Starting phenix.real_space_refine on Mon Jun 16 07:24:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dhr_46874/06_2025/9dhr_46874.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dhr_46874/06_2025/9dhr_46874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dhr_46874/06_2025/9dhr_46874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dhr_46874/06_2025/9dhr_46874.map" model { file = "/net/cci-nas-00/data/ceres_data/9dhr_46874/06_2025/9dhr_46874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dhr_46874/06_2025/9dhr_46874.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 3318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18298 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': 3, 'PTRANS': 10, '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': 3, 'PTRANS': 10, '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': 3, 'PTRANS': 10, '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': 3, 'PTRANS': 10, '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: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "F" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "G" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "H" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} 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: 13.04, per 1000 atoms: 0.71 Number of scatterers: 18298 At special positions: 0 Unit cell: (113.49, 130.95, 147.44, 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 3318 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.04 Conformation dependent library (CDL) restraints added in 2.5 seconds 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 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: 98 helices and 24 sheets defined 56.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.774A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 484 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.509A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 4.097A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.648A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 624 removed outlier: 3.934A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 617 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 641 removed outlier: 4.290A pdb=" N GLU A 637 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ASP A 638 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.552A pdb=" N SER A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 removed outlier: 4.232A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 715 " --> pdb=" O TYR A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.538A pdb=" N ASN A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.526A 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 820 removed outlier: 3.696A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 4.513A pdb=" N GLU B 413 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.936A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.532A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 515 through 519' Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.818A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.557A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 614 removed outlier: 3.557A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 625 removed outlier: 3.552A pdb=" N THR B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 653 through 662 removed outlier: 3.505A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 675 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 713 removed outlier: 4.379A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 818 removed outlier: 3.659A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 798 " --> pdb=" O GLY B 794 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 799 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.609A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' 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 523 through 545 removed outlier: 4.384A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE C 531 " --> pdb=" O MET C 527 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 532 " --> pdb=" O CYS C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 removed outlier: 4.155A pdb=" N ASN C 569 " --> pdb=" O GLU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.587A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 625 removed outlier: 3.986A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 607 " --> pdb=" O GLY C 603 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER C 615 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 617 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 675 Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.582A pdb=" N SER C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.955A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 4.225A pdb=" N VAL C 746 " --> pdb=" O LEU C 742 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.722A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 798 " --> pdb=" O GLY C 794 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C 811 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 812 " --> pdb=" O LEU C 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 removed outlier: 3.760A pdb=" N LEU D 415 " --> pdb=" O HIS D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 4.083A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.722A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.536A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 544 removed outlier: 3.790A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 586 removed outlier: 3.577A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE D 584 " --> pdb=" O SER D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 614 removed outlier: 3.525A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 625 removed outlier: 3.590A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.534A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 675 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 713 removed outlier: 4.284A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 773 through 781 removed outlier: 4.839A pdb=" N SER D 778 " --> pdb=" O ALA D 775 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLY D 779 " --> pdb=" O LYS D 776 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER D 780 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 818 removed outlier: 4.162A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 799 " --> pdb=" O VAL D 795 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (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: 3.529A pdb=" N PHE E 17 " --> pdb=" O THR E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 104 removed outlier: 4.007A pdb=" N ARG E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 123 removed outlier: 3.727A pdb=" N ILE E 108 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 131 through 159 removed outlier: 3.853A pdb=" N LEU E 135 " --> pdb=" O HIS E 131 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN E 159 " --> pdb=" O TYR E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 206 removed outlier: 3.788A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP E 202 " --> pdb=" O HIS E 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 28 removed outlier: 3.699A pdb=" N PHE F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE F 25 " --> pdb=" O SER F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 104 through 124 removed outlier: 3.746A pdb=" N ILE F 108 " --> pdb=" O SER F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 159 removed outlier: 4.091A pdb=" N GLY F 145 " --> pdb=" O PHE F 141 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU F 146 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER F 147 " --> pdb=" O SER F 143 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE F 150 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN F 159 " --> pdb=" O TYR F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 207 removed outlier: 4.039A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE F 186 " --> pdb=" O GLY F 182 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 187 " --> pdb=" O ALA F 183 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 28 removed outlier: 3.813A pdb=" N LEU G 11 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE G 17 " --> pdb=" O THR G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 104 removed outlier: 3.742A pdb=" N ARG G 98 " --> pdb=" O GLU G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 124 removed outlier: 3.734A pdb=" N ILE G 108 " --> pdb=" O SER G 104 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER G 124 " --> pdb=" O CYS G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 159 removed outlier: 4.142A pdb=" N LEU G 135 " --> pdb=" O HIS G 131 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY G 138 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE G 139 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN G 159 " --> pdb=" O TYR G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 206 removed outlier: 3.783A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE G 187 " --> pdb=" O ALA G 183 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL G 197 " --> pdb=" O GLY G 193 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP G 202 " --> pdb=" O HIS G 198 " (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 5 through 6 No H-bonds generated for 'chain 'H' and resid 5 through 6' Processing helix chain 'H' and resid 7 through 28 removed outlier: 3.714A pdb=" N PHE H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.763A pdb=" N ILE H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA H 122 " --> pdb=" O GLY H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 159 removed outlier: 3.965A pdb=" N GLY H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU H 146 " --> pdb=" O VAL H 142 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER H 147 " --> pdb=" O SER H 143 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN H 159 " --> pdb=" O TYR H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 204 removed outlier: 3.961A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE H 186 " --> pdb=" O GLY H 182 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE H 187 " --> pdb=" O ALA H 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 441 removed outlier: 6.280A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.663A 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 497 through 498 Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.402A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.463A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 702 " --> pdb=" O MET A 503 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.069A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.510A 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: 4.092A 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: 6.403A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 504 " --> pdb=" O MET B 721 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 721 " --> pdb=" O ILE B 504 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 441 removed outlier: 6.181A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) 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: 4.489A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR C 732 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.222A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 440 through 444 removed outlier: 5.909A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.171A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.420A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 504 " --> pdb=" O MET D 721 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 76 through 78 removed outlier: 3.516A pdb=" N SER E 174 " --> pdb=" O TYR E 34 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 76 through 78 Processing sheet with id=AC5, first strand: chain 'G' and resid 76 through 78 removed outlier: 3.557A pdb=" N SER G 174 " --> pdb=" O TYR G 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 76 through 78 removed outlier: 3.544A pdb=" N SER H 174 " --> pdb=" O TYR H 34 " (cutoff:3.500A) 934 hydrogen bonds defined for protein. 2673 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 5.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.46: 10219 1.46 - 1.74: 8260 1.74 - 2.01: 208 2.01 - 2.29: 1 2.29 - 2.56: 2 Bond restraints: 18690 Sorted by residual: bond pdb=" C THR B 625 " pdb=" N VAL B 626 " ideal model delta sigma weight residual 1.331 2.560 -1.229 1.01e-02 9.80e+03 1.48e+04 bond pdb=" C THR D 625 " pdb=" N VAL D 626 " ideal model delta sigma weight residual 1.328 2.158 -0.830 1.04e-02 9.25e+03 6.37e+03 bond pdb=" C THR A 625 " pdb=" N VAL A 626 " ideal model delta sigma weight residual 1.332 2.330 -0.998 1.36e-02 5.41e+03 5.39e+03 bond pdb=" C THR C 625 " pdb=" N VAL C 626 " ideal model delta sigma weight residual 1.330 1.568 -0.238 1.05e-02 9.07e+03 5.15e+02 bond pdb=" C GLY B 572 " pdb=" N ILE B 573 " ideal model delta sigma weight residual 1.335 1.539 -0.204 1.26e-02 6.30e+03 2.63e+02 ... (remaining 18685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 25137 4.61 - 9.22: 64 9.22 - 13.84: 6 13.84 - 18.45: 2 18.45 - 23.06: 1 Bond angle restraints: 25210 Sorted by residual: angle pdb=" C THR B 625 " pdb=" N VAL B 626 " pdb=" CA VAL B 626 " ideal model delta sigma weight residual 122.14 145.20 -23.06 1.11e+00 8.12e-01 4.32e+02 angle pdb=" C THR D 625 " pdb=" N VAL D 626 " pdb=" CA VAL D 626 " ideal model delta sigma weight residual 122.63 140.86 -18.23 1.19e+00 7.06e-01 2.35e+02 angle pdb=" O THR B 625 " pdb=" C THR B 625 " pdb=" N VAL B 626 " ideal model delta sigma weight residual 123.12 107.08 16.04 1.32e+00 5.74e-01 1.48e+02 angle pdb=" O THR C 625 " pdb=" C THR C 625 " pdb=" N VAL C 626 " ideal model delta sigma weight residual 122.03 109.59 12.44 1.04e+00 9.25e-01 1.43e+02 angle pdb=" CA THR C 625 " pdb=" C THR C 625 " pdb=" N VAL C 626 " ideal model delta sigma weight residual 116.92 128.78 -11.86 1.16e+00 7.43e-01 1.05e+02 ... (remaining 25205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 10315 18.05 - 36.11: 532 36.11 - 54.16: 97 54.16 - 72.21: 22 72.21 - 90.27: 14 Dihedral angle restraints: 10980 sinusoidal: 4274 harmonic: 6706 Sorted by residual: dihedral pdb=" CB CYS D 718 " pdb=" SG CYS D 718 " pdb=" SG CYS D 773 " pdb=" CB CYS D 773 " ideal model delta sinusoidal sigma weight residual 93.00 -176.73 -90.27 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 153.51 -60.51 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" CA THR D 625 " pdb=" C THR D 625 " pdb=" N VAL D 626 " pdb=" CA VAL D 626 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 10977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2544 0.077 - 0.155: 255 0.155 - 0.232: 20 0.232 - 0.309: 2 0.309 - 0.387: 5 Chirality restraints: 2826 Sorted by residual: chirality pdb=" CA PRO B 593 " pdb=" N PRO B 593 " pdb=" C PRO B 593 " pdb=" CB PRO B 593 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CA ARG D 594 " pdb=" N ARG D 594 " pdb=" C ARG D 594 " pdb=" CB ARG D 594 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA GLN D 586 " pdb=" N GLN D 586 " pdb=" C GLN D 586 " pdb=" CB GLN D 586 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 2823 not shown) Planarity restraints: 3106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 578 " -0.115 2.00e-02 2.50e+03 5.98e-02 8.95e+01 pdb=" CG TRP A 578 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP A 578 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP A 578 " 0.048 2.00e-02 2.50e+03 pdb=" NE1 TRP A 578 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP A 578 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 578 " 0.080 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 578 " -0.072 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 578 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP A 578 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 625 " -0.045 2.00e-02 2.50e+03 8.69e-02 7.54e+01 pdb=" C THR A 625 " 0.149 2.00e-02 2.50e+03 pdb=" O THR A 625 " -0.071 2.00e-02 2.50e+03 pdb=" N VAL A 626 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 578 " -0.098 2.00e-02 2.50e+03 5.04e-02 6.36e+01 pdb=" CG TRP C 578 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP C 578 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP C 578 " 0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP C 578 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP C 578 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP C 578 " 0.060 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 578 " -0.068 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 578 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP C 578 " -0.043 2.00e-02 2.50e+03 ... (remaining 3103 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 174 2.66 - 3.22: 17930 3.22 - 3.78: 25365 3.78 - 4.34: 34765 4.34 - 4.90: 57248 Nonbonded interactions: 135482 Sorted by model distance: nonbonded pdb=" CG2 THR D 625 " pdb=" ND2 ASN D 791 " model vdw 2.101 3.540 nonbonded pdb=" OE1 GLU B 705 " pdb=" OH TYR B 732 " model vdw 2.144 3.040 nonbonded pdb=" OE1 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.150 3.040 nonbonded pdb=" OE1 GLU D 705 " pdb=" OH TYR D 732 " model vdw 2.179 3.040 nonbonded pdb=" OD1 ASP A 490 " pdb=" NZ LYS A 738 " model vdw 2.270 3.120 ... (remaining 135477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 \ and (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = (chain 'B' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 819 or resid 1301)) selection = (chain 'C' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 \ and (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 45.060 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 0.014 1.229 18703 Z= 1.268 Angle : 0.837 23.060 25234 Z= 0.566 Chirality : 0.050 0.387 2826 Planarity : 0.008 0.087 3106 Dihedral : 12.240 89.027 6668 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.62 % Favored : 95.03 % Rotamer: Outliers : 0.72 % Allowed : 0.87 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.16), residues: 2292 helix: -0.85 (0.13), residues: 1181 sheet: -0.97 (0.39), residues: 166 loop : -1.18 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.115 0.009 TRP A 578 HIS 0.004 0.001 HIS E 131 PHE 0.027 0.002 PHE B 608 TYR 0.013 0.002 TYR H 155 ARG 0.020 0.003 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.17746 ( 934) hydrogen bonds : angle 6.07610 ( 2673) SS BOND : bond 0.00135 ( 12) SS BOND : angle 0.93731 ( 24) covalent geometry : bond 0.01419 (18690) covalent geometry : angle 0.83731 (25210) Misc. bond : bond 0.30842 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 510 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 VAL cc_start: 0.8186 (t) cc_final: 0.7665 (m) REVERT: A 412 HIS cc_start: 0.7737 (p90) cc_final: 0.7491 (p-80) REVERT: A 610 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7582 (mp) REVERT: A 651 ASP cc_start: 0.7443 (t0) cc_final: 0.6289 (p0) REVERT: A 674 MET cc_start: 0.8654 (mtm) cc_final: 0.8451 (mtp) REVERT: A 703 LEU cc_start: 0.8649 (mt) cc_final: 0.8398 (mp) REVERT: A 819 ARG cc_start: 0.4705 (mmt-90) cc_final: 0.4255 (ttm170) REVERT: B 651 ASP cc_start: 0.8634 (m-30) cc_final: 0.8363 (m-30) REVERT: B 660 ARG cc_start: 0.9306 (ttm170) cc_final: 0.8977 (ttm110) REVERT: B 661 ARG cc_start: 0.8996 (ttm170) cc_final: 0.8586 (tmt170) REVERT: B 671 TRP cc_start: 0.7752 (t-100) cc_final: 0.7344 (t-100) REVERT: B 714 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8280 (mt0) REVERT: B 726 ASN cc_start: 0.7495 (m-40) cc_final: 0.6848 (t0) REVERT: C 406 VAL cc_start: 0.8139 (t) cc_final: 0.7820 (m) REVERT: C 748 LEU cc_start: 0.9021 (mt) cc_final: 0.8714 (mp) REVERT: C 819 ARG cc_start: 0.5112 (mmt-90) cc_final: 0.4259 (ttm170) REVERT: D 613 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8117 (mt) REVERT: D 659 PHE cc_start: 0.8926 (m-80) cc_final: 0.8656 (m-80) REVERT: D 660 ARG cc_start: 0.9248 (ttm170) cc_final: 0.8916 (ttm110) REVERT: D 671 TRP cc_start: 0.7757 (t-100) cc_final: 0.7430 (t-100) REVERT: D 693 VAL cc_start: 0.6291 (t) cc_final: 0.6079 (t) REVERT: D 714 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8025 (mt0) REVERT: F 75 LEU cc_start: 0.7256 (tp) cc_final: 0.7026 (tp) REVERT: F 81 HIS cc_start: 0.6720 (m90) cc_final: 0.6376 (m-70) REVERT: F 130 ARG cc_start: 0.7735 (mtt180) cc_final: 0.7125 (mmm160) REVERT: H 81 HIS cc_start: 0.6436 (m90) cc_final: 0.5777 (m-70) REVERT: H 100 VAL cc_start: 0.9138 (t) cc_final: 0.8922 (m) REVERT: H 120 CYS cc_start: 0.6992 (m) cc_final: 0.6786 (m) REVERT: H 203 ARG cc_start: 0.7294 (ttp-170) cc_final: 0.6793 (ttp-170) outliers start: 14 outliers final: 5 residues processed: 523 average time/residue: 0.3823 time to fit residues: 279.4573 Evaluate side-chains 288 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 281 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 620 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 118 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 181 optimal weight: 0.0570 chunk 70 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 210 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 ASN C 435 HIS D 587 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.193102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126198 restraints weight = 29221.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.121390 restraints weight = 21905.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121586 restraints weight = 18130.135| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 18703 Z= 0.157 Angle : 0.655 11.646 25234 Z= 0.348 Chirality : 0.043 0.197 2826 Planarity : 0.004 0.048 3106 Dihedral : 5.574 62.966 2542 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.44 % Favored : 97.35 % Rotamer: Outliers : 1.99 % Allowed : 9.57 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2298 helix: 1.03 (0.15), residues: 1234 sheet: -0.61 (0.45), residues: 122 loop : -1.08 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 767 HIS 0.007 0.001 HIS H 204 PHE 0.024 0.002 PHE C 495 TYR 0.015 0.001 TYR C 523 ARG 0.009 0.001 ARG D 661 Details of bonding type rmsd hydrogen bonds : bond 0.05631 ( 934) hydrogen bonds : angle 4.27065 ( 2673) SS BOND : bond 0.00544 ( 12) SS BOND : angle 1.48116 ( 24) covalent geometry : bond 0.00357 (18690) covalent geometry : angle 0.65391 (25210) Misc. bond : bond 0.00192 ( 1) *********************** 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 405 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 366 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8670 (mm) REVERT: A 503 MET cc_start: 0.5644 (ttt) cc_final: 0.4962 (tmm) REVERT: A 819 ARG cc_start: 0.5010 (mmt-90) cc_final: 0.4695 (ttm170) REVERT: B 659 PHE cc_start: 0.8621 (m-80) cc_final: 0.8363 (t80) REVERT: B 660 ARG cc_start: 0.9182 (ttm170) cc_final: 0.8915 (ttm110) REVERT: B 661 ARG cc_start: 0.9080 (ttm170) cc_final: 0.8776 (tmt170) REVERT: B 671 TRP cc_start: 0.7624 (t-100) cc_final: 0.7242 (t-100) REVERT: B 705 GLU cc_start: 0.6940 (mp0) cc_final: 0.6679 (mp0) REVERT: B 714 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8590 (mt0) REVERT: C 784 THR cc_start: 0.7435 (m) cc_final: 0.7126 (t) REVERT: C 807 MET cc_start: 0.8818 (ttp) cc_final: 0.8598 (ttm) REVERT: C 819 ARG cc_start: 0.5176 (mmt-90) cc_final: 0.4484 (ttm170) REVERT: D 411 ASN cc_start: 0.9342 (t0) cc_final: 0.9123 (t0) REVERT: D 537 SER cc_start: 0.8840 (t) cc_final: 0.8616 (t) REVERT: D 629 MET cc_start: 0.6653 (ppp) cc_final: 0.6301 (mtp) REVERT: D 660 ARG cc_start: 0.9283 (ttm170) cc_final: 0.8965 (ttm110) REVERT: D 678 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6848 (mm-30) REVERT: D 714 GLN cc_start: 0.8626 (mm-40) cc_final: 0.7917 (mt0) REVERT: D 747 ASN cc_start: 0.7362 (t0) cc_final: 0.7118 (t0) REVERT: D 751 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7746 (mp) REVERT: E 81 HIS cc_start: 0.6427 (m90) cc_final: 0.5837 (m-70) REVERT: F 81 HIS cc_start: 0.6481 (m90) cc_final: 0.6086 (m-70) REVERT: F 98 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.8038 (mmm-85) REVERT: F 130 ARG cc_start: 0.7728 (mtt180) cc_final: 0.7368 (mmm160) REVERT: H 81 HIS cc_start: 0.6229 (m90) cc_final: 0.5757 (m-70) REVERT: H 98 ARG cc_start: 0.8340 (mmm-85) cc_final: 0.8016 (mmm-85) REVERT: H 100 VAL cc_start: 0.9287 (t) cc_final: 0.9071 (m) REVERT: H 203 ARG cc_start: 0.7444 (ttp-170) cc_final: 0.7108 (ttp-170) outliers start: 39 outliers final: 20 residues processed: 392 average time/residue: 0.3433 time to fit residues: 194.5457 Evaluate side-chains 300 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 278 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 815 CYS Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 587 GLN Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 180 optimal weight: 0.2980 chunk 223 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN D 726 ASN D 791 ASN G 81 HIS ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.188676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126721 restraints weight = 29568.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125560 restraints weight = 29295.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.117364 restraints weight = 18693.149| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18703 Z= 0.191 Angle : 0.664 12.260 25234 Z= 0.349 Chirality : 0.043 0.214 2826 Planarity : 0.004 0.053 3106 Dihedral : 5.037 56.073 2531 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.92 % Favored : 96.91 % Rotamer: Outliers : 3.02 % Allowed : 12.74 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2298 helix: 1.39 (0.15), residues: 1240 sheet: -0.43 (0.41), residues: 158 loop : -1.02 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 767 HIS 0.005 0.001 HIS E 59 PHE 0.020 0.002 PHE D 608 TYR 0.017 0.002 TYR C 702 ARG 0.008 0.001 ARG D 661 Details of bonding type rmsd hydrogen bonds : bond 0.06727 ( 934) hydrogen bonds : angle 4.30717 ( 2673) SS BOND : bond 0.00514 ( 12) SS BOND : angle 1.87615 ( 24) covalent geometry : bond 0.00450 (18690) covalent geometry : angle 0.66145 (25210) Misc. bond : bond 0.00484 ( 1) *********************** 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 350 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 291 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 VAL cc_start: 0.8393 (t) cc_final: 0.7982 (m) REVERT: A 503 MET cc_start: 0.5500 (ttt) cc_final: 0.5183 (tmm) REVERT: A 816 TYR cc_start: 0.6064 (t80) cc_final: 0.5596 (t80) REVERT: A 819 ARG cc_start: 0.5349 (mmt-90) cc_final: 0.4813 (ttm170) REVERT: B 668 ASP cc_start: 0.8671 (t0) cc_final: 0.8393 (m-30) REVERT: B 670 MET cc_start: 0.6562 (mpp) cc_final: 0.6200 (mmm) REVERT: B 671 TRP cc_start: 0.7487 (t-100) cc_final: 0.6989 (t-100) REVERT: B 705 GLU cc_start: 0.6704 (mp0) cc_final: 0.6470 (mp0) REVERT: B 756 GLN cc_start: 0.6143 (OUTLIER) cc_final: 0.5768 (mp10) REVERT: C 397 VAL cc_start: 0.8280 (t) cc_final: 0.7864 (m) REVERT: C 401 LEU cc_start: 0.8287 (pp) cc_final: 0.7971 (mm) REVERT: C 766 TRP cc_start: 0.6000 (m100) cc_final: 0.5540 (m100) REVERT: C 816 TYR cc_start: 0.5933 (t80) cc_final: 0.5564 (t80) REVERT: C 819 ARG cc_start: 0.5578 (mmt-90) cc_final: 0.4644 (ttm170) REVERT: D 411 ASN cc_start: 0.9097 (t0) cc_final: 0.8731 (t0) REVERT: D 668 ASP cc_start: 0.8694 (t0) cc_final: 0.8490 (m-30) REVERT: D 671 TRP cc_start: 0.7138 (t-100) cc_final: 0.6464 (t-100) REVERT: D 714 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8426 (mt0) REVERT: D 756 GLN cc_start: 0.6266 (OUTLIER) cc_final: 0.5967 (mp10) REVERT: E 81 HIS cc_start: 0.6517 (m90) cc_final: 0.6022 (m-70) REVERT: F 81 HIS cc_start: 0.6375 (m90) cc_final: 0.5895 (m90) REVERT: F 98 ARG cc_start: 0.8202 (mmm-85) cc_final: 0.7869 (mmm-85) REVERT: F 130 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7440 (mmm160) REVERT: H 57 MET cc_start: 0.7117 (tpp) cc_final: 0.6703 (mmt) REVERT: H 81 HIS cc_start: 0.6191 (m90) cc_final: 0.5734 (m-70) REVERT: H 98 ARG cc_start: 0.8173 (mmm-85) cc_final: 0.7875 (mmm-85) outliers start: 59 outliers final: 36 residues processed: 329 average time/residue: 0.3138 time to fit residues: 153.5324 Evaluate side-chains 282 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 815 CYS Chi-restraints excluded: chain D residue 587 GLN Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 39 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 227 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 216 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 ASN E 198 HIS G 78 GLN H 8 GLN H 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.189332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130150 restraints weight = 29699.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123462 restraints weight = 33745.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.116700 restraints weight = 20581.693| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18703 Z= 0.151 Angle : 0.599 10.233 25234 Z= 0.314 Chirality : 0.042 0.236 2826 Planarity : 0.004 0.044 3106 Dihedral : 4.761 55.705 2531 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.70 % Favored : 97.17 % Rotamer: Outliers : 2.81 % Allowed : 14.12 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2298 helix: 1.79 (0.15), residues: 1238 sheet: -0.55 (0.41), residues: 158 loop : -1.05 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 671 HIS 0.007 0.001 HIS H 204 PHE 0.021 0.002 PHE C 659 TYR 0.025 0.001 TYR A 450 ARG 0.006 0.000 ARG D 661 Details of bonding type rmsd hydrogen bonds : bond 0.05756 ( 934) hydrogen bonds : angle 4.10324 ( 2673) SS BOND : bond 0.00399 ( 12) SS BOND : angle 1.50003 ( 24) covalent geometry : bond 0.00349 (18690) covalent geometry : angle 0.59741 (25210) Misc. bond : bond 0.00299 ( 1) *********************** 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 316 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 VAL cc_start: 0.8494 (t) cc_final: 0.8064 (m) REVERT: A 407 MET cc_start: 0.6085 (mpp) cc_final: 0.5819 (mpp) REVERT: A 503 MET cc_start: 0.5787 (ttt) cc_final: 0.5366 (tmm) REVERT: A 670 MET cc_start: 0.8104 (mmm) cc_final: 0.7881 (mmm) REVERT: A 816 TYR cc_start: 0.6023 (t80) cc_final: 0.5619 (t80) REVERT: A 819 ARG cc_start: 0.5368 (mmt-90) cc_final: 0.4828 (ttm170) REVERT: B 659 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.7799 (t80) REVERT: B 670 MET cc_start: 0.6568 (tpp) cc_final: 0.5863 (mmt) REVERT: B 671 TRP cc_start: 0.7438 (t-100) cc_final: 0.6903 (t-100) REVERT: B 705 GLU cc_start: 0.6726 (mp0) cc_final: 0.6443 (mp0) REVERT: B 756 GLN cc_start: 0.6102 (OUTLIER) cc_final: 0.5702 (mp10) REVERT: C 397 VAL cc_start: 0.8382 (t) cc_final: 0.7987 (m) REVERT: C 401 LEU cc_start: 0.8354 (pp) cc_final: 0.7983 (mm) REVERT: C 496 MET cc_start: 0.7909 (ptm) cc_final: 0.7684 (ptm) REVERT: C 503 MET cc_start: 0.5843 (tmm) cc_final: 0.5486 (tmm) REVERT: C 702 TYR cc_start: 0.7879 (t80) cc_final: 0.7234 (t80) REVERT: C 816 TYR cc_start: 0.5812 (t80) cc_final: 0.5504 (t80) REVERT: C 819 ARG cc_start: 0.5603 (mmt-90) cc_final: 0.4663 (ttm170) REVERT: D 411 ASN cc_start: 0.9201 (t0) cc_final: 0.8911 (t0) REVERT: D 668 ASP cc_start: 0.8799 (t0) cc_final: 0.8511 (m-30) REVERT: D 671 TRP cc_start: 0.7168 (t-100) cc_final: 0.6779 (t-100) REVERT: D 714 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8505 (mt0) REVERT: D 756 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.5905 (mp10) REVERT: E 81 HIS cc_start: 0.6598 (m90) cc_final: 0.5855 (m-70) REVERT: F 81 HIS cc_start: 0.6384 (m90) cc_final: 0.5898 (m90) REVERT: F 98 ARG cc_start: 0.8201 (mmm-85) cc_final: 0.7899 (mmm-85) REVERT: F 130 ARG cc_start: 0.7801 (mtt180) cc_final: 0.7425 (mmm160) REVERT: H 57 MET cc_start: 0.7091 (tpp) cc_final: 0.6666 (mmt) REVERT: H 81 HIS cc_start: 0.6176 (m90) cc_final: 0.5623 (m-70) REVERT: H 98 ARG cc_start: 0.8214 (mmm-85) cc_final: 0.7949 (mmm-85) REVERT: H 121 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8180 (tp) REVERT: H 206 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7940 (tp40) outliers start: 55 outliers final: 37 residues processed: 291 average time/residue: 0.3060 time to fit residues: 134.5781 Evaluate side-chains 281 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 815 CYS Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 96 PHE Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 206 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 119 optimal weight: 0.0020 chunk 181 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN D 726 ASN E 198 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.187560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.125935 restraints weight = 29821.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.121715 restraints weight = 29188.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114683 restraints weight = 17715.024| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18703 Z= 0.183 Angle : 0.621 9.836 25234 Z= 0.326 Chirality : 0.043 0.317 2826 Planarity : 0.004 0.047 3106 Dihedral : 4.545 52.450 2528 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.09 % Favored : 96.82 % Rotamer: Outliers : 3.22 % Allowed : 14.94 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2298 helix: 1.77 (0.15), residues: 1238 sheet: -0.46 (0.43), residues: 148 loop : -1.04 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 578 HIS 0.022 0.001 HIS E 198 PHE 0.031 0.002 PHE E 126 TYR 0.028 0.002 TYR E 127 ARG 0.005 0.000 ARG H 36 Details of bonding type rmsd hydrogen bonds : bond 0.06509 ( 934) hydrogen bonds : angle 4.26795 ( 2673) SS BOND : bond 0.00467 ( 12) SS BOND : angle 1.45345 ( 24) covalent geometry : bond 0.00432 (18690) covalent geometry : angle 0.62016 (25210) Misc. bond : bond 0.00437 ( 1) *********************** 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 312 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 249 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 VAL cc_start: 0.8559 (t) cc_final: 0.8207 (m) REVERT: A 503 MET cc_start: 0.5655 (ttt) cc_final: 0.5408 (tmm) REVERT: A 816 TYR cc_start: 0.6123 (t80) cc_final: 0.5762 (t80) REVERT: A 819 ARG cc_start: 0.5581 (mmt-90) cc_final: 0.4925 (ttm170) REVERT: B 659 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7881 (t80) REVERT: B 670 MET cc_start: 0.6651 (tpp) cc_final: 0.6129 (mmt) REVERT: B 671 TRP cc_start: 0.7374 (t-100) cc_final: 0.6917 (t-100) REVERT: B 705 GLU cc_start: 0.6620 (mp0) cc_final: 0.6331 (mp0) REVERT: B 756 GLN cc_start: 0.6241 (OUTLIER) cc_final: 0.5796 (mp10) REVERT: B 767 TRP cc_start: 0.7660 (OUTLIER) cc_final: 0.6617 (m-10) REVERT: C 397 VAL cc_start: 0.8506 (t) cc_final: 0.8093 (m) REVERT: C 401 LEU cc_start: 0.8391 (pp) cc_final: 0.8085 (mm) REVERT: C 702 TYR cc_start: 0.7779 (t80) cc_final: 0.7278 (t80) REVERT: C 816 TYR cc_start: 0.5924 (t80) cc_final: 0.5524 (t80) REVERT: C 819 ARG cc_start: 0.5568 (mmt-90) cc_final: 0.4644 (ttm170) REVERT: D 411 ASN cc_start: 0.9014 (t0) cc_final: 0.8794 (t0) REVERT: D 668 ASP cc_start: 0.8729 (t0) cc_final: 0.8442 (m-30) REVERT: D 671 TRP cc_start: 0.7082 (t-100) cc_final: 0.6651 (t-100) REVERT: D 714 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8550 (mt0) REVERT: D 756 GLN cc_start: 0.6309 (OUTLIER) cc_final: 0.6010 (mp10) REVERT: E 198 HIS cc_start: 0.8342 (t70) cc_final: 0.7999 (t70) REVERT: F 98 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7791 (mtt180) REVERT: F 130 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7544 (mmm160) REVERT: F 199 MET cc_start: 0.8118 (ttm) cc_final: 0.7888 (mtp) REVERT: H 57 MET cc_start: 0.7070 (tpp) cc_final: 0.6646 (mmt) REVERT: H 81 HIS cc_start: 0.6259 (m90) cc_final: 0.5944 (m-70) REVERT: H 98 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7909 (mmm-85) REVERT: H 121 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8194 (tp) REVERT: H 206 GLN cc_start: 0.8119 (tp40) cc_final: 0.7881 (tp40) outliers start: 63 outliers final: 48 residues processed: 295 average time/residue: 0.3325 time to fit residues: 146.8676 Evaluate side-chains 285 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 815 CYS Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 212 optimal weight: 0.3980 chunk 95 optimal weight: 0.5980 chunk 223 optimal weight: 0.9980 chunk 98 optimal weight: 0.0000 chunk 83 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.189928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.131149 restraints weight = 29936.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124148 restraints weight = 32008.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117352 restraints weight = 24744.498| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18703 Z= 0.124 Angle : 0.577 11.960 25234 Z= 0.294 Chirality : 0.041 0.285 2826 Planarity : 0.003 0.044 3106 Dihedral : 4.240 52.824 2528 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.48 % Favored : 97.43 % Rotamer: Outliers : 3.38 % Allowed : 15.14 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.18), residues: 2298 helix: 2.10 (0.15), residues: 1234 sheet: -0.42 (0.48), residues: 112 loop : -1.12 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 766 HIS 0.004 0.001 HIS H 204 PHE 0.014 0.001 PHE B 546 TYR 0.022 0.001 TYR E 127 ARG 0.006 0.000 ARG H 36 Details of bonding type rmsd hydrogen bonds : bond 0.05070 ( 934) hydrogen bonds : angle 4.00147 ( 2673) SS BOND : bond 0.00398 ( 12) SS BOND : angle 1.27425 ( 24) covalent geometry : bond 0.00278 (18690) covalent geometry : angle 0.57595 (25210) Misc. bond : bond 0.00338 ( 1) *********************** 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 313 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 247 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 VAL cc_start: 0.8576 (t) cc_final: 0.8146 (m) REVERT: A 503 MET cc_start: 0.5840 (ttt) cc_final: 0.5591 (tmm) REVERT: A 816 TYR cc_start: 0.6073 (t80) cc_final: 0.5606 (t80) REVERT: A 819 ARG cc_start: 0.5598 (mmt-90) cc_final: 0.4999 (ttm170) REVERT: B 466 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: B 629 MET cc_start: 0.3769 (pmm) cc_final: 0.3399 (pmm) REVERT: B 659 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.7971 (t80) REVERT: B 670 MET cc_start: 0.6751 (tpp) cc_final: 0.6266 (mmt) REVERT: B 671 TRP cc_start: 0.7520 (t-100) cc_final: 0.7055 (t-100) REVERT: B 705 GLU cc_start: 0.6824 (mp0) cc_final: 0.6599 (mp0) REVERT: B 756 GLN cc_start: 0.5862 (OUTLIER) cc_final: 0.5428 (mp10) REVERT: B 767 TRP cc_start: 0.7698 (OUTLIER) cc_final: 0.6335 (m-10) REVERT: C 397 VAL cc_start: 0.8470 (t) cc_final: 0.8012 (m) REVERT: C 401 LEU cc_start: 0.8415 (pp) cc_final: 0.8031 (mm) REVERT: C 702 TYR cc_start: 0.7723 (t80) cc_final: 0.7344 (t80) REVERT: C 766 TRP cc_start: 0.5761 (m100) cc_final: 0.5277 (m100) REVERT: C 816 TYR cc_start: 0.5879 (t80) cc_final: 0.5430 (t80) REVERT: C 819 ARG cc_start: 0.5538 (mmt-90) cc_final: 0.4630 (ttm170) REVERT: D 411 ASN cc_start: 0.9178 (t0) cc_final: 0.8811 (t0) REVERT: D 668 ASP cc_start: 0.8937 (t0) cc_final: 0.8469 (m-30) REVERT: D 671 TRP cc_start: 0.7439 (t-100) cc_final: 0.7048 (t-100) REVERT: D 714 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8520 (mt0) REVERT: D 756 GLN cc_start: 0.6116 (OUTLIER) cc_final: 0.5855 (mp10) REVERT: E 198 HIS cc_start: 0.8207 (t70) cc_final: 0.7791 (t70) REVERT: F 98 ARG cc_start: 0.8239 (mmm-85) cc_final: 0.7870 (mmm-85) REVERT: F 130 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7432 (mmm160) REVERT: F 199 MET cc_start: 0.8173 (ttm) cc_final: 0.7785 (mtp) REVERT: H 57 MET cc_start: 0.7142 (tpp) cc_final: 0.6702 (mmt) REVERT: H 65 THR cc_start: 0.8424 (m) cc_final: 0.7944 (p) REVERT: H 81 HIS cc_start: 0.6175 (m90) cc_final: 0.5605 (m-70) REVERT: H 98 ARG cc_start: 0.8301 (mmm-85) cc_final: 0.7912 (mmm-85) REVERT: H 121 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8047 (tp) outliers start: 66 outliers final: 43 residues processed: 292 average time/residue: 0.3915 time to fit residues: 173.0301 Evaluate side-chains 276 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 227 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 815 CYS Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 659 PHE Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 171 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 0.0030 chunk 198 optimal weight: 0.2980 chunk 109 optimal weight: 0.1980 chunk 93 optimal weight: 8.9990 chunk 59 optimal weight: 0.0030 chunk 132 optimal weight: 6.9990 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 ASN E 204 HIS H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.193183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3672 r_free = 0.3672 target = 0.127939 restraints weight = 29968.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122060 restraints weight = 22575.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122628 restraints weight = 18991.751| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18703 Z= 0.104 Angle : 0.561 11.456 25234 Z= 0.282 Chirality : 0.040 0.260 2826 Planarity : 0.003 0.040 3106 Dihedral : 4.009 54.252 2528 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.52 % Favored : 97.39 % Rotamer: Outliers : 2.10 % Allowed : 17.29 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 2298 helix: 2.31 (0.15), residues: 1236 sheet: -0.44 (0.49), residues: 112 loop : -1.04 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 767 HIS 0.003 0.001 HIS D 412 PHE 0.024 0.001 PHE E 126 TYR 0.021 0.001 TYR A 702 ARG 0.008 0.000 ARG H 36 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 934) hydrogen bonds : angle 3.89823 ( 2673) SS BOND : bond 0.00377 ( 12) SS BOND : angle 1.14038 ( 24) covalent geometry : bond 0.00219 (18690) covalent geometry : angle 0.56029 (25210) Misc. bond : bond 0.00258 ( 1) *********************** 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 302 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 VAL cc_start: 0.8672 (t) cc_final: 0.8251 (m) REVERT: A 407 MET cc_start: 0.5929 (mpp) cc_final: 0.5635 (mpp) REVERT: A 816 TYR cc_start: 0.5901 (t80) cc_final: 0.5502 (t80) REVERT: A 819 ARG cc_start: 0.5248 (mmt-90) cc_final: 0.4594 (ttm170) REVERT: B 629 MET cc_start: 0.3601 (pmm) cc_final: 0.3273 (pmm) REVERT: B 659 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.7951 (t80) REVERT: B 670 MET cc_start: 0.6711 (tpp) cc_final: 0.6246 (mmt) REVERT: B 671 TRP cc_start: 0.7508 (t-100) cc_final: 0.7045 (t-100) REVERT: B 705 GLU cc_start: 0.6861 (mp0) cc_final: 0.6537 (mp0) REVERT: B 756 GLN cc_start: 0.5948 (OUTLIER) cc_final: 0.5497 (mp10) REVERT: B 767 TRP cc_start: 0.7769 (OUTLIER) cc_final: 0.6599 (m-10) REVERT: C 397 VAL cc_start: 0.8506 (t) cc_final: 0.8120 (m) REVERT: C 401 LEU cc_start: 0.8258 (pp) cc_final: 0.8020 (mm) REVERT: C 651 ASP cc_start: 0.7264 (t70) cc_final: 0.6863 (p0) REVERT: C 674 MET cc_start: 0.7670 (mmm) cc_final: 0.7461 (mmm) REVERT: C 702 TYR cc_start: 0.7717 (t80) cc_final: 0.7251 (t80) REVERT: C 816 TYR cc_start: 0.5818 (t80) cc_final: 0.5468 (t80) REVERT: C 819 ARG cc_start: 0.5342 (mmt-90) cc_final: 0.4545 (ttm170) REVERT: D 411 ASN cc_start: 0.9196 (t0) cc_final: 0.8850 (t0) REVERT: D 668 ASP cc_start: 0.8938 (t0) cc_final: 0.8473 (m-30) REVERT: D 705 GLU cc_start: 0.7034 (mp0) cc_final: 0.6675 (mp0) REVERT: D 714 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8566 (mt0) REVERT: D 756 GLN cc_start: 0.6101 (OUTLIER) cc_final: 0.5890 (mp10) REVERT: E 198 HIS cc_start: 0.8024 (t70) cc_final: 0.7613 (t70) REVERT: F 65 THR cc_start: 0.8596 (m) cc_final: 0.7906 (p) REVERT: F 81 HIS cc_start: 0.6248 (m90) cc_final: 0.6043 (m90) REVERT: F 98 ARG cc_start: 0.8182 (mmm-85) cc_final: 0.7685 (mtp85) REVERT: F 130 ARG cc_start: 0.7839 (mtt180) cc_final: 0.7492 (mmm160) REVERT: H 65 THR cc_start: 0.8522 (m) cc_final: 0.8053 (p) REVERT: H 81 HIS cc_start: 0.6271 (m90) cc_final: 0.5692 (m90) REVERT: H 98 ARG cc_start: 0.8242 (mmm-85) cc_final: 0.7767 (mmm-85) REVERT: H 121 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7938 (tp) outliers start: 41 outliers final: 29 residues processed: 288 average time/residue: 0.3263 time to fit residues: 139.4976 Evaluate side-chains 269 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 815 CYS Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 659 PHE Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain H residue 121 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 128 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 139 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 230 optimal weight: 1.9990 chunk 198 optimal weight: 0.5980 chunk 171 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 ASN H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.190487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121603 restraints weight = 29898.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116308 restraints weight = 22207.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116838 restraints weight = 18675.701| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18703 Z= 0.131 Angle : 0.602 11.202 25234 Z= 0.303 Chirality : 0.042 0.322 2826 Planarity : 0.003 0.041 3106 Dihedral : 4.063 53.080 2528 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 2.71 % Allowed : 17.70 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.18), residues: 2298 helix: 2.15 (0.15), residues: 1250 sheet: -0.43 (0.50), residues: 110 loop : -1.09 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 671 HIS 0.004 0.001 HIS H 204 PHE 0.021 0.001 PHE E 126 TYR 0.024 0.001 TYR E 127 ARG 0.007 0.000 ARG H 36 Details of bonding type rmsd hydrogen bonds : bond 0.05145 ( 934) hydrogen bonds : angle 4.10362 ( 2673) SS BOND : bond 0.00387 ( 12) SS BOND : angle 1.09190 ( 24) covalent geometry : bond 0.00298 (18690) covalent geometry : angle 0.60178 (25210) Misc. bond : bond 0.00290 ( 1) *********************** 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 298 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 245 time to evaluate : 2.151 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: A 397 VAL cc_start: 0.8644 (t) cc_final: 0.8262 (m) REVERT: A 407 MET cc_start: 0.5888 (mpp) cc_final: 0.5613 (mpp) REVERT: A 702 TYR cc_start: 0.8196 (t80) cc_final: 0.7932 (t80) REVERT: A 816 TYR cc_start: 0.6026 (t80) cc_final: 0.5577 (t80) REVERT: A 819 ARG cc_start: 0.5411 (mmt-90) cc_final: 0.4754 (ttm170) REVERT: B 466 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: B 629 MET cc_start: 0.3859 (pmm) cc_final: 0.3556 (pmm) REVERT: B 659 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8013 (t80) REVERT: B 670 MET cc_start: 0.6697 (tpp) cc_final: 0.6264 (mmt) REVERT: B 671 TRP cc_start: 0.7549 (t-100) cc_final: 0.7095 (t-100) REVERT: B 705 GLU cc_start: 0.6936 (mp0) cc_final: 0.6584 (mp0) REVERT: B 756 GLN cc_start: 0.5906 (OUTLIER) cc_final: 0.5447 (mp10) REVERT: B 767 TRP cc_start: 0.7716 (OUTLIER) cc_final: 0.6331 (m-10) REVERT: C 397 VAL cc_start: 0.8567 (t) cc_final: 0.8175 (m) REVERT: C 401 LEU cc_start: 0.8332 (pp) cc_final: 0.8054 (mm) REVERT: C 702 TYR cc_start: 0.7655 (t80) cc_final: 0.7141 (t80) REVERT: C 703 LEU cc_start: 0.8441 (pt) cc_final: 0.8187 (pp) REVERT: C 816 TYR cc_start: 0.5889 (t80) cc_final: 0.5516 (t80) REVERT: C 819 ARG cc_start: 0.5470 (mmt-90) cc_final: 0.4621 (ttm170) REVERT: D 407 MET cc_start: 0.7534 (ppp) cc_final: 0.6538 (ppp) REVERT: D 411 ASN cc_start: 0.9228 (t0) cc_final: 0.8893 (t0) REVERT: D 668 ASP cc_start: 0.8980 (t0) cc_final: 0.8527 (m-30) REVERT: D 705 GLU cc_start: 0.7108 (mp0) cc_final: 0.6766 (mp0) REVERT: D 714 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8508 (mt0) REVERT: D 756 GLN cc_start: 0.6048 (OUTLIER) cc_final: 0.5845 (mp10) REVERT: E 198 HIS cc_start: 0.8091 (t70) cc_final: 0.7694 (t70) REVERT: F 65 THR cc_start: 0.8586 (m) cc_final: 0.7900 (p) REVERT: F 81 HIS cc_start: 0.6149 (m90) cc_final: 0.5893 (m90) REVERT: F 98 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7758 (mtp85) REVERT: F 130 ARG cc_start: 0.7863 (mtt180) cc_final: 0.7483 (mmm160) REVERT: H 65 THR cc_start: 0.8389 (m) cc_final: 0.7921 (p) REVERT: H 81 HIS cc_start: 0.6287 (m90) cc_final: 0.6024 (m-70) REVERT: H 98 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.7878 (mtp85) outliers start: 53 outliers final: 42 residues processed: 280 average time/residue: 0.3286 time to fit residues: 137.7062 Evaluate side-chains 284 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 237 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 815 CYS Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 76 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 184 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 95 optimal weight: 0.0980 chunk 163 optimal weight: 0.9980 chunk 226 optimal weight: 0.7980 chunk 41 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.189872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.133127 restraints weight = 30201.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122387 restraints weight = 36003.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.118226 restraints weight = 25094.374| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18703 Z= 0.139 Angle : 0.608 11.512 25234 Z= 0.309 Chirality : 0.042 0.326 2826 Planarity : 0.004 0.045 3106 Dihedral : 4.094 50.901 2528 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 2.92 % Allowed : 17.44 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.18), residues: 2298 helix: 2.12 (0.15), residues: 1240 sheet: -0.40 (0.50), residues: 110 loop : -1.11 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 671 HIS 0.006 0.001 HIS H 204 PHE 0.043 0.001 PHE E 126 TYR 0.020 0.001 TYR E 127 ARG 0.008 0.000 ARG H 36 Details of bonding type rmsd hydrogen bonds : bond 0.05447 ( 934) hydrogen bonds : angle 4.17781 ( 2673) SS BOND : bond 0.00378 ( 12) SS BOND : angle 1.05020 ( 24) covalent geometry : bond 0.00321 (18690) covalent geometry : angle 0.60742 (25210) Misc. bond : bond 0.00403 ( 1) *********************** 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 293 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 VAL cc_start: 0.8465 (t) cc_final: 0.8039 (m) REVERT: A 816 TYR cc_start: 0.5940 (t80) cc_final: 0.5567 (t80) REVERT: A 819 ARG cc_start: 0.5711 (mmt-90) cc_final: 0.4976 (ttm170) REVERT: B 659 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8043 (t80) REVERT: B 670 MET cc_start: 0.6638 (tpp) cc_final: 0.6219 (mmt) REVERT: B 671 TRP cc_start: 0.7561 (t-100) cc_final: 0.7110 (t-100) REVERT: B 705 GLU cc_start: 0.6937 (mp0) cc_final: 0.6590 (mp0) REVERT: B 767 TRP cc_start: 0.7729 (OUTLIER) cc_final: 0.6238 (m-10) REVERT: C 397 VAL cc_start: 0.8608 (t) cc_final: 0.8238 (m) REVERT: C 401 LEU cc_start: 0.8344 (pp) cc_final: 0.8040 (mm) REVERT: C 674 MET cc_start: 0.7460 (mmm) cc_final: 0.6978 (mmm) REVERT: C 702 TYR cc_start: 0.7741 (t80) cc_final: 0.7352 (t80) REVERT: C 816 TYR cc_start: 0.5922 (t80) cc_final: 0.5534 (t80) REVERT: C 819 ARG cc_start: 0.5540 (mmt-90) cc_final: 0.4680 (ttm170) REVERT: D 407 MET cc_start: 0.7539 (ppp) cc_final: 0.6490 (ppp) REVERT: D 411 ASN cc_start: 0.9235 (t0) cc_final: 0.9020 (t0) REVERT: D 668 ASP cc_start: 0.9043 (t0) cc_final: 0.8470 (m-30) REVERT: D 705 GLU cc_start: 0.7209 (mp0) cc_final: 0.6810 (mp0) REVERT: D 714 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8511 (mt0) REVERT: E 198 HIS cc_start: 0.8042 (t70) cc_final: 0.7657 (t70) REVERT: F 65 THR cc_start: 0.8558 (m) cc_final: 0.7857 (p) REVERT: F 81 HIS cc_start: 0.6224 (m90) cc_final: 0.6018 (m-70) REVERT: F 98 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7840 (mtp85) REVERT: F 130 ARG cc_start: 0.7881 (mtt180) cc_final: 0.7452 (mmm160) REVERT: F 199 MET cc_start: 0.7905 (ttm) cc_final: 0.7671 (mtp) REVERT: H 57 MET cc_start: 0.7172 (tpp) cc_final: 0.6749 (mmt) REVERT: H 65 THR cc_start: 0.8464 (m) cc_final: 0.7965 (p) REVERT: H 98 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.7943 (mtp85) outliers start: 57 outliers final: 50 residues processed: 276 average time/residue: 0.3291 time to fit residues: 135.6491 Evaluate side-chains 276 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 224 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 815 CYS Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 659 PHE Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 135 optimal weight: 0.0970 chunk 112 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.188297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.127248 restraints weight = 29925.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.127017 restraints weight = 28865.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122149 restraints weight = 20969.025| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18703 Z= 0.163 Angle : 0.642 11.488 25234 Z= 0.325 Chirality : 0.043 0.379 2826 Planarity : 0.004 0.047 3106 Dihedral : 4.240 48.759 2528 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.00 % Favored : 96.91 % Rotamer: Outliers : 2.81 % Allowed : 18.06 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.17), residues: 2298 helix: 1.99 (0.15), residues: 1244 sheet: -0.33 (0.50), residues: 110 loop : -1.12 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 671 HIS 0.005 0.001 HIS H 204 PHE 0.038 0.002 PHE E 126 TYR 0.024 0.002 TYR A 702 ARG 0.008 0.000 ARG H 36 Details of bonding type rmsd hydrogen bonds : bond 0.06075 ( 934) hydrogen bonds : angle 4.35848 ( 2673) SS BOND : bond 0.00386 ( 12) SS BOND : angle 1.08771 ( 24) covalent geometry : bond 0.00383 (18690) covalent geometry : angle 0.64182 (25210) Misc. bond : bond 0.00514 ( 1) ********************** 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 288 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 233 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 VAL cc_start: 0.8563 (t) cc_final: 0.8252 (m) REVERT: A 816 TYR cc_start: 0.6085 (t80) cc_final: 0.5412 (t80) REVERT: A 819 ARG cc_start: 0.5788 (mmt-90) cc_final: 0.4991 (ttm170) REVERT: B 629 MET cc_start: 0.3265 (pmm) cc_final: 0.2896 (pmm) REVERT: B 659 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7857 (t80) REVERT: B 670 MET cc_start: 0.6544 (tpp) cc_final: 0.6286 (mmt) REVERT: B 671 TRP cc_start: 0.7216 (t-100) cc_final: 0.6905 (t-100) REVERT: B 705 GLU cc_start: 0.6337 (mp0) cc_final: 0.6109 (mp0) REVERT: B 767 TRP cc_start: 0.7533 (OUTLIER) cc_final: 0.5764 (m-10) REVERT: C 397 VAL cc_start: 0.8695 (t) cc_final: 0.8421 (m) REVERT: C 674 MET cc_start: 0.6916 (mmm) cc_final: 0.6652 (mmm) REVERT: C 702 TYR cc_start: 0.7408 (t80) cc_final: 0.7189 (t80) REVERT: C 816 TYR cc_start: 0.6029 (t80) cc_final: 0.5576 (t80) REVERT: C 819 ARG cc_start: 0.5671 (mmt-90) cc_final: 0.4779 (ttm170) REVERT: D 407 MET cc_start: 0.7698 (ppp) cc_final: 0.6522 (ppp) REVERT: D 411 ASN cc_start: 0.8848 (t0) cc_final: 0.8644 (t0) REVERT: E 198 HIS cc_start: 0.8188 (t70) cc_final: 0.7799 (t70) REVERT: F 81 HIS cc_start: 0.6262 (m90) cc_final: 0.5789 (m-70) REVERT: F 98 ARG cc_start: 0.8165 (mmm-85) cc_final: 0.7779 (mtt180) REVERT: F 199 MET cc_start: 0.7988 (ttm) cc_final: 0.7702 (mtp) REVERT: G 198 HIS cc_start: 0.8001 (t-90) cc_final: 0.7529 (t70) REVERT: H 57 MET cc_start: 0.7078 (tpp) cc_final: 0.6682 (mmt) REVERT: H 65 THR cc_start: 0.8569 (m) cc_final: 0.8060 (p) REVERT: H 98 ARG cc_start: 0.8226 (mmm-85) cc_final: 0.7936 (mtp85) outliers start: 55 outliers final: 51 residues processed: 273 average time/residue: 0.3062 time to fit residues: 126.2275 Evaluate side-chains 272 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 815 CYS Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 659 PHE Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 225 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 120 optimal weight: 0.0030 chunk 20 optimal weight: 0.8980 chunk 189 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 642 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.190540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 125)---------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118083 restraints weight = 30000.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.116519 restraints weight = 19506.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116976 restraints weight = 17274.900| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18703 Z= 0.126 Angle : 0.622 11.665 25234 Z= 0.311 Chirality : 0.042 0.322 2826 Planarity : 0.004 0.044 3106 Dihedral : 4.101 49.733 2528 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 2.46 % Allowed : 18.93 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.18), residues: 2298 helix: 2.16 (0.15), residues: 1238 sheet: -0.32 (0.48), residues: 122 loop : -1.13 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 766 HIS 0.004 0.001 HIS H 204 PHE 0.037 0.001 PHE E 126 TYR 0.015 0.001 TYR A 523 ARG 0.008 0.000 ARG H 36 Details of bonding type rmsd hydrogen bonds : bond 0.05002 ( 934) hydrogen bonds : angle 4.17066 ( 2673) SS BOND : bond 0.00338 ( 12) SS BOND : angle 0.99771 ( 24) covalent geometry : bond 0.00279 (18690) covalent geometry : angle 0.62196 (25210) Misc. bond : bond 0.00382 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7275.65 seconds wall clock time: 128 minutes 17.11 seconds (7697.11 seconds total)