.47 % Rotamer: Outliers : 0.05 % Allowed : 2.20 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.18), residues: 2298 helix: 1.48 (0.15), residues: 1221 sheet: -1.47 (0.40), residues: 149 loop : -1.06 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 675 TYR 0.013 0.001 TYR C 816 PHE 0.023 0.001 PHE F 106 TRP 0.045 0.002 TRP D 460 HIS 0.012 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00339 (18686) covalent geometry : angle 0.60680 (25202) SS BOND : bond 0.00370 ( 12) SS BOND : angle 1.31043 ( 24) hydrogen bonds : bond 0.05217 ( 954) hydrogen bonds : angle 4.65017 ( 2730) *********************** 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 321 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 0.643 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 425 CYS cc_start: 0.9193 (m) cc_final: 0.8832 (m) REVERT: A 428 LEU cc_start: 0.9357 (pp) cc_final: 0.9057 (mm) REVERT: A 587 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7568 (mm110) REVERT: A 600 ILE cc_start: 0.8993 (mt) cc_final: 0.8663 (mm) REVERT: A 650 LEU cc_start: 0.9303 (tp) cc_final: 0.8772 (tp) REVERT: B 408 MET cc_start: 0.8668 (mmp) cc_final: 0.7355 (mmp) REVERT: B 421 TYR cc_start: 0.5916 (m-80) cc_final: 0.5593 (m-80) REVERT: B 503 MET cc_start: 0.8959 (tmm) cc_final: 0.8436 (tmm) REVERT: B 670 MET cc_start: 0.8801 (mmm) cc_final: 0.8552 (mmm) REVERT: C 405 TYR cc_start: 0.8223 (m-80) cc_final: 0.7941 (m-80) REVERT: C 425 CYS cc_start: 0.9557 (m) cc_final: 0.9356 (m) REVERT: C 463 MET cc_start: 0.8447 (ttt) cc_final: 0.8201 (ptm) REVERT: C 516 SER cc_start: 0.9507 (p) cc_final: 0.9192 (t) REVERT: D 534 ILE cc_start: 0.9095 (mt) cc_final: 0.8726 (tt) REVERT: D 573 ILE cc_start: 0.9283 (mp) cc_final: 0.9017 (mm) REVERT: D 587 GLN cc_start: 0.7265 (mm110) cc_final: 0.6910 (mp10) REVERT: D 693 VAL cc_start: 0.8817 (t) cc_final: 0.8197 (p) REVERT: D 713 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8629 (pt0) REVERT: E 10 LEU cc_start: 0.8643 (mm) cc_final: 0.8153 (pp) REVERT: E 25 ILE cc_start: 0.8948 (mt) cc_final: 0.8655 (tp) REVERT: E 127 TYR cc_start: 0.6584 (m-80) cc_final: 0.6248 (m-10) REVERT: F 148 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8635 (t0) REVERT: F 188 ILE cc_start: 0.8890 (tp) cc_final: 0.8620 (tp) REVERT: F 191 MET cc_start: 0.8529 (mtp) cc_final: 0.7915 (tpt) REVERT: G 23 MET cc_start: 0.8514 (mmm) cc_final: 0.8173 (mmt) REVERT: G 101 ARG cc_start: 0.8413 (tpt90) cc_final: 0.7978 (tpt90) REVERT: G 191 MET cc_start: 0.8401 (mtp) cc_final: 0.7867 (tpt) REVERT: H 10 LEU cc_start: 0.8655 (mm) cc_final: 0.8260 (pp) REVERT: H 11 LEU cc_start: 0.8915 (mm) cc_final: 0.8712 (mm) REVERT: H 25 ILE cc_start: 0.8808 (mt) cc_final: 0.8564 (tp) REVERT: H 101 ARG cc_start: 0.9113 (tpt90) cc_final: 0.8826 (tpt170) REVERT: H 127 TYR cc_start: 0.6459 (m-80) cc_final: 0.6211 (m-10) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.1194 time to fit residues: 61.8384 Evaluate side-chains 248 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 179 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS B 586 GLN B 619 ASN B 756 GLN E 131 HIS ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.128392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.098978 restraints weight = 53128.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096948 restraints weight = 70283.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.098100 restraints weight = 61358.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.098275 restraints weight = 41642.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.100435 restraints weight = 39794.335| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18698 Z= 0.135 Angle : 0.594 11.014 25226 Z= 0.316 Chirality : 0.042 0.174 2826 Planarity : 0.004 0.059 3102 Dihedral : 5.047 55.715 2522 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.35 % Favored : 95.43 % Rotamer: Outliers : 0.10 % Allowed : 1.23 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.18), residues: 2298 helix: 1.51 (0.15), residues: 1227 sheet: -1.47 (0.40), residues: 149 loop : -1.08 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 675 TYR 0.012 0.001 TYR C 424 PHE 0.019 0.001 PHE E 20 TRP 0.038 0.002 TRP C 767 HIS 0.006 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00292 (18686) covalent geometry : angle 0.59291 (25202) SS BOND : bond 0.00248 ( 12) SS BOND : angle 1.10674 ( 24) hydrogen bonds : bond 0.04921 ( 954) hydrogen bonds : angle 4.46518 ( 2730) *********************** 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 325 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 323 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 CYS cc_start: 0.9251 (m) cc_final: 0.8884 (m) REVERT: A 428 LEU cc_start: 0.9383 (pp) cc_final: 0.9084 (mm) REVERT: A 533 TYR cc_start: 0.8100 (t80) cc_final: 0.7769 (t80) REVERT: A 574 PHE cc_start: 0.8133 (t80) cc_final: 0.7043 (m-80) REVERT: A 587 GLN cc_start: 0.8499 (mm-40) cc_final: 0.7490 (mm110) REVERT: A 600 ILE cc_start: 0.8950 (mt) cc_final: 0.8646 (mm) REVERT: A 650 LEU cc_start: 0.9295 (tp) cc_final: 0.8753 (tp) REVERT: A 667 PHE cc_start: 0.8798 (m-80) cc_final: 0.8368 (m-80) REVERT: B 408 MET cc_start: 0.8724 (mmp) cc_final: 0.7499 (mmp) REVERT: B 421 TYR cc_start: 0.6102 (m-80) cc_final: 0.5654 (m-80) REVERT: B 503 MET cc_start: 0.8973 (tmm) cc_final: 0.8407 (tmm) REVERT: B 534 ILE cc_start: 0.8994 (mt) cc_final: 0.8664 (tt) REVERT: B 645 ILE cc_start: 0.8006 (mm) cc_final: 0.7734 (mm) REVERT: B 667 PHE cc_start: 0.9169 (m-10) cc_final: 0.8967 (m-80) REVERT: B 807 MET cc_start: 0.8846 (ttm) cc_final: 0.8531 (tpp) REVERT: C 405 TYR cc_start: 0.8256 (m-80) cc_final: 0.7973 (m-80) REVERT: C 463 MET cc_start: 0.8648 (ttt) cc_final: 0.8256 (ptm) REVERT: C 674 MET cc_start: 0.7886 (tpp) cc_final: 0.7654 (mmp) REVERT: D 414 MET cc_start: 0.6744 (ppp) cc_final: 0.5661 (ppp) REVERT: D 527 MET cc_start: 0.8653 (ttp) cc_final: 0.7920 (tpp) REVERT: D 534 ILE cc_start: 0.9062 (mt) cc_final: 0.8702 (tt) REVERT: D 573 ILE cc_start: 0.9297 (mp) cc_final: 0.9038 (mm) REVERT: D 585 MET cc_start: 0.7468 (mmm) cc_final: 0.6850 (mmt) REVERT: D 693 VAL cc_start: 0.8819 (t) cc_final: 0.8202 (p) REVERT: D 713 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8629 (pt0) REVERT: D 721 MET cc_start: 0.7630 (pmm) cc_final: 0.7429 (pmm) REVERT: E 127 TYR cc_start: 0.6599 (m-80) cc_final: 0.6263 (m-10) REVERT: F 191 MET cc_start: 0.8562 (mtp) cc_final: 0.7973 (tpt) REVERT: F 199 MET cc_start: 0.8718 (mmm) cc_final: 0.8504 (mmm) REVERT: G 23 MET cc_start: 0.8657 (mmm) cc_final: 0.8301 (mmt) REVERT: G 101 ARG cc_start: 0.8427 (tpt90) cc_final: 0.8001 (tpt90) REVERT: G 191 MET cc_start: 0.8378 (mtp) cc_final: 0.7864 (tpt) REVERT: H 10 LEU cc_start: 0.8630 (mm) cc_final: 0.8193 (pp) REVERT: H 25 ILE cc_start: 0.8879 (mt) cc_final: 0.8624 (tp) REVERT: H 101 ARG cc_start: 0.9114 (tpt90) cc_final: 0.8797 (tpt170) REVERT: H 127 TYR cc_start: 0.6506 (m-80) cc_final: 0.6221 (m-10) outliers start: 2 outliers final: 0 residues processed: 324 average time/residue: 0.1187 time to fit residues: 62.1863 Evaluate side-chains 252 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 192 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** A 714 GLN B 435 HIS B 619 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.124275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.091991 restraints weight = 54237.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.088229 restraints weight = 70636.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.086511 restraints weight = 57457.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.086070 restraints weight = 54916.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.086256 restraints weight = 52896.535| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 18698 Z= 0.269 Angle : 0.727 9.154 25226 Z= 0.393 Chirality : 0.046 0.194 2826 Planarity : 0.005 0.060 3102 Dihedral : 5.565 57.414 2522 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.96 % Favored : 94.78 % Rotamer: Outliers : 0.05 % Allowed : 1.84 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.18), residues: 2298 helix: 1.01 (0.15), residues: 1241 sheet: -1.53 (0.41), residues: 149 loop : -1.26 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 64 TYR 0.023 0.002 TYR A 616 PHE 0.036 0.002 PHE B 517 TRP 0.027 0.002 TRP D 460 HIS 0.007 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00581 (18686) covalent geometry : angle 0.72609 (25202) SS BOND : bond 0.00251 ( 12) SS BOND : angle 1.21774 ( 24) hydrogen bonds : bond 0.06027 ( 954) hydrogen bonds : angle 5.11311 ( 2730) *********************** 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 310 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 0.710 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: A 405 TYR cc_start: 0.8558 (m-80) cc_final: 0.7982 (m-80) REVERT: A 425 CYS cc_start: 0.9324 (m) cc_final: 0.8950 (m) REVERT: A 428 LEU cc_start: 0.9446 (pp) cc_final: 0.9129 (mm) REVERT: A 463 MET cc_start: 0.8519 (ttp) cc_final: 0.8276 (ptt) REVERT: A 489 ILE cc_start: 0.9114 (pt) cc_final: 0.8899 (pt) REVERT: A 533 TYR cc_start: 0.8273 (t80) cc_final: 0.7991 (t80) REVERT: A 585 MET cc_start: 0.7958 (mtp) cc_final: 0.7579 (mtt) REVERT: A 587 GLN cc_start: 0.8447 (mm-40) cc_final: 0.7572 (mm110) REVERT: A 600 ILE cc_start: 0.9144 (mt) cc_final: 0.8802 (mm) REVERT: A 667 PHE cc_start: 0.8907 (m-80) cc_final: 0.8378 (m-80) REVERT: B 503 MET cc_start: 0.8989 (tmm) cc_final: 0.8285 (tmm) REVERT: B 645 ILE cc_start: 0.8096 (mm) cc_final: 0.7793 (mm) REVERT: B 670 MET cc_start: 0.8652 (mmt) cc_final: 0.8151 (mmm) REVERT: C 405 TYR cc_start: 0.8584 (m-80) cc_final: 0.8215 (m-80) REVERT: C 463 MET cc_start: 0.8811 (ttt) cc_final: 0.8414 (mtm) REVERT: C 503 MET cc_start: 0.8357 (ptp) cc_final: 0.8014 (ptp) REVERT: C 586 GLN cc_start: 0.8619 (mt0) cc_final: 0.8347 (mt0) REVERT: D 414 MET cc_start: 0.7029 (ppp) cc_final: 0.5992 (ppp) REVERT: D 527 MET cc_start: 0.8741 (ttp) cc_final: 0.8374 (tpp) REVERT: D 534 ILE cc_start: 0.9108 (mt) cc_final: 0.8715 (tt) REVERT: D 573 ILE cc_start: 0.9327 (mp) cc_final: 0.9102 (mm) REVERT: D 585 MET cc_start: 0.8006 (mmm) cc_final: 0.7125 (tpp) REVERT: D 587 GLN cc_start: 0.7535 (mm110) cc_final: 0.6816 (mp10) REVERT: E 127 TYR cc_start: 0.6697 (m-80) cc_final: 0.6306 (m-10) REVERT: F 188 ILE cc_start: 0.8972 (tp) cc_final: 0.8722 (tp) REVERT: F 191 MET cc_start: 0.8642 (mtp) cc_final: 0.8073 (tpt) REVERT: G 23 MET cc_start: 0.8697 (mmm) cc_final: 0.8365 (mmt) REVERT: G 191 MET cc_start: 0.8388 (mtp) cc_final: 0.7937 (tpt) REVERT: H 10 LEU cc_start: 0.8779 (mm) cc_final: 0.8261 (pp) REVERT: H 25 ILE cc_start: 0.8934 (mt) cc_final: 0.8718 (tp) REVERT: H 127 TYR cc_start: 0.6541 (m-80) cc_final: 0.6126 (m-10) outliers start: 1 outliers final: 0 residues processed: 309 average time/residue: 0.1212 time to fit residues: 60.1560 Evaluate side-chains 237 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 67 optimal weight: 7.9990 chunk 226 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 169 optimal weight: 0.0060 chunk 73 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN A 791 ASN B 435 HIS B 586 GLN B 756 GLN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.128912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.100358 restraints weight = 53422.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.098691 restraints weight = 79709.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.100599 restraints weight = 60611.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.101258 restraints weight = 40405.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101903 restraints weight = 38675.156| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18698 Z= 0.124 Angle : 0.617 8.185 25226 Z= 0.322 Chirality : 0.042 0.173 2826 Planarity : 0.004 0.058 3102 Dihedral : 4.989 53.879 2522 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.66 % Favored : 96.08 % Rotamer: Outliers : 0.05 % Allowed : 0.72 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.18), residues: 2298 helix: 1.49 (0.15), residues: 1218 sheet: -1.50 (0.40), residues: 150 loop : -1.18 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 36 TYR 0.011 0.001 TYR C 424 PHE 0.024 0.001 PHE H 20 TRP 0.038 0.002 TRP D 460 HIS 0.008 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00258 (18686) covalent geometry : angle 0.61680 (25202) SS BOND : bond 0.00229 ( 12) SS BOND : angle 1.00989 ( 24) hydrogen bonds : bond 0.04769 ( 954) hydrogen bonds : angle 4.46846 ( 2730) *********************** 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 340 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 339 time to evaluate : 0.549 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: A 405 TYR cc_start: 0.8182 (m-80) cc_final: 0.7629 (m-80) REVERT: A 425 CYS cc_start: 0.9226 (m) cc_final: 0.8842 (m) REVERT: A 428 LEU cc_start: 0.9335 (pp) cc_final: 0.9033 (mm) REVERT: A 587 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7342 (mm110) REVERT: A 600 ILE cc_start: 0.8944 (mt) cc_final: 0.8614 (mm) REVERT: A 667 PHE cc_start: 0.8872 (m-80) cc_final: 0.8484 (m-80) REVERT: B 424 TYR cc_start: 0.7638 (t80) cc_final: 0.7438 (t80) REVERT: B 503 MET cc_start: 0.8967 (tmm) cc_final: 0.8334 (tmm) REVERT: B 534 ILE cc_start: 0.8927 (mt) cc_final: 0.8669 (tt) REVERT: B 645 ILE cc_start: 0.7956 (mm) cc_final: 0.7679 (mm) REVERT: C 538 VAL cc_start: 0.9256 (t) cc_final: 0.9048 (p) REVERT: D 527 MET cc_start: 0.8499 (ttp) cc_final: 0.7980 (tpp) REVERT: D 534 ILE cc_start: 0.8987 (mt) cc_final: 0.8632 (tt) REVERT: D 585 MET cc_start: 0.7652 (mmm) cc_final: 0.6894 (mmt) REVERT: D 587 GLN cc_start: 0.7195 (mm110) cc_final: 0.6768 (mp10) REVERT: D 693 VAL cc_start: 0.8833 (t) cc_final: 0.8215 (p) REVERT: D 713 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8565 (pt0) REVERT: E 101 ARG cc_start: 0.9229 (tpt90) cc_final: 0.8886 (tpt170) REVERT: E 127 TYR cc_start: 0.6405 (m-80) cc_final: 0.6189 (m-10) REVERT: F 191 MET cc_start: 0.8551 (mtp) cc_final: 0.7930 (tpt) REVERT: G 23 MET cc_start: 0.8657 (mmm) cc_final: 0.8312 (mmt) REVERT: G 191 MET cc_start: 0.8312 (mtp) cc_final: 0.7765 (tpt) REVERT: G 199 MET cc_start: 0.8739 (mmm) cc_final: 0.7976 (mmp) REVERT: H 10 LEU cc_start: 0.8523 (mm) cc_final: 0.7971 (pp) REVERT: H 101 ARG cc_start: 0.9050 (tpt90) cc_final: 0.8686 (tpt170) REVERT: H 127 TYR cc_start: 0.6527 (m-80) cc_final: 0.6165 (m-10) REVERT: H 190 GLU cc_start: 0.8670 (tp30) cc_final: 0.8399 (tp30) outliers start: 1 outliers final: 0 residues processed: 339 average time/residue: 0.1148 time to fit residues: 62.5630 Evaluate side-chains 253 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 149 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN A 791 ASN B 435 HIS B 586 GLN B 619 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.126903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.085761 restraints weight = 52881.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.086077 restraints weight = 42809.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.086494 restraints weight = 33450.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.086525 restraints weight = 31904.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.086613 restraints weight = 30213.701| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5161 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= 0.172 Angle : 0.655 7.715 25226 Z= 0.347 Chirality : 0.044 0.248 2826 Planarity : 0.004 0.060 3102 Dihedral : 5.114 53.436 2522 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.70 % Favored : 95.04 % Rotamer: Outliers : 0.10 % Allowed : 0.36 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.18), residues: 2298 helix: 1.39 (0.15), residues: 1218 sheet: -1.40 (0.42), residues: 147 loop : -1.19 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 675 TYR 0.022 0.002 TYR C 533 PHE 0.024 0.002 PHE E 20 TRP 0.040 0.002 TRP A 767 HIS 0.005 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00382 (18686) covalent geometry : angle 0.65418 (25202) SS BOND : bond 0.00215 ( 12) SS BOND : angle 1.04427 ( 24) hydrogen bonds : bond 0.05148 ( 954) hydrogen bonds : angle 4.65551 ( 2730) ********************** 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 312 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 310 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 TYR cc_start: 0.8620 (m-80) cc_final: 0.7868 (m-80) REVERT: A 425 CYS cc_start: 0.9394 (m) cc_final: 0.8971 (m) REVERT: A 428 LEU cc_start: 0.9454 (pp) cc_final: 0.9127 (mm) REVERT: A 463 MET cc_start: 0.8299 (ptt) cc_final: 0.7977 (pmm) REVERT: A 533 TYR cc_start: 0.8235 (t80) cc_final: 0.7834 (t80) REVERT: A 574 PHE cc_start: 0.8110 (t80) cc_final: 0.7035 (m-80) REVERT: A 587 GLN cc_start: 0.8340 (mm-40) cc_final: 0.7417 (mm110) REVERT: A 600 ILE cc_start: 0.8952 (mt) cc_final: 0.8619 (mm) REVERT: A 667 PHE cc_start: 0.8960 (m-80) cc_final: 0.8418 (m-80) REVERT: A 763 LYS cc_start: 0.9218 (ttpt) cc_final: 0.8988 (tptt) REVERT: B 408 MET cc_start: 0.8957 (mmp) cc_final: 0.8328 (mmm) REVERT: B 503 MET cc_start: 0.9027 (tmm) cc_final: 0.8224 (tmm) REVERT: B 534 ILE cc_start: 0.8968 (mt) cc_final: 0.8633 (tt) REVERT: B 645 ILE cc_start: 0.7994 (mm) cc_final: 0.7724 (mm) REVERT: B 667 PHE cc_start: 0.9234 (m-80) cc_final: 0.8892 (m-80) REVERT: B 670 MET cc_start: 0.9053 (mmp) cc_final: 0.8718 (mmt) REVERT: B 674 MET cc_start: 0.9258 (mtm) cc_final: 0.8475 (mtt) REVERT: C 516 SER cc_start: 0.9582 (p) cc_final: 0.9369 (t) REVERT: C 816 TYR cc_start: 0.7563 (t80) cc_final: 0.7203 (t80) REVERT: D 527 MET cc_start: 0.8781 (ttp) cc_final: 0.8312 (tpp) REVERT: D 534 ILE cc_start: 0.9105 (mt) cc_final: 0.8725 (tt) REVERT: D 585 MET cc_start: 0.8142 (mmm) cc_final: 0.7120 (mmt) REVERT: D 587 GLN cc_start: 0.7386 (mm110) cc_final: 0.6964 (mp10) REVERT: D 693 VAL cc_start: 0.8863 (t) cc_final: 0.8329 (p) REVERT: D 708 MET cc_start: 0.9058 (mtt) cc_final: 0.8840 (mtt) REVERT: D 713 GLU cc_start: 0.9368 (tm-30) cc_final: 0.8521 (pt0) REVERT: E 81 HIS cc_start: 0.8634 (m-70) cc_final: 0.8405 (m-70) REVERT: E 127 TYR cc_start: 0.6325 (m-80) cc_final: 0.6049 (m-10) REVERT: F 191 MET cc_start: 0.8648 (mtp) cc_final: 0.8171 (tpt) REVERT: G 23 MET cc_start: 0.8754 (mmm) cc_final: 0.8349 (mmt) REVERT: G 191 MET cc_start: 0.8534 (mtp) cc_final: 0.7977 (tpt) REVERT: G 199 MET cc_start: 0.9028 (mmm) cc_final: 0.8240 (mmp) REVERT: H 101 ARG cc_start: 0.9102 (tpt90) cc_final: 0.8695 (tpt170) REVERT: H 127 TYR cc_start: 0.6334 (m-80) cc_final: 0.5929 (m-10) outliers start: 2 outliers final: 1 residues processed: 310 average time/residue: 0.1122 time to fit residues: 56.3056 Evaluate side-chains 239 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 172 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 228 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 176 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 69 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN B 435 HIS B 586 GLN B 756 GLN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3913 r_free = 0.3913 target = 0.128219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.098433 restraints weight = 53009.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.096371 restraints weight = 65682.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.097622 restraints weight = 60708.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.097741 restraints weight = 40317.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.099866 restraints weight = 38764.786| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5361 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= 0.131 Angle : 0.624 9.109 25226 Z= 0.325 Chirality : 0.043 0.237 2826 Planarity : 0.004 0.057 3102 Dihedral : 4.900 51.623 2522 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.05 % Favored : 95.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.18), residues: 2298 helix: 1.49 (0.15), residues: 1218 sheet: -1.34 (0.42), residues: 148 loop : -1.15 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 675 TYR 0.016 0.001 TYR C 533 PHE 0.023 0.001 PHE E 20 TRP 0.029 0.001 TRP D 460 HIS 0.005 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00286 (18686) covalent geometry : angle 0.62341 (25202) SS BOND : bond 0.00216 ( 12) SS BOND : angle 0.93821 ( 24) hydrogen bonds : bond 0.04777 ( 954) hydrogen bonds : angle 4.45127 ( 2730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2878.17 seconds wall clock time: 50 minutes 46.49 seconds (3046.49 seconds total)