Starting phenix.real_space_refine on Thu Sep 18 16:40:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mrm_48559/09_2025/9mrm_48559.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mrm_48559/09_2025/9mrm_48559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mrm_48559/09_2025/9mrm_48559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mrm_48559/09_2025/9mrm_48559.map" model { file = "/net/cci-nas-00/data/ceres_data/9mrm_48559/09_2025/9mrm_48559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mrm_48559/09_2025/9mrm_48559.cif" } resolution = 4.52 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 2 residue(s): 0.01s 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: 3.96, per 1000 atoms: 0.22 Number of scatterers: 18294 At special positions: 0 Unit cell: (120.28, 115.43, 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=2.03 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: 1.59 Conformation dependent library (CDL) restraints added in 782.2 milliseconds Enol-peptide restraints added in 476.8 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: 100 helices and 22 sheets defined 59.0% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 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: 3.834A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.856A 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 521 Proline residue: A 520 - end of helix Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.561A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.919A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 629 removed outlier: 3.704A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.823A 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: 3.684A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) removed outlier: 3.871A 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 768 removed outlier: 4.542A pdb=" N LYS A 765 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 3.660A 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: 4.266A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 809 " --> pdb=" O LEU A 805 " (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: 3.908A 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: 3.946A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.740A pdb=" N PHE B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 624 removed outlier: 3.681A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.581A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 removed outlier: 3.734A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 3.504A 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: 3.546A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.637A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.781A pdb=" N ALA B 749 " --> pdb=" O PRO B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 removed outlier: 3.939A pdb=" N LYS B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 Processing helix chain 'B' and resid 773 through 778 removed outlier: 3.535A pdb=" N LYS B 776 " --> pdb=" O CYS B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 817 removed outlier: 3.807A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.577A 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 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: 4.204A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE C 534 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 536 " --> pdb=" O ALA C 532 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 586 removed outlier: 3.988A pdb=" N SER C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 582 " --> pdb=" O TRP C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 629 removed outlier: 3.589A pdb=" N ILE C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.872A 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: 3.808A 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: 3.678A pdb=" N LYS C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 786 removed outlier: 4.388A pdb=" N SER C 785 " --> pdb=" O GLU C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 818 removed outlier: 4.365A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 797 " --> pdb=" O ALA C 793 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.679A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 428 removed outlier: 3.926A 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 461 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: 4.192A pdb=" N ILE D 525 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE D 531 " --> pdb=" O MET D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.576A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.812A 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: 3.767A 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: 3.578A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.840A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 768 removed outlier: 4.300A 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: 4.352A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 28 removed outlier: 3.600A pdb=" N LEU E 11 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ALA E 16 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE E 17 " --> pdb=" O THR E 13 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA E 18 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.902A 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: 3.844A pdb=" N ARG E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 124 removed outlier: 3.938A pdb=" N ILE E 108 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE E 121 " --> pdb=" O GLY E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 160 removed outlier: 4.269A pdb=" N LEU E 135 " --> pdb=" O HIS E 131 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER E 136 " --> pdb=" O ASN E 132 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 209 removed outlier: 4.038A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS E 204 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU E 207 " --> pdb=" O ARG E 203 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR E 208 " --> pdb=" O HIS E 204 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 28 Processing helix chain 'F' and resid 94 through 104 removed outlier: 4.459A pdb=" N ALA F 99 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL F 100 " --> pdb=" O PHE F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 4.250A 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: 3.917A pdb=" N ALA F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE F 140 " --> pdb=" O SER F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 206 removed outlier: 3.979A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU F 195 " --> pdb=" O MET F 191 " (cutoff:3.500A) removed outlier: 3.739A 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: 4.694A pdb=" N ALA G 99 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL G 100 " --> pdb=" O PHE G 96 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG G 101 " --> pdb=" O LEU G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 123 removed outlier: 3.527A pdb=" N ILE G 108 " --> pdb=" O SER G 104 " (cutoff:3.500A) 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 161 removed outlier: 3.812A pdb=" N LEU G 135 " --> pdb=" O HIS G 131 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE G 149 " --> pdb=" O GLY G 145 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 160 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY G 161 " --> pdb=" O SER G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 206 removed outlier: 3.946A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL G 194 " --> pdb=" O GLU G 190 " (cutoff:3.500A) removed outlier: 3.619A 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 6 through 28 removed outlier: 4.198A pdb=" N LEU H 10 " --> pdb=" O GLY H 6 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 11 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY H 15 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA H 16 " --> pdb=" O THR H 12 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N PHE H 17 " --> pdb=" O THR H 13 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA H 18 " --> pdb=" O VAL H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 removed outlier: 3.943A 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: 3.831A pdb=" N ARG H 101 " --> pdb=" O LEU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.987A pdb=" N ILE H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE H 121 " --> pdb=" O GLY H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 160 removed outlier: 4.219A pdb=" N LEU H 135 " --> pdb=" O HIS H 131 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA H 137 " --> pdb=" O ILE H 133 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY H 138 " --> pdb=" O ILE H 134 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 206 removed outlier: 4.104A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS H 204 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 3.738A 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: 3.852A 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: 4.230A 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: 8.752A pdb=" N VAL A 683 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 649 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU A 650 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLU A 705 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 removed outlier: 3.751A 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 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.566A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.639A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.652A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 444 removed outlier: 5.971A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL C 396 " --> pdb=" O ILE C 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.285A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.363A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 439 through 444 removed outlier: 7.050A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 476 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 439 through 444 removed outlier: 7.050A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 476 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.334A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE D 504 " --> pdb=" O MET D 721 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 Processing sheet with id=AC2, first strand: chain 'F' and resid 76 through 78 removed outlier: 3.605A pdb=" N LEU F 33 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 76 through 78 removed outlier: 3.745A pdb=" N LEU G 33 " --> pdb=" O SER G 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 76 through 78 978 hydrogen bonds defined for protein. 2796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5607 1.34 - 1.46: 4805 1.46 - 1.58: 8066 1.58 - 1.70: 0 1.70 - 1.82: 208 Bond restraints: 18686 Sorted by residual: bond pdb=" CG1 ILE E 188 " pdb=" CD1 ILE E 188 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.29e+00 bond pdb=" CG1 ILE F 188 " pdb=" CD1 ILE F 188 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.07e+00 bond pdb=" C GLN C 508 " pdb=" N LYS C 509 " ideal model delta sigma weight residual 1.333 1.350 -0.017 1.30e-02 5.92e+03 1.71e+00 bond pdb=" CA GLN B 586 " pdb=" C GLN B 586 " ideal model delta sigma weight residual 1.532 1.520 0.012 9.60e-03 1.09e+04 1.59e+00 bond pdb=" CA ASN B 726 " pdb=" CB ASN B 726 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.22e+00 ... (remaining 18681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 24919 2.39 - 4.79: 260 4.79 - 7.18: 19 7.18 - 9.57: 3 9.57 - 11.96: 1 Bond angle restraints: 25202 Sorted by residual: angle pdb=" C MET B 629 " pdb=" N VAL B 630 " pdb=" CA VAL B 630 " ideal model delta sigma weight residual 121.97 130.35 -8.38 1.80e+00 3.09e-01 2.17e+01 angle pdb=" C GLY B 725 " pdb=" N ASN B 726 " pdb=" CA ASN B 726 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.72e+01 angle pdb=" N ILE D 476 " pdb=" CA ILE D 476 " pdb=" C ILE D 476 " ideal model delta sigma weight residual 111.77 108.16 3.61 1.04e+00 9.25e-01 1.20e+01 angle pdb=" C ARG A 715 " pdb=" N LYS A 716 " pdb=" CA LYS A 716 " ideal model delta sigma weight residual 120.58 125.11 -4.53 1.32e+00 5.74e-01 1.18e+01 angle pdb=" CA LEU H 114 " pdb=" CB LEU H 114 " pdb=" CG LEU H 114 " ideal model delta sigma weight residual 116.30 128.26 -11.96 3.50e+00 8.16e-02 1.17e+01 ... (remaining 25197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 10251 17.62 - 35.24: 606 35.24 - 52.87: 84 52.87 - 70.49: 21 70.49 - 88.11: 14 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 -63.32 63.32 1 1.00e+01 1.00e-02 5.29e+01 dihedral pdb=" CA VAL E 14 " pdb=" C VAL E 14 " pdb=" N GLY E 15 " pdb=" CA GLY E 15 " ideal model delta harmonic sigma weight residual 180.00 -156.61 -23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 131.39 -38.39 1 1.00e+01 1.00e-02 2.08e+01 ... (remaining 10973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1968 0.042 - 0.085: 678 0.085 - 0.127: 157 0.127 - 0.170: 20 0.170 - 0.212: 3 Chirality restraints: 2826 Sorted by residual: chirality pdb=" CA THR B 744 " pdb=" N THR B 744 " pdb=" C THR B 744 " pdb=" CB THR B 744 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.12e+00 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 2.32 0.21 2.00e-01 2.50e+01 1.06e+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 2.33 0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 2823 not shown) Planarity restraints: 3102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 628 " -0.792 9.50e-02 1.11e+02 3.57e-01 9.06e+01 pdb=" NE ARG A 628 " 0.071 2.00e-02 2.50e+03 pdb=" CZ ARG A 628 " -0.055 2.00e-02 2.50e+03 pdb=" NH1 ARG A 628 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG A 628 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 97 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C LEU F 97 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU F 97 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG F 98 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 519 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO C 520 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.030 5.00e-02 4.00e+02 ... (remaining 3099 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 308 2.67 - 3.23: 19334 3.23 - 3.79: 27468 3.79 - 4.34: 35341 4.34 - 4.90: 57916 Nonbonded interactions: 140367 Sorted by model distance: nonbonded pdb=" OE2 GLU B 657 " pdb=" NH1 ARG B 660 " model vdw 2.118 3.120 nonbonded pdb=" OE1 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.164 3.040 nonbonded pdb=" OG SER D 547 " pdb=" OE2 GLU D 566 " model vdw 2.223 3.040 nonbonded pdb=" O VAL B 397 " pdb=" OG1 THR B 443 " model vdw 2.231 3.040 nonbonded pdb=" N GLU G 94 " pdb=" OE1 GLU G 94 " model vdw 2.243 3.120 ... (remaining 140362 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.230 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.110 Find NCS groups from input model: 0.310 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 0.081 18698 Z= 0.150 Angle : 0.650 11.965 25226 Z= 0.372 Chirality : 0.044 0.212 2826 Planarity : 0.009 0.357 3102 Dihedral : 12.052 88.110 6664 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.18 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -0.82 (0.16), residues: 2298 helix: -0.04 (0.14), residues: 1170 sheet: -0.99 (0.42), residues: 142 loop : -0.97 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.064 0.003 ARG A 628 TYR 0.019 0.003 TYR C 533 PHE 0.023 0.002 PHE C 531 TRP 0.034 0.002 TRP D 606 HIS 0.004 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00304 (18686) covalent geometry : angle 0.64951 (25202) SS BOND : bond 0.00319 ( 12) SS BOND : angle 0.66658 ( 24) hydrogen bonds : bond 0.15874 ( 975) hydrogen bonds : angle 6.47774 ( 2796) *********************** 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 626 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 626 time to evaluate : 0.751 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: symmetry clash REVERT: A 424 TYR cc_start: 0.8668 (t80) cc_final: 0.8040 (t80) REVERT: A 463 MET cc_start: 0.8471 (mtm) cc_final: 0.8002 (mmt) REVERT: A 534 ILE cc_start: 0.9624 (mt) cc_final: 0.9407 (mm) REVERT: A 537 SER cc_start: 0.9601 (m) cc_final: 0.9311 (t) REVERT: A 609 THR cc_start: 0.9102 (t) cc_final: 0.8894 (t) REVERT: A 625 THR cc_start: 0.9474 (m) cc_final: 0.9162 (p) REVERT: A 642 GLN cc_start: 0.8764 (tp-100) cc_final: 0.7819 (tm-30) REVERT: A 645 ILE cc_start: 0.7079 (mm) cc_final: 0.6858 (mm) REVERT: A 657 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8567 (mp0) REVERT: A 702 TYR cc_start: 0.8020 (t80) cc_final: 0.7625 (t80) REVERT: B 486 GLU cc_start: 0.8500 (tt0) cc_final: 0.8077 (tp30) REVERT: B 527 MET cc_start: 0.8878 (mtm) cc_final: 0.7987 (mtt) REVERT: B 609 THR cc_start: 0.9226 (t) cc_final: 0.8942 (t) REVERT: B 674 MET cc_start: 0.3470 (mtp) cc_final: 0.2054 (tmm) REVERT: B 769 ASP cc_start: 0.8981 (m-30) cc_final: 0.8393 (p0) REVERT: C 474 ILE cc_start: 0.8670 (tt) cc_final: 0.8398 (tp) REVERT: C 508 GLN cc_start: 0.7299 (pp30) cc_final: 0.6497 (mm110) REVERT: C 537 SER cc_start: 0.9338 (m) cc_final: 0.8736 (t) REVERT: C 627 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8407 (mt-10) REVERT: C 642 GLN cc_start: 0.9270 (tp-100) cc_final: 0.8858 (tm-30) REVERT: C 668 ASP cc_start: 0.9282 (t0) cc_final: 0.8943 (m-30) REVERT: D 503 MET cc_start: 0.7320 (ttp) cc_final: 0.6624 (ttm) REVERT: D 609 THR cc_start: 0.9236 (t) cc_final: 0.8837 (t) REVERT: D 612 ILE cc_start: 0.9574 (mm) cc_final: 0.9319 (tp) REVERT: D 614 SER cc_start: 0.9526 (m) cc_final: 0.9233 (t) REVERT: D 651 ASP cc_start: 0.7071 (t0) cc_final: 0.6421 (p0) REVERT: D 767 TRP cc_start: 0.8676 (m-90) cc_final: 0.8208 (m-90) REVERT: E 8 GLN cc_start: 0.7573 (mp10) cc_final: 0.7333 (mp10) REVERT: E 35 SER cc_start: 0.7267 (m) cc_final: 0.7048 (t) REVERT: F 60 SER cc_start: 0.9012 (m) cc_final: 0.8718 (t) REVERT: F 149 ILE cc_start: 0.8153 (mt) cc_final: 0.7863 (mt) REVERT: F 173 TYR cc_start: 0.8115 (p90) cc_final: 0.7563 (p90) REVERT: F 205 LYS cc_start: 0.8811 (tttt) cc_final: 0.8311 (tptt) REVERT: G 23 MET cc_start: 0.8528 (tpt) cc_final: 0.8253 (tpt) REVERT: G 97 LEU cc_start: 0.7491 (tt) cc_final: 0.6799 (mt) REVERT: G 116 MET cc_start: 0.3319 (mmm) cc_final: 0.3093 (mmm) REVERT: G 124 SER cc_start: 0.7051 (t) cc_final: 0.6588 (m) REVERT: H 23 MET cc_start: 0.8688 (tpt) cc_final: 0.8382 (ttt) REVERT: H 63 TRP cc_start: 0.6850 (m100) cc_final: 0.6616 (m100) outliers start: 0 outliers final: 0 residues processed: 626 average time/residue: 0.1307 time to fit residues: 123.7175 Evaluate side-chains 334 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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: 5.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.137455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094376 restraints weight = 55849.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.093004 restraints weight = 46339.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.092557 restraints weight = 43178.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.092789 restraints weight = 39124.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.092950 restraints weight = 36388.967| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 18698 Z= 0.383 Angle : 0.886 10.815 25226 Z= 0.484 Chirality : 0.052 0.201 2826 Planarity : 0.006 0.073 3102 Dihedral : 6.265 86.698 2522 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.70 % Favored : 95.00 % Rotamer: Outliers : 0.31 % Allowed : 5.17 % Favored : 94.53 % 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: -0.64 (0.17), residues: 2298 helix: 0.28 (0.14), residues: 1179 sheet: -1.05 (0.37), residues: 186 loop : -1.10 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 420 TYR 0.034 0.003 TYR C 523 PHE 0.049 0.003 PHE D 546 TRP 0.027 0.003 TRP B 671 HIS 0.013 0.002 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00806 (18686) covalent geometry : angle 0.88592 (25202) SS BOND : bond 0.00332 ( 12) SS BOND : angle 0.91085 ( 24) hydrogen bonds : bond 0.07378 ( 975) hydrogen bonds : angle 6.17665 ( 2796) *********************** 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 354 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 348 time to evaluate : 0.702 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: A 419 GLU cc_start: 0.9048 (mp0) cc_final: 0.8698 (pp20) REVERT: A 496 MET cc_start: 0.8698 (tpt) cc_final: 0.8468 (tpp) REVERT: A 527 MET cc_start: 0.8409 (ttp) cc_final: 0.8093 (ttt) REVERT: A 537 SER cc_start: 0.9770 (m) cc_final: 0.9306 (t) REVERT: A 625 THR cc_start: 0.9452 (m) cc_final: 0.9163 (p) REVERT: A 642 GLN cc_start: 0.8746 (tp-100) cc_final: 0.7949 (tm-30) REVERT: A 710 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8124 (pp20) REVERT: A 721 MET cc_start: 0.5842 (pmm) cc_final: 0.5288 (pmm) REVERT: B 651 ASP cc_start: 0.6916 (t0) cc_final: 0.6605 (p0) REVERT: B 674 MET cc_start: 0.4658 (mtp) cc_final: 0.3148 (tmm) REVERT: B 721 MET cc_start: 0.8666 (ptp) cc_final: 0.8303 (ptm) REVERT: C 398 THR cc_start: 0.8493 (p) cc_final: 0.8252 (p) REVERT: C 485 ARG cc_start: 0.8589 (ptp-170) cc_final: 0.7973 (mtm110) REVERT: C 508 GLN cc_start: 0.7221 (pp30) cc_final: 0.6651 (mm-40) REVERT: C 537 SER cc_start: 0.9609 (m) cc_final: 0.9139 (t) REVERT: C 625 THR cc_start: 0.9378 (m) cc_final: 0.9123 (p) REVERT: C 627 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8555 (mt-10) REVERT: C 642 GLN cc_start: 0.9285 (tp-100) cc_final: 0.8713 (tm-30) REVERT: C 668 ASP cc_start: 0.9433 (t0) cc_final: 0.9093 (m-30) REVERT: C 670 MET cc_start: 0.9506 (mmp) cc_final: 0.9040 (mmm) REVERT: C 702 TYR cc_start: 0.8310 (t80) cc_final: 0.7921 (t80) REVERT: C 710 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7659 (pp20) REVERT: C 721 MET cc_start: 0.6626 (pmm) cc_final: 0.6311 (pmm) REVERT: C 726 ASN cc_start: 0.8911 (p0) cc_final: 0.8589 (p0) REVERT: D 503 MET cc_start: 0.7814 (ttp) cc_final: 0.7496 (ttm) REVERT: D 612 ILE cc_start: 0.9537 (mm) cc_final: 0.9318 (tp) REVERT: D 658 PHE cc_start: 0.8066 (t80) cc_final: 0.7866 (t80) REVERT: D 670 MET cc_start: 0.8746 (mmp) cc_final: 0.8343 (mmm) REVERT: D 767 TRP cc_start: 0.8111 (m-90) cc_final: 0.7275 (m-90) REVERT: E 8 GLN cc_start: 0.8510 (mp10) cc_final: 0.8023 (mp10) REVERT: F 22 LEU cc_start: 0.8687 (mt) cc_final: 0.8322 (mt) REVERT: F 134 ILE cc_start: 0.9280 (pt) cc_final: 0.9026 (pt) REVERT: F 190 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8556 (mm-30) REVERT: F 205 LYS cc_start: 0.8953 (tttt) cc_final: 0.8466 (tptt) REVERT: G 23 MET cc_start: 0.8760 (tpt) cc_final: 0.8423 (tpt) REVERT: G 190 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8524 (mm-30) REVERT: H 73 LYS cc_start: 0.7499 (ttpp) cc_final: 0.7184 (mtmm) REVERT: H 190 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8870 (mm-30) outliers start: 6 outliers final: 2 residues processed: 353 average time/residue: 0.1289 time to fit residues: 69.6464 Evaluate side-chains 271 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 269 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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: 0.6980 chunk 71 optimal weight: 3.9990 chunk 186 optimal weight: 0.0980 chunk 123 optimal weight: 30.0000 chunk 60 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 586 GLN C 587 GLN C 764 ASN D 747 ASN F 81 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.143448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.099079 restraints weight = 55301.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099689 restraints weight = 43595.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.099693 restraints weight = 36901.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.099848 restraints weight = 35018.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099969 restraints weight = 33091.635| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18698 Z= 0.135 Angle : 0.599 9.203 25226 Z= 0.322 Chirality : 0.043 0.207 2826 Planarity : 0.004 0.041 3102 Dihedral : 5.329 83.616 2522 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.44 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.47 (0.18), residues: 2298 helix: 1.42 (0.15), residues: 1204 sheet: -0.69 (0.40), residues: 167 loop : -0.96 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 545 TYR 0.022 0.002 TYR C 732 PHE 0.023 0.001 PHE G 181 TRP 0.027 0.002 TRP H 177 HIS 0.006 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00277 (18686) covalent geometry : angle 0.59935 (25202) SS BOND : bond 0.00330 ( 12) SS BOND : angle 0.64845 ( 24) hydrogen bonds : bond 0.05353 ( 975) hydrogen bonds : angle 4.87965 ( 2796) *********************** 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 366 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.741 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 419 GLU cc_start: 0.8977 (mp0) cc_final: 0.8659 (pp20) REVERT: A 471 LYS cc_start: 0.7577 (mtmt) cc_final: 0.7205 (tppt) REVERT: A 489 ILE cc_start: 0.9152 (mm) cc_final: 0.8947 (tp) REVERT: A 496 MET cc_start: 0.8629 (tpt) cc_final: 0.8369 (tpp) REVERT: A 537 SER cc_start: 0.9711 (m) cc_final: 0.9181 (t) REVERT: A 587 GLN cc_start: 0.8663 (mm110) cc_final: 0.8441 (mm110) REVERT: A 625 THR cc_start: 0.9304 (m) cc_final: 0.9022 (p) REVERT: A 642 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8055 (tm-30) REVERT: A 710 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8159 (pt0) REVERT: A 721 MET cc_start: 0.6021 (pmm) cc_final: 0.5327 (pmm) REVERT: B 674 MET cc_start: 0.4709 (mtp) cc_final: 0.3309 (tmm) REVERT: C 398 THR cc_start: 0.8203 (p) cc_final: 0.7997 (p) REVERT: C 489 ILE cc_start: 0.8955 (mm) cc_final: 0.8717 (tp) REVERT: C 508 GLN cc_start: 0.7594 (pp30) cc_final: 0.7249 (mm-40) REVERT: C 537 SER cc_start: 0.9271 (m) cc_final: 0.8823 (t) REVERT: C 625 THR cc_start: 0.9318 (m) cc_final: 0.9004 (p) REVERT: C 627 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8456 (mt-10) REVERT: C 642 GLN cc_start: 0.9295 (tp-100) cc_final: 0.8663 (tm-30) REVERT: C 668 ASP cc_start: 0.9373 (t0) cc_final: 0.9080 (m-30) REVERT: C 670 MET cc_start: 0.9524 (mmp) cc_final: 0.9073 (mmm) REVERT: C 674 MET cc_start: 0.9314 (tpp) cc_final: 0.9061 (tpp) REVERT: C 710 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7718 (pp20) REVERT: C 721 MET cc_start: 0.6726 (pmm) cc_final: 0.6514 (pmm) REVERT: C 764 ASN cc_start: 0.9182 (m110) cc_final: 0.8970 (m-40) REVERT: D 503 MET cc_start: 0.7631 (ttp) cc_final: 0.7420 (ttt) REVERT: D 546 PHE cc_start: 0.6915 (t80) cc_final: 0.6444 (t80) REVERT: D 612 ILE cc_start: 0.9512 (mm) cc_final: 0.9271 (tp) REVERT: D 638 ASP cc_start: 0.8198 (m-30) cc_final: 0.7684 (m-30) REVERT: D 641 LYS cc_start: 0.9203 (pptt) cc_final: 0.8872 (mmtm) REVERT: D 670 MET cc_start: 0.8566 (mmp) cc_final: 0.8288 (mmm) REVERT: D 767 TRP cc_start: 0.8260 (m-90) cc_final: 0.7448 (m-90) REVERT: E 8 GLN cc_start: 0.8578 (mp10) cc_final: 0.8108 (mp10) REVERT: E 64 ARG cc_start: 0.5761 (ptm-80) cc_final: 0.3434 (ptp-170) REVERT: E 73 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7804 (mtmm) REVERT: F 9 MET cc_start: 0.7618 (mtm) cc_final: 0.7006 (tmm) REVERT: F 22 LEU cc_start: 0.8501 (mt) cc_final: 0.8115 (mt) REVERT: F 134 ILE cc_start: 0.9182 (pt) cc_final: 0.8847 (pt) REVERT: F 173 TYR cc_start: 0.8125 (p90) cc_final: 0.7685 (p90) REVERT: F 190 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8576 (mm-30) REVERT: F 205 LYS cc_start: 0.8913 (tttt) cc_final: 0.8412 (tptt) REVERT: G 23 MET cc_start: 0.8658 (tpt) cc_final: 0.8218 (tpt) REVERT: G 134 ILE cc_start: 0.8973 (mp) cc_final: 0.8765 (mp) REVERT: G 175 TYR cc_start: 0.8739 (m-80) cc_final: 0.8338 (m-80) REVERT: G 190 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8416 (mm-30) REVERT: H 73 LYS cc_start: 0.7305 (ttpp) cc_final: 0.6984 (mtmm) REVERT: H 190 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8765 (mm-30) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.1191 time to fit residues: 68.4132 Evaluate side-chains 277 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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: 0.7980 chunk 201 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 125 optimal weight: 0.0470 chunk 123 optimal weight: 40.0000 chunk 52 optimal weight: 9.9990 chunk 194 optimal weight: 0.0010 chunk 65 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 217 optimal weight: 0.6980 overall best weight: 0.5086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 791 ASN E 148 ASN H 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.144371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099672 restraints weight = 55189.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.100513 restraints weight = 41127.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100439 restraints weight = 34130.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100633 restraints weight = 32259.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.100767 restraints weight = 30889.591| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 18698 Z= 0.121 Angle : 0.570 7.919 25226 Z= 0.304 Chirality : 0.042 0.198 2826 Planarity : 0.003 0.036 3102 Dihedral : 5.019 88.538 2522 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.74 % Favored : 96.04 % Rotamer: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.19 % 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: 0.73 (0.18), residues: 2298 helix: 1.69 (0.15), residues: 1219 sheet: -1.00 (0.37), residues: 177 loop : -0.87 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 420 TYR 0.020 0.001 TYR A 702 PHE 0.027 0.001 PHE H 179 TRP 0.033 0.001 TRP D 460 HIS 0.005 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00248 (18686) covalent geometry : angle 0.57033 (25202) SS BOND : bond 0.00347 ( 12) SS BOND : angle 0.67158 ( 24) hydrogen bonds : bond 0.04689 ( 975) hydrogen bonds : angle 4.49535 ( 2796) *********************** 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 355 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 354 time to evaluate : 0.630 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 419 GLU cc_start: 0.8957 (mp0) cc_final: 0.8620 (pp20) REVERT: A 463 MET cc_start: 0.8180 (mtt) cc_final: 0.7963 (mmt) REVERT: A 471 LYS cc_start: 0.7818 (mtmt) cc_final: 0.7301 (tppt) REVERT: A 489 ILE cc_start: 0.9093 (mm) cc_final: 0.8825 (tp) REVERT: A 496 MET cc_start: 0.8544 (tpt) cc_final: 0.8295 (tpp) REVERT: A 521 LEU cc_start: 0.8815 (mt) cc_final: 0.8568 (mt) REVERT: A 537 SER cc_start: 0.9671 (m) cc_final: 0.9236 (t) REVERT: A 587 GLN cc_start: 0.8588 (mm110) cc_final: 0.8313 (mm110) REVERT: A 642 GLN cc_start: 0.8828 (tp-100) cc_final: 0.8197 (tm-30) REVERT: A 702 TYR cc_start: 0.8194 (t80) cc_final: 0.7940 (t80) REVERT: A 721 MET cc_start: 0.5832 (pmm) cc_final: 0.5301 (pmm) REVERT: B 414 MET cc_start: 0.9275 (pmm) cc_final: 0.9042 (pmm) REVERT: B 503 MET cc_start: 0.8259 (ttp) cc_final: 0.7905 (ttt) REVERT: B 534 ILE cc_start: 0.9416 (mt) cc_final: 0.8950 (tp) REVERT: B 674 MET cc_start: 0.4729 (mtp) cc_final: 0.3300 (tmm) REVERT: C 489 ILE cc_start: 0.8988 (mm) cc_final: 0.8709 (tp) REVERT: C 508 GLN cc_start: 0.7319 (pp30) cc_final: 0.7018 (mm-40) REVERT: C 537 SER cc_start: 0.9300 (m) cc_final: 0.8679 (t) REVERT: C 627 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8499 (mt-10) REVERT: C 642 GLN cc_start: 0.9284 (tp-100) cc_final: 0.8673 (tm-30) REVERT: C 668 ASP cc_start: 0.9365 (t0) cc_final: 0.9096 (m-30) REVERT: C 670 MET cc_start: 0.9501 (mmp) cc_final: 0.9070 (mmm) REVERT: C 702 TYR cc_start: 0.8456 (t80) cc_final: 0.8110 (t80) REVERT: C 710 GLU cc_start: 0.8588 (mt-10) cc_final: 0.7817 (pp20) REVERT: C 726 ASN cc_start: 0.9010 (m-40) cc_final: 0.8791 (m-40) REVERT: C 803 LEU cc_start: 0.9338 (mt) cc_final: 0.9028 (mm) REVERT: D 546 PHE cc_start: 0.6697 (t80) cc_final: 0.6194 (t80) REVERT: D 612 ILE cc_start: 0.9418 (mm) cc_final: 0.9151 (tp) REVERT: D 638 ASP cc_start: 0.8087 (m-30) cc_final: 0.7555 (m-30) REVERT: D 641 LYS cc_start: 0.9285 (pptt) cc_final: 0.9022 (mmtm) REVERT: D 670 MET cc_start: 0.8561 (mmp) cc_final: 0.8341 (mmm) REVERT: D 767 TRP cc_start: 0.8227 (m-90) cc_final: 0.7495 (m-90) REVERT: E 8 GLN cc_start: 0.8645 (mp10) cc_final: 0.8284 (mp10) REVERT: E 64 ARG cc_start: 0.5691 (ptm-80) cc_final: 0.3319 (ptp-170) REVERT: E 73 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7763 (mtmm) REVERT: E 177 TRP cc_start: 0.7280 (p90) cc_final: 0.6697 (p90) REVERT: F 134 ILE cc_start: 0.9209 (pt) cc_final: 0.8819 (pt) REVERT: F 173 TYR cc_start: 0.8059 (p90) cc_final: 0.7642 (p90) REVERT: F 190 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8715 (mm-30) REVERT: F 205 LYS cc_start: 0.8913 (tttt) cc_final: 0.8393 (tptp) REVERT: G 23 MET cc_start: 0.8740 (tpt) cc_final: 0.8529 (tpt) REVERT: G 190 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8379 (mm-30) outliers start: 1 outliers final: 0 residues processed: 354 average time/residue: 0.1176 time to fit residues: 65.0734 Evaluate side-chains 281 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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: 9.9990 chunk 59 optimal weight: 2.9990 chunk 54 optimal weight: 0.0670 chunk 215 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 183 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 135 optimal weight: 0.0470 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN G 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.143869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.096904 restraints weight = 55740.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.099765 restraints weight = 36609.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.101533 restraints weight = 27788.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.102610 restraints weight = 23425.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.103163 restraints weight = 21106.616| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18698 Z= 0.117 Angle : 0.562 8.666 25226 Z= 0.298 Chirality : 0.042 0.192 2826 Planarity : 0.003 0.035 3102 Dihedral : 4.836 86.997 2522 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.61 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.78 (0.18), residues: 2298 helix: 1.73 (0.15), residues: 1222 sheet: -1.12 (0.37), residues: 177 loop : -0.82 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 545 TYR 0.019 0.001 TYR H 31 PHE 0.023 0.001 PHE E 179 TRP 0.050 0.002 TRP D 460 HIS 0.003 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00244 (18686) covalent geometry : angle 0.56118 (25202) SS BOND : bond 0.00278 ( 12) SS BOND : angle 0.95167 ( 24) hydrogen bonds : bond 0.04414 ( 975) hydrogen bonds : angle 4.38152 ( 2796) *********************** 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 353 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.787 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 419 GLU cc_start: 0.8971 (mp0) cc_final: 0.8632 (pp20) REVERT: A 427 ASP cc_start: 0.9148 (m-30) cc_final: 0.8912 (m-30) REVERT: A 431 GLU cc_start: 0.8745 (pt0) cc_final: 0.8526 (pm20) REVERT: A 471 LYS cc_start: 0.7879 (mtmt) cc_final: 0.7410 (tppt) REVERT: A 489 ILE cc_start: 0.9178 (mm) cc_final: 0.8868 (tp) REVERT: A 496 MET cc_start: 0.8581 (tpt) cc_final: 0.8278 (tpp) REVERT: A 537 SER cc_start: 0.9680 (m) cc_final: 0.9335 (t) REVERT: A 587 GLN cc_start: 0.8533 (mm110) cc_final: 0.8293 (mm110) REVERT: A 642 GLN cc_start: 0.8816 (tp-100) cc_final: 0.7952 (pp30) REVERT: A 702 TYR cc_start: 0.8218 (t80) cc_final: 0.7669 (t80) REVERT: B 534 ILE cc_start: 0.9422 (mt) cc_final: 0.8991 (tp) REVERT: B 546 PHE cc_start: 0.8059 (t80) cc_final: 0.7749 (t80) REVERT: B 674 MET cc_start: 0.4729 (mtp) cc_final: 0.3373 (tmm) REVERT: C 489 ILE cc_start: 0.9057 (mm) cc_final: 0.8724 (tp) REVERT: C 537 SER cc_start: 0.9333 (m) cc_final: 0.8794 (t) REVERT: C 627 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8372 (mt-10) REVERT: C 642 GLN cc_start: 0.9271 (tp-100) cc_final: 0.7978 (pp30) REVERT: C 668 ASP cc_start: 0.9331 (t0) cc_final: 0.9089 (m-30) REVERT: C 670 MET cc_start: 0.9461 (mmp) cc_final: 0.8995 (mmm) REVERT: C 674 MET cc_start: 0.9339 (tpp) cc_final: 0.9088 (tpp) REVERT: C 702 TYR cc_start: 0.8514 (t80) cc_final: 0.8108 (t80) REVERT: C 710 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7818 (pp20) REVERT: C 726 ASN cc_start: 0.9062 (m-40) cc_final: 0.8844 (t0) REVERT: C 803 LEU cc_start: 0.9350 (mt) cc_final: 0.9076 (mm) REVERT: D 408 MET cc_start: 0.7234 (tpt) cc_final: 0.6867 (tpt) REVERT: D 546 PHE cc_start: 0.6636 (t80) cc_final: 0.6206 (t80) REVERT: D 612 ILE cc_start: 0.9476 (mm) cc_final: 0.9250 (tp) REVERT: D 638 ASP cc_start: 0.8094 (m-30) cc_final: 0.7623 (m-30) REVERT: D 641 LYS cc_start: 0.9308 (pptt) cc_final: 0.9050 (mmtm) REVERT: D 670 MET cc_start: 0.8595 (mmp) cc_final: 0.8373 (mmm) REVERT: D 708 MET cc_start: 0.9410 (ptp) cc_final: 0.9159 (ptt) REVERT: D 767 TRP cc_start: 0.8133 (m-90) cc_final: 0.7352 (m-90) REVERT: E 8 GLN cc_start: 0.8712 (mp10) cc_final: 0.8401 (mp10) REVERT: E 64 ARG cc_start: 0.5728 (ptm-80) cc_final: 0.3108 (ptp-170) REVERT: E 78 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7801 (mm-40) REVERT: E 148 ASN cc_start: 0.9021 (m-40) cc_final: 0.8786 (m110) REVERT: E 177 TRP cc_start: 0.7297 (p90) cc_final: 0.6714 (p90) REVERT: F 173 TYR cc_start: 0.7979 (p90) cc_final: 0.7560 (p90) REVERT: F 190 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8785 (mm-30) REVERT: F 205 LYS cc_start: 0.8835 (tttt) cc_final: 0.8321 (tptp) REVERT: G 103 SER cc_start: 0.9183 (t) cc_final: 0.8805 (p) REVERT: G 190 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8471 (mm-30) REVERT: H 23 MET cc_start: 0.8228 (ttt) cc_final: 0.7513 (tpt) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.1340 time to fit residues: 74.9061 Evaluate side-chains 270 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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: 0.9990 chunk 179 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 134 optimal weight: 0.4980 chunk 117 optimal weight: 4.9990 chunk 94 optimal weight: 0.0970 chunk 200 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.0270 chunk 224 optimal weight: 0.0170 chunk 216 optimal weight: 4.9990 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN B 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.145526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.101029 restraints weight = 56839.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.101223 restraints weight = 45358.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.101869 restraints weight = 36072.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.102287 restraints weight = 32001.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.102426 restraints weight = 30528.868| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 18698 Z= 0.112 Angle : 0.567 8.948 25226 Z= 0.297 Chirality : 0.042 0.247 2826 Planarity : 0.003 0.036 3102 Dihedral : 4.509 55.686 2522 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.79 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: 0.75 (0.18), residues: 2298 helix: 1.70 (0.15), residues: 1228 sheet: -1.12 (0.37), residues: 182 loop : -0.83 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 660 TYR 0.017 0.001 TYR A 533 PHE 0.023 0.001 PHE E 179 TRP 0.027 0.001 TRP B 671 HIS 0.005 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00231 (18686) covalent geometry : angle 0.56556 (25202) SS BOND : bond 0.00243 ( 12) SS BOND : angle 1.27012 ( 24) hydrogen bonds : bond 0.04028 ( 975) hydrogen bonds : angle 4.28686 ( 2796) *********************** 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 351 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.801 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: A 419 GLU cc_start: 0.9009 (mp0) cc_final: 0.8635 (pp20) REVERT: A 471 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7465 (tppt) REVERT: A 496 MET cc_start: 0.8571 (tpt) cc_final: 0.8229 (tpp) REVERT: A 537 SER cc_start: 0.9640 (m) cc_final: 0.9293 (t) REVERT: A 587 GLN cc_start: 0.8514 (mm110) cc_final: 0.8286 (mm110) REVERT: A 642 GLN cc_start: 0.8823 (tp-100) cc_final: 0.7439 (pp30) REVERT: A 721 MET cc_start: 0.6376 (pmm) cc_final: 0.5979 (pmm) REVERT: B 441 LYS cc_start: 0.6327 (mmmt) cc_final: 0.6119 (tptp) REVERT: B 534 ILE cc_start: 0.9383 (mt) cc_final: 0.8971 (tp) REVERT: B 546 PHE cc_start: 0.8036 (t80) cc_final: 0.7739 (t80) REVERT: B 674 MET cc_start: 0.4519 (mtp) cc_final: 0.3418 (tmm) REVERT: C 398 THR cc_start: 0.8189 (p) cc_final: 0.7903 (p) REVERT: C 489 ILE cc_start: 0.9152 (mm) cc_final: 0.8772 (tp) REVERT: C 537 SER cc_start: 0.9204 (m) cc_final: 0.8640 (t) REVERT: C 619 ASN cc_start: 0.9269 (t0) cc_final: 0.8903 (t0) REVERT: C 627 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8225 (mt-10) REVERT: C 642 GLN cc_start: 0.9292 (tp-100) cc_final: 0.7929 (pp30) REVERT: C 668 ASP cc_start: 0.9331 (t0) cc_final: 0.9052 (m-30) REVERT: C 670 MET cc_start: 0.9413 (mmp) cc_final: 0.8876 (mmm) REVERT: C 702 TYR cc_start: 0.8366 (t80) cc_final: 0.7686 (t80) REVERT: C 710 GLU cc_start: 0.8533 (mt-10) cc_final: 0.7939 (pp20) REVERT: C 726 ASN cc_start: 0.8985 (m-40) cc_final: 0.8642 (t0) REVERT: C 803 LEU cc_start: 0.9308 (mt) cc_final: 0.9056 (mm) REVERT: D 546 PHE cc_start: 0.6621 (t80) cc_final: 0.6239 (t80) REVERT: D 612 ILE cc_start: 0.9452 (mm) cc_final: 0.9239 (tp) REVERT: D 638 ASP cc_start: 0.8199 (m-30) cc_final: 0.7660 (m-30) REVERT: D 767 TRP cc_start: 0.8262 (m-90) cc_final: 0.7415 (m-90) REVERT: E 8 GLN cc_start: 0.8740 (mp10) cc_final: 0.8481 (mp10) REVERT: E 64 ARG cc_start: 0.5792 (ptm-80) cc_final: 0.3272 (ptp-170) REVERT: E 73 LYS cc_start: 0.8019 (ttpp) cc_final: 0.7789 (mttp) REVERT: E 78 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7880 (mm-40) REVERT: E 148 ASN cc_start: 0.8933 (m-40) cc_final: 0.8722 (m-40) REVERT: E 177 TRP cc_start: 0.7131 (p90) cc_final: 0.6785 (p90) REVERT: F 173 TYR cc_start: 0.7939 (p90) cc_final: 0.7673 (p90) REVERT: F 177 TRP cc_start: 0.7263 (m100) cc_final: 0.6976 (m100) REVERT: F 205 LYS cc_start: 0.8911 (tttt) cc_final: 0.8394 (tptp) REVERT: G 152 ILE cc_start: 0.9195 (tp) cc_final: 0.8917 (mm) REVERT: G 190 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8400 (mm-30) REVERT: H 23 MET cc_start: 0.8179 (ttt) cc_final: 0.7413 (tpt) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1279 time to fit residues: 71.2008 Evaluate side-chains 281 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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: 2.9990 chunk 51 optimal weight: 0.0980 chunk 76 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 HIS ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.144479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.101461 restraints weight = 56727.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.102062 restraints weight = 43770.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101172 restraints weight = 41260.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.101373 restraints weight = 38678.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.101449 restraints weight = 35087.987| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18698 Z= 0.121 Angle : 0.573 9.571 25226 Z= 0.297 Chirality : 0.041 0.192 2826 Planarity : 0.003 0.036 3102 Dihedral : 4.426 50.335 2522 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.87 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.73 (0.18), residues: 2298 helix: 1.71 (0.15), residues: 1230 sheet: -1.22 (0.35), residues: 189 loop : -0.86 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 420 TYR 0.016 0.001 TYR A 533 PHE 0.022 0.001 PHE E 179 TRP 0.028 0.001 TRP B 671 HIS 0.004 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00259 (18686) covalent geometry : angle 0.57226 (25202) SS BOND : bond 0.00437 ( 12) SS BOND : angle 1.28745 ( 24) hydrogen bonds : bond 0.04085 ( 975) hydrogen bonds : angle 4.29036 ( 2796) *********************** 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 333 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.759 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 419 GLU cc_start: 0.8963 (mp0) cc_final: 0.8643 (pp20) REVERT: A 463 MET cc_start: 0.7897 (mmt) cc_final: 0.6968 (mmm) REVERT: A 471 LYS cc_start: 0.8043 (mtmt) cc_final: 0.7541 (tppt) REVERT: A 496 MET cc_start: 0.8473 (tpt) cc_final: 0.8128 (tpp) REVERT: A 642 GLN cc_start: 0.8732 (tp-100) cc_final: 0.7531 (pp30) REVERT: A 702 TYR cc_start: 0.8427 (t80) cc_final: 0.8181 (t80) REVERT: A 721 MET cc_start: 0.6322 (pmm) cc_final: 0.5851 (pmm) REVERT: B 441 LYS cc_start: 0.6797 (mmmt) cc_final: 0.6437 (tptp) REVERT: B 534 ILE cc_start: 0.9423 (mt) cc_final: 0.8977 (tp) REVERT: B 546 PHE cc_start: 0.8068 (t80) cc_final: 0.7790 (t80) REVERT: B 674 MET cc_start: 0.4557 (mtp) cc_final: 0.3475 (tmm) REVERT: C 489 ILE cc_start: 0.9078 (mm) cc_final: 0.8695 (tp) REVERT: C 537 SER cc_start: 0.9311 (m) cc_final: 0.8764 (t) REVERT: C 619 ASN cc_start: 0.9323 (t0) cc_final: 0.8968 (t0) REVERT: C 627 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8293 (mt-10) REVERT: C 642 GLN cc_start: 0.9279 (tp-100) cc_final: 0.8745 (tm-30) REVERT: C 668 ASP cc_start: 0.9328 (t0) cc_final: 0.9056 (m-30) REVERT: C 670 MET cc_start: 0.9415 (mmp) cc_final: 0.8846 (mmm) REVERT: C 674 MET cc_start: 0.9360 (tpp) cc_final: 0.9136 (tpp) REVERT: C 710 GLU cc_start: 0.8567 (mt-10) cc_final: 0.7985 (pp20) REVERT: C 726 ASN cc_start: 0.9050 (m-40) cc_final: 0.8652 (t0) REVERT: C 803 LEU cc_start: 0.9337 (mt) cc_final: 0.9113 (mm) REVERT: D 546 PHE cc_start: 0.6514 (t80) cc_final: 0.6032 (t80) REVERT: D 612 ILE cc_start: 0.9507 (mm) cc_final: 0.9255 (tp) REVERT: D 767 TRP cc_start: 0.8342 (m-90) cc_final: 0.7430 (m-90) REVERT: E 64 ARG cc_start: 0.5861 (ptm-80) cc_final: 0.3394 (ptp-170) REVERT: E 73 LYS cc_start: 0.8011 (ttpp) cc_final: 0.7755 (mttp) REVERT: E 177 TRP cc_start: 0.7113 (p90) cc_final: 0.6689 (p90) REVERT: E 199 MET cc_start: 0.9066 (ppp) cc_final: 0.8718 (ppp) REVERT: F 139 ILE cc_start: 0.8610 (mt) cc_final: 0.8396 (mt) REVERT: F 188 ILE cc_start: 0.7640 (mm) cc_final: 0.7430 (mm) REVERT: F 205 LYS cc_start: 0.8927 (tttt) cc_final: 0.8402 (tptp) REVERT: G 152 ILE cc_start: 0.9132 (tp) cc_final: 0.8884 (mm) REVERT: G 190 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8361 (mm-30) REVERT: H 140 PHE cc_start: 0.8408 (m-80) cc_final: 0.7947 (m-80) REVERT: H 181 PHE cc_start: 0.6968 (m-80) cc_final: 0.6378 (m-80) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.1293 time to fit residues: 68.4498 Evaluate side-chains 273 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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: 20.0000 chunk 81 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 225 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 69 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN E 148 ASN H 131 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.139861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.094596 restraints weight = 55535.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.096243 restraints weight = 42190.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.095999 restraints weight = 31826.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096173 restraints weight = 31925.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096370 restraints weight = 30138.710| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18698 Z= 0.183 Angle : 0.638 9.457 25226 Z= 0.338 Chirality : 0.043 0.202 2826 Planarity : 0.004 0.034 3102 Dihedral : 4.675 50.363 2522 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.44 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.51 (0.18), residues: 2298 helix: 1.45 (0.15), residues: 1228 sheet: -1.28 (0.37), residues: 186 loop : -0.84 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 101 TYR 0.033 0.002 TYR F 34 PHE 0.020 0.002 PHE E 179 TRP 0.041 0.002 TRP D 460 HIS 0.004 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00389 (18686) covalent geometry : angle 0.63764 (25202) SS BOND : bond 0.00383 ( 12) SS BOND : angle 1.12616 ( 24) hydrogen bonds : bond 0.05142 ( 975) hydrogen bonds : angle 4.58205 ( 2796) *********************** 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 327 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 GLU cc_start: 0.9005 (mp0) cc_final: 0.8705 (pp20) REVERT: A 463 MET cc_start: 0.7841 (mmt) cc_final: 0.6867 (mmm) REVERT: A 471 LYS cc_start: 0.7964 (mtmt) cc_final: 0.7573 (tppt) REVERT: A 496 MET cc_start: 0.8588 (tpt) cc_final: 0.8278 (tpp) REVERT: A 585 MET cc_start: 0.9124 (mmm) cc_final: 0.8830 (mmt) REVERT: A 637 GLU cc_start: 0.8991 (pp20) cc_final: 0.8673 (mm-30) REVERT: A 642 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8087 (tm-30) REVERT: A 721 MET cc_start: 0.6666 (pmm) cc_final: 0.6151 (pmm) REVERT: A 722 LYS cc_start: 0.8337 (tmmt) cc_final: 0.7934 (ptpt) REVERT: B 408 MET cc_start: 0.7671 (tpt) cc_final: 0.7440 (tpt) REVERT: B 546 PHE cc_start: 0.8105 (t80) cc_final: 0.7873 (t80) REVERT: B 674 MET cc_start: 0.5029 (mtp) cc_final: 0.3755 (tmm) REVERT: C 489 ILE cc_start: 0.9160 (mm) cc_final: 0.8821 (tp) REVERT: C 537 SER cc_start: 0.9545 (m) cc_final: 0.9009 (t) REVERT: C 627 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8552 (mt-10) REVERT: C 642 GLN cc_start: 0.9244 (tp-100) cc_final: 0.7821 (pp30) REVERT: C 670 MET cc_start: 0.9428 (mmp) cc_final: 0.8975 (mmm) REVERT: C 674 MET cc_start: 0.9370 (tpp) cc_final: 0.9094 (tpp) REVERT: C 702 TYR cc_start: 0.8663 (t80) cc_final: 0.8348 (t80) REVERT: C 710 GLU cc_start: 0.8570 (mt-10) cc_final: 0.7963 (pp20) REVERT: C 726 ASN cc_start: 0.9086 (m-40) cc_final: 0.8819 (m-40) REVERT: C 764 ASN cc_start: 0.9253 (m110) cc_final: 0.8979 (m-40) REVERT: D 473 ASP cc_start: 0.8752 (t0) cc_final: 0.8521 (t70) REVERT: D 546 PHE cc_start: 0.6860 (t80) cc_final: 0.6253 (t80) REVERT: D 637 GLU cc_start: 0.9287 (mp0) cc_final: 0.8907 (pm20) REVERT: D 651 ASP cc_start: 0.7221 (t0) cc_final: 0.6863 (p0) REVERT: D 767 TRP cc_start: 0.8437 (m-90) cc_final: 0.7540 (m-90) REVERT: E 64 ARG cc_start: 0.6071 (ptm-80) cc_final: 0.3515 (ptp-170) REVERT: E 73 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7957 (mtpp) REVERT: E 177 TRP cc_start: 0.7176 (p90) cc_final: 0.6910 (p90) REVERT: F 173 TYR cc_start: 0.8095 (p90) cc_final: 0.7785 (p90) REVERT: F 188 ILE cc_start: 0.7726 (mm) cc_final: 0.7505 (mm) REVERT: F 190 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8527 (mm-30) REVERT: F 205 LYS cc_start: 0.8851 (tttt) cc_final: 0.8342 (tptp) REVERT: G 152 ILE cc_start: 0.9238 (tp) cc_final: 0.8990 (mm) REVERT: G 190 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8531 (mm-30) REVERT: H 127 TYR cc_start: 0.7015 (m-80) cc_final: 0.6509 (m-80) REVERT: H 205 LYS cc_start: 0.8879 (mttp) cc_final: 0.8533 (mmtm) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1349 time to fit residues: 69.4669 Evaluate side-chains 263 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 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: 2.9990 chunk 226 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 79 optimal weight: 0.0020 chunk 49 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 HIS ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.142002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.095256 restraints weight = 54303.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097559 restraints weight = 38182.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.099070 restraints weight = 30315.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099604 restraints weight = 26375.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.100346 restraints weight = 24504.032| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 18698 Z= 0.133 Angle : 0.601 10.540 25226 Z= 0.313 Chirality : 0.042 0.220 2826 Planarity : 0.003 0.035 3102 Dihedral : 4.500 49.049 2522 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.66 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: 0.67 (0.18), residues: 2298 helix: 1.62 (0.15), residues: 1221 sheet: -1.01 (0.39), residues: 171 loop : -0.87 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 64 TYR 0.020 0.001 TYR C 533 PHE 0.025 0.001 PHE E 179 TRP 0.031 0.001 TRP D 460 HIS 0.004 0.001 HIS G 81 Details of bonding type rmsd covalent geometry : bond 0.00290 (18686) covalent geometry : angle 0.59908 (25202) SS BOND : bond 0.00468 ( 12) SS BOND : angle 1.72427 ( 24) hydrogen bonds : bond 0.04567 ( 975) hydrogen bonds : angle 4.40239 ( 2796) *********************** 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 336 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.732 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: A 419 GLU cc_start: 0.8958 (mp0) cc_final: 0.8675 (pp20) REVERT: A 463 MET cc_start: 0.7689 (mmt) cc_final: 0.6825 (mmm) REVERT: A 471 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7477 (tppt) REVERT: A 496 MET cc_start: 0.8500 (tpt) cc_final: 0.8166 (tpp) REVERT: A 585 MET cc_start: 0.9056 (mmm) cc_final: 0.8829 (mmt) REVERT: A 642 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8342 (tm-30) REVERT: A 702 TYR cc_start: 0.8371 (t80) cc_final: 0.8163 (t80) REVERT: A 721 MET cc_start: 0.6348 (pmm) cc_final: 0.5921 (pmm) REVERT: A 722 LYS cc_start: 0.8324 (tmmt) cc_final: 0.7934 (ptpt) REVERT: B 534 ILE cc_start: 0.9432 (mt) cc_final: 0.8986 (tp) REVERT: B 546 PHE cc_start: 0.7987 (t80) cc_final: 0.7754 (t80) REVERT: B 674 MET cc_start: 0.4904 (mtp) cc_final: 0.3751 (tmm) REVERT: C 489 ILE cc_start: 0.9179 (mm) cc_final: 0.8764 (tp) REVERT: C 537 SER cc_start: 0.9432 (m) cc_final: 0.8813 (t) REVERT: C 627 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8337 (mt-10) REVERT: C 642 GLN cc_start: 0.9191 (tp-100) cc_final: 0.7831 (pp30) REVERT: C 670 MET cc_start: 0.9366 (mmp) cc_final: 0.8917 (mmm) REVERT: C 674 MET cc_start: 0.9325 (tpp) cc_final: 0.9020 (tpp) REVERT: C 710 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8044 (pp20) REVERT: C 726 ASN cc_start: 0.9080 (m-40) cc_final: 0.8574 (t0) REVERT: D 473 ASP cc_start: 0.8814 (t0) cc_final: 0.8582 (t70) REVERT: D 546 PHE cc_start: 0.6373 (t80) cc_final: 0.6009 (t80) REVERT: D 637 GLU cc_start: 0.9173 (mp0) cc_final: 0.8962 (pm20) REVERT: D 767 TRP cc_start: 0.8290 (m-90) cc_final: 0.7405 (m-90) REVERT: E 64 ARG cc_start: 0.5968 (ptm-80) cc_final: 0.3323 (ptp-170) REVERT: E 181 PHE cc_start: 0.7373 (m-80) cc_final: 0.7164 (m-80) REVERT: F 190 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8615 (mm-30) REVERT: F 205 LYS cc_start: 0.8773 (tttt) cc_final: 0.8263 (tptp) REVERT: G 97 LEU cc_start: 0.7589 (tt) cc_final: 0.7128 (mt) REVERT: G 152 ILE cc_start: 0.9215 (tp) cc_final: 0.8932 (mm) REVERT: G 190 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8533 (mm-30) REVERT: H 23 MET cc_start: 0.8213 (ttt) cc_final: 0.7247 (tpt) REVERT: H 127 TYR cc_start: 0.6676 (m-80) cc_final: 0.6230 (m-80) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.1304 time to fit residues: 69.2917 Evaluate side-chains 272 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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: 8.9990 chunk 112 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 HIS ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.139200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.093907 restraints weight = 54634.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094933 restraints weight = 39988.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.095438 restraints weight = 31036.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.095805 restraints weight = 28649.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.095963 restraints weight = 27874.144| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18698 Z= 0.195 Angle : 0.664 10.550 25226 Z= 0.351 Chirality : 0.044 0.211 2826 Planarity : 0.004 0.035 3102 Dihedral : 4.744 49.083 2522 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.40 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 1.39 (0.15), residues: 1218 sheet: -1.33 (0.37), residues: 188 loop : -0.90 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 660 TYR 0.019 0.002 TYR C 533 PHE 0.024 0.002 PHE E 179 TRP 0.034 0.002 TRP E 177 HIS 0.008 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00421 (18686) covalent geometry : angle 0.66288 (25202) SS BOND : bond 0.00551 ( 12) SS BOND : angle 1.38453 ( 24) hydrogen bonds : bond 0.05268 ( 975) hydrogen bonds : angle 4.70144 ( 2796) ********************** 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 324 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.753 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 419 GLU cc_start: 0.9024 (mp0) cc_final: 0.8533 (pt0) REVERT: A 471 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7664 (tppt) REVERT: A 496 MET cc_start: 0.8547 (tpt) cc_final: 0.8246 (tpp) REVERT: A 585 MET cc_start: 0.9066 (mmm) cc_final: 0.8790 (mmt) REVERT: A 642 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8437 (tm-30) REVERT: A 674 MET cc_start: 0.9062 (tpp) cc_final: 0.8824 (tpp) REVERT: A 721 MET cc_start: 0.6836 (pmm) cc_final: 0.6344 (pmm) REVERT: A 734 ILE cc_start: 0.7283 (tp) cc_final: 0.7023 (tp) REVERT: B 674 MET cc_start: 0.5417 (mtp) cc_final: 0.4251 (tmm) REVERT: C 489 ILE cc_start: 0.9337 (mm) cc_final: 0.8866 (tp) REVERT: C 537 SER cc_start: 0.9572 (m) cc_final: 0.9094 (t) REVERT: C 627 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8498 (mt-10) REVERT: C 642 GLN cc_start: 0.9192 (tp-100) cc_final: 0.8556 (tm-30) REVERT: C 670 MET cc_start: 0.9386 (mmp) cc_final: 0.8912 (mmm) REVERT: C 674 MET cc_start: 0.9397 (tpp) cc_final: 0.9163 (tpp) REVERT: C 710 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8233 (pp20) REVERT: C 764 ASN cc_start: 0.9399 (m110) cc_final: 0.9060 (m-40) REVERT: D 473 ASP cc_start: 0.8819 (t0) cc_final: 0.8572 (t70) REVERT: D 546 PHE cc_start: 0.6785 (t80) cc_final: 0.6402 (t80) REVERT: D 641 LYS cc_start: 0.9686 (tptp) cc_final: 0.9446 (mmtm) REVERT: D 651 ASP cc_start: 0.7210 (t0) cc_final: 0.6907 (p0) REVERT: D 659 PHE cc_start: 0.7223 (m-80) cc_final: 0.6986 (m-80) REVERT: D 721 MET cc_start: 0.8788 (pmm) cc_final: 0.8527 (pmm) REVERT: D 767 TRP cc_start: 0.8485 (m-90) cc_final: 0.7545 (m-90) REVERT: E 64 ARG cc_start: 0.5880 (ptm-80) cc_final: 0.5523 (ptp-110) REVERT: E 181 PHE cc_start: 0.7196 (m-80) cc_final: 0.6479 (m-80) REVERT: F 190 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8491 (mm-30) REVERT: F 205 LYS cc_start: 0.8853 (tttt) cc_final: 0.8346 (tptp) REVERT: G 97 LEU cc_start: 0.7534 (tt) cc_final: 0.7106 (mt) REVERT: G 190 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8645 (mm-30) REVERT: H 127 TYR cc_start: 0.7079 (m-80) cc_final: 0.6600 (m-80) REVERT: H 205 LYS cc_start: 0.8872 (mttp) cc_final: 0.8392 (mmmt) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.1313 time to fit residues: 67.3260 Evaluate side-chains 263 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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: 3.9990 chunk 46 optimal weight: 0.0050 chunk 57 optimal weight: 0.0570 chunk 123 optimal weight: 20.0000 chunk 228 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 170 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.138779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094740 restraints weight = 55125.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094655 restraints weight = 46511.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094109 restraints weight = 37396.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.094289 restraints weight = 36815.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094553 restraints weight = 32187.807| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.6704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18698 Z= 0.181 Angle : 0.654 10.289 25226 Z= 0.345 Chirality : 0.044 0.198 2826 Planarity : 0.004 0.039 3102 Dihedral : 4.719 48.390 2522 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.57 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 1.38 (0.15), residues: 1216 sheet: -1.26 (0.38), residues: 177 loop : -0.95 (0.22), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 660 TYR 0.030 0.002 TYR E 31 PHE 0.026 0.002 PHE E 179 TRP 0.036 0.002 TRP E 177 HIS 0.015 0.002 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00391 (18686) covalent geometry : angle 0.65358 (25202) SS BOND : bond 0.00590 ( 12) SS BOND : angle 1.10952 ( 24) hydrogen bonds : bond 0.05125 ( 975) hydrogen bonds : angle 4.71270 ( 2796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3286.12 seconds wall clock time: 57 minutes 44.96 seconds (3464.96 seconds total)