Starting phenix.real_space_refine on Sun Aug 24 08:23:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dhr_46874/08_2025/9dhr_46874.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dhr_46874/08_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_46874/08_2025/9dhr_46874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dhr_46874/08_2025/9dhr_46874.map" model { file = "/net/cci-nas-00/data/ceres_data/9dhr_46874/08_2025/9dhr_46874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dhr_46874/08_2025/9dhr_46874.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.74, per 1000 atoms: 0.26 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: 1.58 Conformation dependent library (CDL) restraints added in 803.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.52 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: 3.28 Time building geometry restraints manager: 2.04 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 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: 8.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.640 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.910 ------------------------------------------------------------------------------- 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 : 3.08 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (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 ARG 0.020 0.003 ARG B 453 TYR 0.013 0.002 TYR H 155 PHE 0.027 0.002 PHE B 608 TRP 0.115 0.009 TRP A 578 HIS 0.004 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.01419 (18690) covalent geometry : angle 0.83731 (25210) SS BOND : bond 0.00135 ( 12) SS BOND : angle 0.93731 ( 24) hydrogen bonds : bond 0.17746 ( 934) hydrogen bonds : angle 6.07610 ( 2673) 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 : 0.648 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: 0.1801 time to fit residues: 131.8057 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 : 0.754 ------------------------------------------------------------------------------- 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 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 194 optimal weight: 0.0570 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.4449 r_free = 0.4449 target = 0.195447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3646 r_free = 0.3646 target = 0.127462 restraints weight = 29247.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125191 restraints weight = 20203.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124880 restraints weight = 17395.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125400 restraints weight = 17378.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.125503 restraints weight = 15203.877| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 18703 Z= 0.137 Angle : 0.633 11.895 25234 Z= 0.334 Chirality : 0.042 0.174 2826 Planarity : 0.004 0.048 3106 Dihedral : 5.472 60.518 2542 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.35 % Favored : 97.43 % Rotamer: Outliers : 1.79 % Allowed : 9.62 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.17), residues: 2298 helix: 1.19 (0.15), residues: 1220 sheet: -0.60 (0.45), residues: 122 loop : -0.97 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 661 TYR 0.015 0.001 TYR C 732 PHE 0.024 0.002 PHE C 495 TRP 0.018 0.002 TRP A 671 HIS 0.006 0.001 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00300 (18690) covalent geometry : angle 0.63198 (25210) SS BOND : bond 0.00555 ( 12) SS BOND : angle 1.50884 ( 24) hydrogen bonds : bond 0.04935 ( 934) hydrogen bonds : angle 4.15258 ( 2673) Misc. bond : bond 0.00185 ( 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 403 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 368 time to evaluate : 0.598 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: A 428 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8586 (mm) REVERT: A 503 MET cc_start: 0.5709 (ttt) cc_final: 0.5424 (tmm) REVERT: A 674 MET cc_start: 0.8529 (mtm) cc_final: 0.8285 (ttm) REVERT: B 486 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8227 (pt0) REVERT: B 651 ASP cc_start: 0.8493 (m-30) cc_final: 0.8231 (m-30) REVERT: B 659 PHE cc_start: 0.8785 (m-80) cc_final: 0.8475 (t80) REVERT: B 660 ARG cc_start: 0.9253 (ttm170) cc_final: 0.8947 (ttm110) REVERT: B 661 ARG cc_start: 0.9227 (ttm170) cc_final: 0.8806 (tmt170) REVERT: B 671 TRP cc_start: 0.7679 (t-100) cc_final: 0.7295 (t-100) REVERT: B 684 ARG cc_start: 0.7017 (tpt170) cc_final: 0.6788 (tpt170) REVERT: B 705 GLU cc_start: 0.7085 (mp0) cc_final: 0.6838 (mp0) REVERT: B 714 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8599 (mt0) REVERT: C 401 LEU cc_start: 0.8380 (pp) cc_final: 0.7576 (mm) REVERT: C 503 MET cc_start: 0.5936 (ttt) cc_final: 0.5702 (tmm) REVERT: C 807 MET cc_start: 0.8671 (ttp) cc_final: 0.8450 (ttm) REVERT: C 819 ARG cc_start: 0.4980 (mmt-90) cc_final: 0.4333 (ttm170) REVERT: D 411 ASN cc_start: 0.9419 (t0) cc_final: 0.9203 (t0) REVERT: D 629 MET cc_start: 0.6612 (ppp) cc_final: 0.6336 (mtp) REVERT: D 660 ARG cc_start: 0.9377 (ttm170) cc_final: 0.9010 (ttm110) REVERT: D 678 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6987 (mm-30) REVERT: D 714 GLN cc_start: 0.8723 (mm-40) cc_final: 0.7872 (mt0) REVERT: D 751 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7685 (mp) REVERT: F 81 HIS cc_start: 0.6493 (m90) cc_final: 0.5998 (m-70) REVERT: F 98 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.8033 (mmm-85) REVERT: F 130 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7321 (mmm160) REVERT: H 81 HIS cc_start: 0.6215 (m90) cc_final: 0.5602 (m-70) REVERT: H 98 ARG cc_start: 0.8312 (mmm-85) cc_final: 0.7970 (mmm-85) REVERT: H 100 VAL cc_start: 0.9260 (t) cc_final: 0.9026 (m) outliers start: 35 outliers final: 16 residues processed: 389 average time/residue: 0.1613 time to fit residues: 90.0492 Evaluate side-chains 290 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 272 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 585 MET Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain B residue 412 HIS 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 58 THR 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 60 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 93 optimal weight: 0.0050 chunk 188 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 109 optimal weight: 0.0370 overall best weight: 1.0078 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.189309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118182 restraints weight = 29312.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114767 restraints weight = 20933.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114971 restraints weight = 16879.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115447 restraints weight = 15858.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.115562 restraints weight = 14960.589| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18703 Z= 0.174 Angle : 0.655 13.164 25234 Z= 0.341 Chirality : 0.043 0.240 2826 Planarity : 0.004 0.049 3106 Dihedral : 4.926 56.626 2531 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.96 % Favored : 96.87 % Rotamer: Outliers : 2.66 % Allowed : 13.30 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.17), residues: 2298 helix: 1.49 (0.15), residues: 1240 sheet: -0.45 (0.44), residues: 144 loop : -0.94 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 661 TYR 0.019 0.002 TYR H 31 PHE 0.019 0.002 PHE D 608 TRP 0.024 0.002 TRP B 767 HIS 0.005 0.001 HIS E 59 Details of bonding type rmsd covalent geometry : bond 0.00407 (18690) covalent geometry : angle 0.65275 (25210) SS BOND : bond 0.00461 ( 12) SS BOND : angle 1.82522 ( 24) hydrogen bonds : bond 0.06453 ( 934) hydrogen bonds : angle 4.26716 ( 2673) Misc. bond : bond 0.00607 ( 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 346 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 294 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 VAL cc_start: 0.8375 (t) cc_final: 0.7923 (m) REVERT: A 428 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8633 (mm) REVERT: A 463 MET cc_start: 0.7533 (mtp) cc_final: 0.7200 (mtp) REVERT: A 503 MET cc_start: 0.5562 (ttt) cc_final: 0.5076 (tmm) REVERT: A 816 TYR cc_start: 0.6022 (t80) cc_final: 0.5581 (t80) REVERT: B 651 ASP cc_start: 0.8324 (m-30) cc_final: 0.7816 (p0) REVERT: B 659 PHE cc_start: 0.8810 (m-80) cc_final: 0.8527 (t80) REVERT: B 661 ARG cc_start: 0.9114 (ttm170) cc_final: 0.8759 (tmt170) REVERT: B 670 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.6209 (mmm) REVERT: B 671 TRP cc_start: 0.7699 (t-100) cc_final: 0.7196 (t-100) REVERT: B 705 GLU cc_start: 0.6962 (mp0) cc_final: 0.6668 (mp0) REVERT: B 714 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8658 (mt0) REVERT: B 756 GLN cc_start: 0.5867 (mp10) cc_final: 0.5513 (mp10) REVERT: C 397 VAL cc_start: 0.8212 (t) cc_final: 0.7771 (m) REVERT: C 401 LEU cc_start: 0.8335 (pp) cc_final: 0.7984 (mm) REVERT: C 766 TRP cc_start: 0.5756 (m100) cc_final: 0.5262 (m100) REVERT: C 816 TYR cc_start: 0.5915 (t80) cc_final: 0.5577 (t80) REVERT: C 819 ARG cc_start: 0.5381 (mmt-90) cc_final: 0.4553 (ttm170) REVERT: D 411 ASN cc_start: 0.9347 (t0) cc_final: 0.8977 (t0) REVERT: D 463 MET cc_start: 0.7619 (mpp) cc_final: 0.6607 (mmt) REVERT: D 668 ASP cc_start: 0.9065 (t0) cc_final: 0.8633 (m-30) REVERT: D 671 TRP cc_start: 0.7334 (t-100) cc_final: 0.6673 (t-100) REVERT: D 714 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8364 (mt0) REVERT: D 756 GLN cc_start: 0.6054 (OUTLIER) cc_final: 0.5757 (mp10) REVERT: F 81 HIS cc_start: 0.6353 (m90) cc_final: 0.5824 (m90) REVERT: F 98 ARG cc_start: 0.8218 (mmm-85) cc_final: 0.7903 (mmm-85) REVERT: F 130 ARG cc_start: 0.7744 (mtt180) cc_final: 0.7387 (mmm160) REVERT: H 81 HIS cc_start: 0.6205 (m90) cc_final: 0.5854 (m-70) REVERT: H 98 ARG cc_start: 0.8186 (mmm-85) cc_final: 0.7881 (mmm-85) REVERT: H 206 GLN cc_start: 0.8181 (tp40) cc_final: 0.7236 (tp-100) outliers start: 52 outliers final: 34 residues processed: 324 average time/residue: 0.1461 time to fit residues: 70.7879 Evaluate side-chains 285 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 248 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 651 ASP 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 589 CYS Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 767 TRP 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 486 GLU 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 30 ASP Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 96 PHE Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain H residue 7 VAL 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 217 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 E 198 HIS G 78 GLN H 8 GLN ** 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 = 0.4336 r_free = 0.4336 target = 0.184260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121608 restraints weight = 29217.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119076 restraints weight = 36997.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.119254 restraints weight = 32512.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116493 restraints weight = 26251.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116856 restraints weight = 28129.541| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 18703 Z= 0.265 Angle : 0.706 10.568 25234 Z= 0.374 Chirality : 0.046 0.305 2826 Planarity : 0.005 0.053 3106 Dihedral : 4.969 49.820 2528 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.22 % Favored : 96.65 % Rotamer: Outliers : 3.38 % Allowed : 14.42 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.17), residues: 2298 helix: 1.37 (0.15), residues: 1238 sheet: -0.78 (0.42), residues: 148 loop : -1.12 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 661 TYR 0.025 0.002 TYR A 450 PHE 0.025 0.003 PHE A 608 TRP 0.026 0.002 TRP B 578 HIS 0.006 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00636 (18690) covalent geometry : angle 0.70482 (25210) SS BOND : bond 0.00634 ( 12) SS BOND : angle 1.67886 ( 24) hydrogen bonds : bond 0.07857 ( 934) hydrogen bonds : angle 4.58694 ( 2673) Misc. bond : bond 0.00349 ( 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 334 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 268 time to evaluate : 0.650 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: B 670 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.6117 (mmm) REVERT: B 671 TRP cc_start: 0.7299 (t-100) cc_final: 0.6942 (t-100) REVERT: B 756 GLN cc_start: 0.6636 (OUTLIER) cc_final: 0.6219 (mp10) REVERT: C 397 VAL cc_start: 0.8528 (t) cc_final: 0.8166 (m) REVERT: C 401 LEU cc_start: 0.8424 (pp) cc_final: 0.8182 (mm) REVERT: C 487 GLU cc_start: 0.7921 (pp20) cc_final: 0.7699 (pp20) REVERT: C 702 TYR cc_start: 0.7624 (t80) cc_final: 0.7155 (t80) REVERT: C 819 ARG cc_start: 0.5382 (mmt-90) cc_final: 0.4603 (ttm170) REVERT: D 463 MET cc_start: 0.7384 (mpp) cc_final: 0.6404 (mmt) REVERT: D 587 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8456 (mp10) REVERT: D 671 TRP cc_start: 0.6871 (t-100) cc_final: 0.6480 (t-100) REVERT: D 756 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.6282 (mp10) REVERT: E 81 HIS cc_start: 0.6441 (m90) cc_final: 0.6129 (m-70) REVERT: G 198 HIS cc_start: 0.8056 (t-90) cc_final: 0.7660 (t70) REVERT: H 57 MET cc_start: 0.7128 (tpp) cc_final: 0.6750 (mmt) REVERT: H 81 HIS cc_start: 0.6478 (m90) cc_final: 0.6060 (m-70) REVERT: H 98 ARG cc_start: 0.8193 (mmm-85) cc_final: 0.7851 (mmm-85) REVERT: H 206 GLN cc_start: 0.7994 (tp40) cc_final: 0.7662 (tp40) outliers start: 66 outliers final: 42 residues processed: 313 average time/residue: 0.1398 time to fit residues: 65.2567 Evaluate side-chains 277 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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 815 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 670 MET 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 613 ILE Chi-restraints excluded: chain C residue 788 SER 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 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 188 ILE Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 198 HIS 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 G residue 188 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 40 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 188 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 57 optimal weight: 0.0980 chunk 117 optimal weight: 0.5980 chunk 172 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** C 714 GLN D 726 ASN E 198 HIS H 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.189362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.130790 restraints weight = 29833.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127253 restraints weight = 37979.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118183 restraints weight = 25810.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117190 restraints weight = 24312.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.118146 restraints weight = 21107.773| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5510 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= 0.134 Angle : 0.590 10.213 25234 Z= 0.308 Chirality : 0.041 0.289 2826 Planarity : 0.004 0.047 3106 Dihedral : 4.482 53.031 2528 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % Rotamer: Outliers : 2.86 % Allowed : 16.42 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.18), residues: 2298 helix: 1.85 (0.15), residues: 1236 sheet: -0.54 (0.46), residues: 122 loop : -1.17 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 36 TYR 0.023 0.001 TYR G 127 PHE 0.032 0.001 PHE F 126 TRP 0.019 0.001 TRP D 767 HIS 0.021 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00299 (18690) covalent geometry : angle 0.58853 (25210) SS BOND : bond 0.00416 ( 12) SS BOND : angle 1.32554 ( 24) hydrogen bonds : bond 0.05453 ( 934) hydrogen bonds : angle 4.10478 ( 2673) Misc. bond : bond 0.00446 ( 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 308 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 252 time to evaluate : 0.847 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 816 TYR cc_start: 0.6115 (t80) cc_final: 0.5746 (t80) REVERT: B 629 MET cc_start: 0.4098 (pmm) cc_final: 0.3788 (pmm) REVERT: B 659 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7693 (t80) REVERT: B 670 MET cc_start: 0.6356 (mpp) cc_final: 0.5767 (mmm) REVERT: B 671 TRP cc_start: 0.7380 (t-100) cc_final: 0.6895 (t-100) REVERT: B 756 GLN cc_start: 0.6323 (OUTLIER) cc_final: 0.5916 (mp10) REVERT: C 397 VAL cc_start: 0.8548 (t) cc_final: 0.8191 (m) REVERT: C 401 LEU cc_start: 0.8489 (pp) cc_final: 0.8213 (mm) REVERT: C 496 MET cc_start: 0.7906 (ptm) cc_final: 0.7678 (ptm) REVERT: C 702 TYR cc_start: 0.7556 (t80) cc_final: 0.7197 (t80) REVERT: C 816 TYR cc_start: 0.5869 (t80) cc_final: 0.5532 (t80) REVERT: C 819 ARG cc_start: 0.5650 (mmt-90) cc_final: 0.4725 (ttm170) REVERT: D 463 MET cc_start: 0.7561 (mpp) cc_final: 0.6798 (mmt) REVERT: D 670 MET cc_start: 0.6262 (mtm) cc_final: 0.6014 (ptt) REVERT: D 671 TRP cc_start: 0.6875 (t-100) cc_final: 0.6548 (t-100) REVERT: D 756 GLN cc_start: 0.6440 (OUTLIER) cc_final: 0.6119 (mp10) REVERT: E 198 HIS cc_start: 0.8365 (t70) cc_final: 0.7933 (t70) REVERT: F 98 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7714 (mtp85) REVERT: H 57 MET cc_start: 0.7063 (tpp) cc_final: 0.6671 (mmt) REVERT: H 81 HIS cc_start: 0.6322 (m90) cc_final: 0.5923 (m-70) REVERT: H 98 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7898 (mmm-85) outliers start: 56 outliers final: 36 residues processed: 290 average time/residue: 0.1449 time to fit residues: 62.7160 Evaluate side-chains 264 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 489 ILE 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 659 PHE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain C residue 425 CYS 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 788 SER 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 612 ILE Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 76 CYS 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 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 33 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 159 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 134 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 210 optimal weight: 0.5980 chunk 151 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 ASN D 726 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.189452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.132515 restraints weight = 29760.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.121911 restraints weight = 39425.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116341 restraints weight = 23630.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116645 restraints weight = 24558.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.116992 restraints weight = 20565.391| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5677 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= 0.130 Angle : 0.578 10.679 25234 Z= 0.298 Chirality : 0.041 0.245 2826 Planarity : 0.003 0.045 3106 Dihedral : 4.254 52.560 2528 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 3.43 % Allowed : 16.16 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.18), residues: 2298 helix: 2.05 (0.15), residues: 1236 sheet: -0.43 (0.47), residues: 120 loop : -1.15 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 36 TYR 0.037 0.001 TYR G 127 PHE 0.029 0.001 PHE G 126 TRP 0.015 0.001 TRP B 578 HIS 0.003 0.001 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00291 (18690) covalent geometry : angle 0.57698 (25210) SS BOND : bond 0.00410 ( 12) SS BOND : angle 1.22342 ( 24) hydrogen bonds : bond 0.05268 ( 934) hydrogen bonds : angle 4.03474 ( 2673) Misc. bond : bond 0.00407 ( 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 304 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 237 time to evaluate : 0.721 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: 0.8262 (t) cc_final: 0.7686 (m) REVERT: A 674 MET cc_start: 0.7726 (mmm) cc_final: 0.7465 (mmm) REVERT: A 816 TYR cc_start: 0.6108 (t80) cc_final: 0.5734 (t80) REVERT: B 629 MET cc_start: 0.4301 (pmm) cc_final: 0.4018 (pmm) REVERT: B 659 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7806 (t80) REVERT: B 670 MET cc_start: 0.6371 (mpp) cc_final: 0.5745 (mmt) REVERT: B 671 TRP cc_start: 0.7497 (t-100) cc_final: 0.6981 (t-100) REVERT: B 705 GLU cc_start: 0.7112 (mp0) cc_final: 0.6885 (mp0) REVERT: B 756 GLN cc_start: 0.5986 (OUTLIER) cc_final: 0.5580 (mp10) REVERT: B 767 TRP cc_start: 0.7613 (OUTLIER) cc_final: 0.6049 (m-10) REVERT: C 397 VAL cc_start: 0.8560 (t) cc_final: 0.8167 (m) REVERT: C 401 LEU cc_start: 0.8521 (pp) cc_final: 0.8187 (mm) REVERT: C 702 TYR cc_start: 0.7645 (t80) cc_final: 0.7135 (t80) REVERT: C 766 TRP cc_start: 0.5806 (m100) cc_final: 0.5312 (m100) REVERT: C 816 TYR cc_start: 0.5825 (t80) cc_final: 0.5422 (t80) REVERT: C 819 ARG cc_start: 0.5579 (mmt-90) cc_final: 0.4697 (ttm170) REVERT: D 671 TRP cc_start: 0.7097 (t-100) cc_final: 0.6829 (t-100) REVERT: D 756 GLN cc_start: 0.6173 (OUTLIER) cc_final: 0.5895 (mp10) REVERT: D 767 TRP cc_start: 0.7667 (OUTLIER) cc_final: 0.6876 (m-10) REVERT: E 198 HIS cc_start: 0.8211 (t70) cc_final: 0.7814 (t70) REVERT: F 98 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7779 (mtp85) REVERT: H 5 ARG cc_start: 0.5919 (tmm160) cc_final: 0.5632 (ttp80) REVERT: H 65 THR cc_start: 0.8664 (m) cc_final: 0.7979 (p) REVERT: H 98 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.7918 (mtp85) outliers start: 67 outliers final: 47 residues processed: 286 average time/residue: 0.1477 time to fit residues: 63.6025 Evaluate side-chains 275 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain A residue 549 TYR 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 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 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 425 CYS 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 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 486 GLU Chi-restraints excluded: chain D residue 543 VAL 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 626 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 767 TRP 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 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 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 158 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 chunk 210 optimal weight: 0.6980 chunk 113 optimal weight: 0.1980 chunk 123 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 230 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.188729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129337 restraints weight = 29761.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.123968 restraints weight = 36926.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114825 restraints weight = 28814.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115219 restraints weight = 27132.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.116038 restraints weight = 22891.107| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5895 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= 0.140 Angle : 0.591 10.811 25234 Z= 0.303 Chirality : 0.041 0.269 2826 Planarity : 0.004 0.046 3106 Dihedral : 4.206 51.097 2528 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.95 % Rotamer: Outliers : 3.17 % Allowed : 17.03 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.18), residues: 2298 helix: 2.06 (0.15), residues: 1238 sheet: -0.32 (0.50), residues: 110 loop : -1.14 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 36 TYR 0.032 0.001 TYR G 127 PHE 0.029 0.001 PHE G 126 TRP 0.016 0.001 TRP B 578 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00322 (18690) covalent geometry : angle 0.59051 (25210) SS BOND : bond 0.00408 ( 12) SS BOND : angle 1.13377 ( 24) hydrogen bonds : bond 0.05560 ( 934) hydrogen bonds : angle 4.09915 ( 2673) Misc. bond : bond 0.00391 ( 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: 62 poor density : 240 time to evaluate : 0.746 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: 0.8292 (t) cc_final: 0.7887 (m) REVERT: A 816 TYR cc_start: 0.6091 (t80) cc_final: 0.5626 (t80) REVERT: B 629 MET cc_start: 0.3815 (pmm) cc_final: 0.3590 (pmm) REVERT: B 659 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7827 (t80) REVERT: B 670 MET cc_start: 0.6524 (tpp) cc_final: 0.6010 (mmt) REVERT: B 671 TRP cc_start: 0.7466 (t-100) cc_final: 0.7009 (t-100) REVERT: B 705 GLU cc_start: 0.6792 (mp0) cc_final: 0.6547 (mp0) REVERT: B 767 TRP cc_start: 0.7575 (OUTLIER) cc_final: 0.5840 (m-10) REVERT: C 397 VAL cc_start: 0.8646 (t) cc_final: 0.8297 (m) REVERT: C 401 LEU cc_start: 0.8519 (pp) cc_final: 0.8252 (mm) REVERT: C 463 MET cc_start: 0.7960 (mmm) cc_final: 0.7744 (mmt) REVERT: C 702 TYR cc_start: 0.7663 (t80) cc_final: 0.7218 (t80) REVERT: C 816 TYR cc_start: 0.5923 (t80) cc_final: 0.5527 (t80) REVERT: C 819 ARG cc_start: 0.5570 (mmt-90) cc_final: 0.4680 (ttm170) REVERT: D 407 MET cc_start: 0.7677 (ppp) cc_final: 0.6556 (ppp) REVERT: D 411 ASN cc_start: 0.9002 (t0) cc_final: 0.8684 (t0) REVERT: D 414 MET cc_start: 0.8903 (pmm) cc_final: 0.8678 (pmm) REVERT: D 670 MET cc_start: 0.6562 (mtm) cc_final: 0.6046 (ptt) REVERT: D 705 GLU cc_start: 0.6886 (mp0) cc_final: 0.6678 (mp0) REVERT: D 756 GLN cc_start: 0.6292 (OUTLIER) cc_final: 0.6022 (mp10) REVERT: D 767 TRP cc_start: 0.7621 (OUTLIER) cc_final: 0.7015 (m-10) REVERT: E 198 HIS cc_start: 0.8177 (t70) cc_final: 0.7766 (t70) REVERT: F 98 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.7990 (mtt-85) REVERT: H 5 ARG cc_start: 0.6000 (tmm160) cc_final: 0.5656 (ttp80) REVERT: H 65 THR cc_start: 0.8737 (m) cc_final: 0.8091 (p) REVERT: H 98 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.7850 (mmm-85) outliers start: 62 outliers final: 48 residues processed: 277 average time/residue: 0.1563 time to fit residues: 64.7241 Evaluate side-chains 275 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain A residue 549 TYR 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 659 PHE Chi-restraints excluded: chain B residue 666 VAL 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 425 CYS Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 549 TYR 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 569 ASN Chi-restraints excluded: chain D residue 587 GLN 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 626 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 76 CYS 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 27 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 100 optimal weight: 0.9990 chunk 179 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 222 optimal weight: 0.2980 chunk 80 optimal weight: 0.6980 chunk 210 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 60 optimal weight: 0.0000 chunk 201 optimal weight: 0.9980 chunk 193 optimal weight: 0.9990 chunk 181 optimal weight: 0.0370 overall best weight: 0.3262 ------------------------------------------------------------------------------- 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 764 ASN E 204 HIS H 78 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 = 0.4425 r_free = 0.4425 target = 0.192280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.129307 restraints weight = 30100.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.121928 restraints weight = 23008.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122439 restraints weight = 22475.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122939 restraints weight = 19610.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123185 restraints weight = 17654.738| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.6026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18703 Z= 0.111 Angle : 0.582 11.537 25234 Z= 0.294 Chirality : 0.041 0.292 2826 Planarity : 0.003 0.042 3106 Dihedral : 4.021 52.782 2528 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 2.20 % Allowed : 18.36 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.18), residues: 2298 helix: 2.19 (0.15), residues: 1244 sheet: -0.37 (0.50), residues: 110 loop : -1.08 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 36 TYR 0.031 0.001 TYR G 127 PHE 0.027 0.001 PHE G 126 TRP 0.010 0.001 TRP C 766 HIS 0.003 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00233 (18690) covalent geometry : angle 0.58166 (25210) SS BOND : bond 0.00363 ( 12) SS BOND : angle 1.01885 ( 24) hydrogen bonds : bond 0.04341 ( 934) hydrogen bonds : angle 3.99129 ( 2673) Misc. bond : bond 0.00403 ( 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 284 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 0.745 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: 0.8285 (t) cc_final: 0.7816 (m) REVERT: A 674 MET cc_start: 0.7718 (mmm) cc_final: 0.7426 (mmm) REVERT: A 816 TYR cc_start: 0.6107 (t80) cc_final: 0.5704 (t80) REVERT: B 659 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7862 (t80) REVERT: B 670 MET cc_start: 0.6477 (tpp) cc_final: 0.5985 (mmt) REVERT: B 671 TRP cc_start: 0.7538 (t-100) cc_final: 0.7060 (t-100) REVERT: B 705 GLU cc_start: 0.6936 (mp0) cc_final: 0.6626 (mp0) REVERT: B 708 MET cc_start: 0.7983 (mpp) cc_final: 0.7781 (mpp) REVERT: B 767 TRP cc_start: 0.7620 (OUTLIER) cc_final: 0.5985 (m-10) REVERT: C 397 VAL cc_start: 0.8579 (t) cc_final: 0.8206 (m) REVERT: C 401 LEU cc_start: 0.8500 (pp) cc_final: 0.8206 (mm) REVERT: C 463 MET cc_start: 0.7986 (mmm) cc_final: 0.7771 (mmt) REVERT: C 702 TYR cc_start: 0.7646 (t80) cc_final: 0.7057 (t80) REVERT: C 703 LEU cc_start: 0.8442 (pt) cc_final: 0.8148 (pp) REVERT: C 816 TYR cc_start: 0.5844 (t80) cc_final: 0.5374 (t80) REVERT: C 819 ARG cc_start: 0.5443 (mmt-90) cc_final: 0.4620 (ttm170) REVERT: D 407 MET cc_start: 0.7567 (ppp) cc_final: 0.6571 (ppp) REVERT: D 411 ASN cc_start: 0.9200 (t0) cc_final: 0.8844 (t0) REVERT: D 414 MET cc_start: 0.9191 (pmm) cc_final: 0.8973 (pmm) REVERT: D 670 MET cc_start: 0.6533 (mtm) cc_final: 0.5411 (ptt) REVERT: D 705 GLU cc_start: 0.7021 (mp0) cc_final: 0.6739 (mp0) REVERT: D 756 GLN cc_start: 0.6138 (OUTLIER) cc_final: 0.5910 (mp10) REVERT: D 767 TRP cc_start: 0.7610 (OUTLIER) cc_final: 0.7246 (m-10) REVERT: E 198 HIS cc_start: 0.8058 (t70) cc_final: 0.7639 (t70) REVERT: F 98 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7793 (mtt180) REVERT: H 5 ARG cc_start: 0.5727 (tmm160) cc_final: 0.5502 (ttp80) REVERT: H 65 THR cc_start: 0.8667 (m) cc_final: 0.8022 (p) REVERT: H 98 ARG cc_start: 0.8229 (mmm-85) cc_final: 0.7830 (mmm-85) outliers start: 43 outliers final: 33 residues processed: 271 average time/residue: 0.1512 time to fit residues: 61.8344 Evaluate side-chains 261 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 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 659 PHE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 425 CYS 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 D residue 412 HIS Chi-restraints excluded: chain D residue 497 SER 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 626 VAL Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 195 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 107 optimal weight: 0.8980 chunk 50 optimal weight: 0.0970 chunk 79 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** H 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.189844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.3605 r_free = 0.3605 target = 0.123486 restraints weight = 29915.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116912 restraints weight = 24039.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117752 restraints weight = 20330.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118246 restraints weight = 18085.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118290 restraints weight = 16849.909| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.6149 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= 0.138 Angle : 0.612 11.283 25234 Z= 0.309 Chirality : 0.042 0.302 2826 Planarity : 0.004 0.044 3106 Dihedral : 4.089 51.530 2528 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.00 % Favored : 96.91 % Rotamer: Outliers : 2.51 % Allowed : 18.57 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.18), residues: 2298 helix: 2.14 (0.15), residues: 1238 sheet: -0.34 (0.50), residues: 110 loop : -1.09 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 36 TYR 0.033 0.001 TYR G 127 PHE 0.026 0.001 PHE G 126 TRP 0.018 0.001 TRP D 671 HIS 0.004 0.001 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00318 (18690) covalent geometry : angle 0.61160 (25210) SS BOND : bond 0.00385 ( 12) SS BOND : angle 0.98292 ( 24) hydrogen bonds : bond 0.05349 ( 934) hydrogen bonds : angle 4.14130 ( 2673) Misc. bond : bond 0.00438 ( 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 278 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 0.738 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: 0.8347 (t) cc_final: 0.7863 (m) REVERT: A 674 MET cc_start: 0.7856 (mmm) cc_final: 0.7492 (mmm) REVERT: A 816 TYR cc_start: 0.6089 (t80) cc_final: 0.5637 (t80) REVERT: B 407 MET cc_start: 0.7620 (ppp) cc_final: 0.6956 (mtm) REVERT: B 659 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.7891 (t80) REVERT: B 670 MET cc_start: 0.6463 (tpp) cc_final: 0.5977 (mmt) REVERT: B 671 TRP cc_start: 0.7548 (t-100) cc_final: 0.7074 (t-100) REVERT: B 705 GLU cc_start: 0.6874 (mp0) cc_final: 0.6479 (mp0) REVERT: B 767 TRP cc_start: 0.7762 (OUTLIER) cc_final: 0.5718 (m-10) REVERT: C 397 VAL cc_start: 0.8606 (t) cc_final: 0.8233 (m) REVERT: C 401 LEU cc_start: 0.8386 (pp) cc_final: 0.8155 (mm) REVERT: C 463 MET cc_start: 0.8124 (mmm) cc_final: 0.7875 (mmt) REVERT: C 674 MET cc_start: 0.7488 (mmm) cc_final: 0.6967 (mmm) REVERT: C 702 TYR cc_start: 0.7721 (t80) cc_final: 0.7220 (t80) REVERT: C 816 TYR cc_start: 0.5995 (t80) cc_final: 0.5503 (t80) REVERT: C 819 ARG cc_start: 0.5510 (mmt-90) cc_final: 0.4644 (ttm170) REVERT: D 407 MET cc_start: 0.7623 (ppp) cc_final: 0.6677 (ppp) REVERT: D 411 ASN cc_start: 0.9215 (t0) cc_final: 0.8925 (t0) REVERT: D 414 MET cc_start: 0.9147 (pmm) cc_final: 0.8931 (pmm) REVERT: D 670 MET cc_start: 0.6355 (mtm) cc_final: 0.6111 (ptt) REVERT: D 705 GLU cc_start: 0.7084 (mp0) cc_final: 0.6770 (mp0) REVERT: D 756 GLN cc_start: 0.6112 (OUTLIER) cc_final: 0.5889 (mp10) REVERT: D 767 TRP cc_start: 0.7709 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: E 198 HIS cc_start: 0.8101 (t70) cc_final: 0.7689 (t70) REVERT: F 98 ARG cc_start: 0.8153 (mmm-85) cc_final: 0.7831 (mtp85) REVERT: H 65 THR cc_start: 0.8662 (m) cc_final: 0.8022 (p) REVERT: H 98 ARG cc_start: 0.8282 (mmm-85) cc_final: 0.7935 (mtp85) outliers start: 49 outliers final: 41 residues processed: 264 average time/residue: 0.1555 time to fit residues: 61.5331 Evaluate side-chains 268 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 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 721 MET 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 425 CYS 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 815 CYS Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 587 GLN 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 626 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 195 LEU 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 121 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.8404 > 50: distance: 67 - 174: 24.755 distance: 70 - 90: 15.267 distance: 74 - 99: 16.547 distance: 80 - 113: 13.743 distance: 84 - 90: 15.063 distance: 85 - 127: 21.243 distance: 90 - 91: 12.375 distance: 91 - 92: 13.657 distance: 91 - 94: 8.645 distance: 92 - 93: 16.152 distance: 92 - 99: 35.700 distance: 94 - 95: 9.845 distance: 95 - 96: 8.761 distance: 96 - 97: 14.332 distance: 97 - 98: 10.707 distance: 99 - 100: 43.703 distance: 100 - 101: 31.473 distance: 100 - 103: 36.962 distance: 101 - 102: 12.864 distance: 101 - 113: 39.598 distance: 103 - 104: 42.921 distance: 104 - 105: 34.448 distance: 104 - 106: 31.580 distance: 105 - 107: 9.612 distance: 106 - 108: 29.649 distance: 106 - 109: 15.601 distance: 107 - 108: 28.428 distance: 108 - 110: 11.387 distance: 109 - 111: 6.296 distance: 110 - 112: 4.138 distance: 111 - 112: 5.067 distance: 113 - 114: 20.164 distance: 114 - 115: 18.717 distance: 114 - 117: 13.462 distance: 115 - 116: 38.134 distance: 115 - 127: 10.428 distance: 117 - 118: 9.864 distance: 118 - 119: 26.288 distance: 118 - 120: 13.624 distance: 119 - 121: 10.341 distance: 120 - 122: 13.703 distance: 120 - 123: 3.959 distance: 121 - 122: 14.324 distance: 122 - 124: 11.002 distance: 124 - 126: 3.961 distance: 127 - 128: 19.532 distance: 128 - 129: 20.075 distance: 128 - 131: 10.978 distance: 129 - 130: 21.478 distance: 129 - 139: 23.958 distance: 131 - 132: 18.947 distance: 132 - 133: 19.631 distance: 132 - 134: 16.629 distance: 133 - 135: 12.721 distance: 134 - 136: 8.824 distance: 135 - 137: 11.632 distance: 136 - 137: 11.961 distance: 137 - 138: 8.004 distance: 139 - 140: 27.729 distance: 140 - 141: 30.528 distance: 140 - 143: 27.954 distance: 141 - 142: 12.294 distance: 141 - 147: 18.141 distance: 143 - 144: 23.271 distance: 144 - 145: 42.408 distance: 144 - 146: 24.132 distance: 147 - 148: 17.142 distance: 148 - 149: 16.451 distance: 148 - 151: 6.730 distance: 149 - 150: 7.238 distance: 149 - 156: 24.087 distance: 151 - 152: 7.478 distance: 152 - 153: 12.237 distance: 153 - 154: 12.623 distance: 154 - 155: 13.349 distance: 156 - 157: 8.359 distance: 157 - 158: 35.926 distance: 158 - 159: 9.252 distance: 158 - 160: 11.111 distance: 160 - 161: 11.158 distance: 161 - 162: 25.489 distance: 161 - 164: 23.000 distance: 162 - 163: 16.429 distance: 162 - 169: 12.726 distance: 164 - 165: 29.139 distance: 165 - 166: 19.215 distance: 166 - 167: 30.945 distance: 166 - 168: 11.278 distance: 169 - 170: 20.472 distance: 170 - 171: 20.214 distance: 170 - 173: 47.947 distance: 171 - 172: 48.960 distance: 171 - 175: 28.569 distance: 173 - 174: 27.475 distance: 175 - 176: 35.507 distance: 176 - 177: 15.281 distance: 177 - 178: 20.876 distance: 177 - 179: 23.950