Starting phenix.real_space_refine on Sat May 24 14:38:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wgy_37522/05_2025/8wgy_37522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wgy_37522/05_2025/8wgy_37522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wgy_37522/05_2025/8wgy_37522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wgy_37522/05_2025/8wgy_37522.map" model { file = "/net/cci-nas-00/data/ceres_data/8wgy_37522/05_2025/8wgy_37522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wgy_37522/05_2025/8wgy_37522.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 18 5.49 5 Mg 4 5.21 5 S 114 5.16 5 C 16345 2.51 5 N 4342 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25643 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 6160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 769, 6160 Classifications: {'peptide': 769} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 734} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 4413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4413 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 27, 'TRANS': 522} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "T" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5844 SG CYS E 282 73.447 60.207 145.031 1.00 64.60 S ATOM 5863 SG CYS E 285 76.095 62.805 146.023 1.00 58.26 S ATOM 6097 SG CYS E 314 72.385 63.830 145.758 1.00 62.98 S ATOM 10257 SG CYS D 282 93.059 80.522 130.719 1.00 56.81 S ATOM 10276 SG CYS D 285 92.691 83.797 132.598 1.00 59.96 S ATOM 10510 SG CYS D 314 90.071 81.077 133.243 1.00 64.65 S Time building chain proxies: 14.34, per 1000 atoms: 0.56 Number of scatterers: 25643 At special positions: 0 Unit cell: (127.68, 133.56, 164.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 114 16.00 P 18 15.00 Mg 4 11.99 O 4818 8.00 N 4342 7.00 C 16345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.05 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 801 " pdb="ZN ZN D 801 " - pdb=" NE2 HIS D 290 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 285 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 282 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 314 " pdb=" ZN E 802 " pdb="ZN ZN E 802 " - pdb=" NE2 HIS E 290 " pdb="ZN ZN E 802 " - pdb=" SG CYS E 282 " pdb="ZN ZN E 802 " - pdb=" SG CYS E 314 " pdb="ZN ZN E 802 " - pdb=" SG CYS E 285 " Number of angles added : 6 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6070 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 48 sheets defined 45.3% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.633A pdb=" N THR B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'B' and resid 376 through 382 removed outlier: 3.637A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.941A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 570 through 578 Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.637A pdb=" N ARG B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.760A pdb=" N PHE B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 695 Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 696 through 703 removed outlier: 3.610A pdb=" N GLY B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 714 Processing helix chain 'B' and resid 716 through 723 Processing helix chain 'B' and resid 735 through 744 Processing helix chain 'B' and resid 752 through 763 Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'E' and resid 20 through 27 Processing helix chain 'E' and resid 36 through 47 Processing helix chain 'E' and resid 78 through 105 Processing helix chain 'E' and resid 108 through 119 removed outlier: 4.435A pdb=" N ASN E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 160 removed outlier: 3.673A pdb=" N LEU E 147 " --> pdb=" O THR E 143 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG E 152 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 168 Processing helix chain 'E' and resid 204 through 208 removed outlier: 3.781A pdb=" N LEU E 208 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 255 Processing helix chain 'E' and resid 324 through 335 Processing helix chain 'E' and resid 363 through 371 Processing helix chain 'E' and resid 372 through 375 removed outlier: 3.600A pdb=" N LEU E 375 " --> pdb=" O ARG E 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 372 through 375' Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'E' and resid 429 through 434 removed outlier: 3.891A pdb=" N ASP E 432 " --> pdb=" O SER E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 475 through 489 removed outlier: 3.700A pdb=" N CYS E 489 " --> pdb=" O THR E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 541 through 546 Processing helix chain 'E' and resid 570 through 578 removed outlier: 3.957A pdb=" N ILE E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR E 578 " --> pdb=" O ILE E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 619 Processing helix chain 'E' and resid 632 through 634 No H-bonds generated for 'chain 'E' and resid 632 through 634' Processing helix chain 'E' and resid 635 through 642 removed outlier: 3.740A pdb=" N ASN E 642 " --> pdb=" O ALA E 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 661 removed outlier: 4.471A pdb=" N GLY E 657 " --> pdb=" O GLU E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 680 Processing helix chain 'E' and resid 694 through 705 removed outlier: 4.131A pdb=" N PHE E 698 " --> pdb=" O PRO E 694 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR E 699 " --> pdb=" O ASP E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 715 No H-bonds generated for 'chain 'E' and resid 713 through 715' Processing helix chain 'E' and resid 716 through 724 removed outlier: 4.237A pdb=" N LEU E 720 " --> pdb=" O LEU E 716 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 744 Processing helix chain 'E' and resid 748 through 763 removed outlier: 3.542A pdb=" N PHE E 752 " --> pdb=" O ASN E 748 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N HIS E 754 " --> pdb=" O ARG E 750 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP E 755 " --> pdb=" O LEU E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 779 through 784 Processing helix chain 'D' and resid 242 through 255 Processing helix chain 'D' and resid 310 through 314 Processing helix chain 'D' and resid 324 through 335 Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.700A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 430 through 435 removed outlier: 3.626A pdb=" N LYS D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 430 through 435' Processing helix chain 'D' and resid 455 through 469 removed outlier: 3.801A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU D 460 " --> pdb=" O PRO D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 474 No H-bonds generated for 'chain 'D' and resid 472 through 474' Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 528 through 533 removed outlier: 3.830A pdb=" N ILE D 531 " --> pdb=" O GLY D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 570 through 578 removed outlier: 3.750A pdb=" N THR D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 619 Processing helix chain 'D' and resid 635 through 641 removed outlier: 3.531A pdb=" N ASN D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 664 through 680 Processing helix chain 'D' and resid 689 through 693 Processing helix chain 'D' and resid 697 through 705 removed outlier: 4.842A pdb=" N GLY D 703 " --> pdb=" O TYR D 699 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR D 704 " --> pdb=" O LEU D 700 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 705 " --> pdb=" O LYS D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 723 removed outlier: 3.964A pdb=" N LEU D 720 " --> pdb=" O LEU D 716 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS D 723 " --> pdb=" O ASP D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 731 Processing helix chain 'D' and resid 735 through 747 Processing helix chain 'D' and resid 753 through 764 removed outlier: 4.371A pdb=" N GLU D 757 " --> pdb=" O GLY D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 784 removed outlier: 3.592A pdb=" N SER D 784 " --> pdb=" O GLU D 780 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.797A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 371 Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.949A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 384 No H-bonds generated for 'chain 'F' and resid 382 through 384' Processing helix chain 'F' and resid 385 through 401 removed outlier: 4.553A pdb=" N VAL F 401 " --> pdb=" O ARG F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 434 removed outlier: 3.583A pdb=" N ASP F 432 " --> pdb=" O SER F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.903A pdb=" N LYS F 450 " --> pdb=" O ASP F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 469 Processing helix chain 'F' and resid 475 through 488 removed outlier: 3.541A pdb=" N ARG F 479 " --> pdb=" O ASN F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 520 Processing helix chain 'F' and resid 530 through 533 Processing helix chain 'F' and resid 542 through 547 Processing helix chain 'F' and resid 570 through 577 Processing helix chain 'F' and resid 614 through 619 removed outlier: 3.525A pdb=" N ARG F 619 " --> pdb=" O ASN F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 635 through 640 Processing helix chain 'F' and resid 654 through 661 Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'F' and resid 689 through 692 removed outlier: 3.950A pdb=" N GLU F 692 " --> pdb=" O THR F 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 689 through 692' Processing helix chain 'F' and resid 693 through 705 removed outlier: 3.664A pdb=" N GLY F 703 " --> pdb=" O TYR F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 710 through 714 Processing helix chain 'F' and resid 717 through 722 Processing helix chain 'F' and resid 735 through 744 Processing helix chain 'F' and resid 748 through 763 removed outlier: 5.851A pdb=" N HIS F 754 " --> pdb=" O ARG F 750 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP F 755 " --> pdb=" O LEU F 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 779 through 784 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.642A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 376 through 382 removed outlier: 4.136A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 400 Processing helix chain 'C' and resid 430 through 435 removed outlier: 3.866A pdb=" N LYS C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 removed outlier: 3.580A pdb=" N LYS C 450 " --> pdb=" O ASP C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.655A pdb=" N GLU C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 474 No H-bonds generated for 'chain 'C' and resid 472 through 474' Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 579 removed outlier: 3.541A pdb=" N GLU C 579 " --> pdb=" O LYS C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 635 through 641 removed outlier: 3.855A pdb=" N ASN C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'C' and resid 693 through 695 No H-bonds generated for 'chain 'C' and resid 693 through 695' Processing helix chain 'C' and resid 696 through 703 removed outlier: 3.584A pdb=" N GLY C 703 " --> pdb=" O TYR C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 715 Proline residue: C 715 - end of helix Processing helix chain 'C' and resid 716 through 724 removed outlier: 3.839A pdb=" N LEU C 720 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS C 722 " --> pdb=" O THR C 718 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS C 723 " --> pdb=" O ASP C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 745 Processing helix chain 'C' and resid 752 through 764 removed outlier: 3.923A pdb=" N ILE C 756 " --> pdb=" O PHE C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 784 Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.643A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.807A pdb=" N LYS A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 635 through 640 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 689 through 695 removed outlier: 3.630A pdb=" N GLU A 692 " --> pdb=" O THR A 689 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 693 " --> pdb=" O PRO A 690 " (cutoff:3.500A) Proline residue: A 694 - end of helix No H-bonds generated for 'chain 'A' and resid 689 through 695' Processing helix chain 'A' and resid 696 through 705 removed outlier: 3.725A pdb=" N GLY A 703 " --> pdb=" O TYR A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 714 removed outlier: 3.551A pdb=" N HIS A 713 " --> pdb=" O SER A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 724 removed outlier: 3.761A pdb=" N LEU A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 747 removed outlier: 3.645A pdb=" N TYR A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 764 removed outlier: 3.618A pdb=" N ILE A 756 " --> pdb=" O PHE A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing sheet with id=AA1, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'B' and resid 412 through 415 Processing sheet with id=AA3, first strand: chain 'B' and resid 601 through 604 removed outlier: 6.256A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AA5, first strand: chain 'B' and resid 629 through 631 Processing sheet with id=AA6, first strand: chain 'B' and resid 706 through 708 Processing sheet with id=AA7, first strand: chain 'B' and resid 726 through 728 Processing sheet with id=AA8, first strand: chain 'E' and resid 32 through 35 Processing sheet with id=AA9, first strand: chain 'E' and resid 65 through 73 removed outlier: 6.953A pdb=" N THR E 140 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N MET E 69 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 11.351A pdb=" N LEU E 138 " --> pdb=" O MET E 69 " (cutoff:3.500A) removed outlier: 12.165A pdb=" N VAL E 71 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 11.028A pdb=" N ILE E 136 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N LEU E 73 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 11.500A pdb=" N HIS E 134 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 65 through 73 removed outlier: 6.953A pdb=" N THR E 140 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N MET E 69 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 11.351A pdb=" N LEU E 138 " --> pdb=" O MET E 69 " (cutoff:3.500A) removed outlier: 12.165A pdb=" N VAL E 71 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 11.028A pdb=" N ILE E 136 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N LEU E 73 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 11.500A pdb=" N HIS E 134 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 124 through 125 Processing sheet with id=AB3, first strand: chain 'E' and resid 294 through 299 Processing sheet with id=AB4, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AB5, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AB6, first strand: chain 'E' and resid 525 through 527 removed outlier: 4.106A pdb=" N SER E 556 " --> pdb=" O THR E 527 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ASP E 603 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N CYS E 555 " --> pdb=" O ASP E 603 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE E 626 " --> pdb=" O PHE E 500 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N PHE E 502 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AB8, first strand: chain 'E' and resid 629 through 631 removed outlier: 5.912A pdb=" N HIS E 629 " --> pdb=" O LYS E 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 706 through 707 Processing sheet with id=AC1, first strand: chain 'E' and resid 727 through 728 removed outlier: 3.640A pdb=" N TYR E 728 " --> pdb=" O VAL E 731 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 295 through 299 Processing sheet with id=AC3, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC4, first strand: chain 'D' and resid 412 through 415 Processing sheet with id=AC5, first strand: chain 'D' and resid 524 through 526 removed outlier: 6.349A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AC7, first strand: chain 'D' and resid 628 through 631 removed outlier: 6.142A pdb=" N HIS D 629 " --> pdb=" O LYS D 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 706 through 707 removed outlier: 4.117A pdb=" N VAL D 707 " --> pdb=" O ILE D 777 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE D 777 " --> pdb=" O VAL D 707 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 339 through 342 removed outlier: 3.927A pdb=" N ASP F 346 " --> pdb=" O THR F 342 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 412 through 415 Processing sheet with id=AD2, first strand: chain 'F' and resid 524 through 528 removed outlier: 6.619A pdb=" N VAL F 525 " --> pdb=" O PHE F 554 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N SER F 556 " --> pdb=" O VAL F 525 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR F 527 " --> pdb=" O SER F 556 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL F 553 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR F 499 " --> pdb=" O ILE F 602 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR F 604 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE F 501 " --> pdb=" O THR F 604 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 581 through 583 Processing sheet with id=AD4, first strand: chain 'F' and resid 628 through 631 Processing sheet with id=AD5, first strand: chain 'F' and resid 706 through 708 Processing sheet with id=AD6, first strand: chain 'F' and resid 726 through 728 Processing sheet with id=AD7, first strand: chain 'F' and resid 765 through 766 removed outlier: 3.530A pdb=" N LYS F 765 " --> pdb=" O TYR F 773 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AD9, first strand: chain 'C' and resid 412 through 415 Processing sheet with id=AE1, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.830A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N SER C 556 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AE3, first strand: chain 'C' and resid 629 through 631 Processing sheet with id=AE4, first strand: chain 'C' and resid 706 through 708 Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AE6, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AE7, first strand: chain 'A' and resid 412 through 415 Processing sheet with id=AE8, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.225A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AF1, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.359A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'A' and resid 706 through 708 Processing sheet with id=AF3, first strand: chain 'A' and resid 726 through 728 954 hydrogen bonds defined for protein. 2676 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: 9.80 Time building geometry restraints manager: 7.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.92 - 1.25: 3855 1.25 - 1.57: 22146 1.57 - 1.90: 199 1.90 - 2.22: 0 2.22 - 2.55: 1 Bond restraints: 26201 Sorted by residual: bond pdb=" CB PRO E 293 " pdb=" CG PRO E 293 " ideal model delta sigma weight residual 1.492 2.546 -1.054 5.00e-02 4.00e+02 4.45e+02 bond pdb=" CG PRO E 293 " pdb=" CD PRO E 293 " ideal model delta sigma weight residual 1.503 0.924 0.579 3.40e-02 8.65e+02 2.90e+02 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" O3A ANP C 801 " pdb=" PB ANP C 801 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.20e+01 ... (remaining 26196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.42: 35482 19.42 - 38.84: 2 38.84 - 58.26: 0 58.26 - 77.68: 0 77.68 - 97.10: 1 Bond angle restraints: 35485 Sorted by residual: angle pdb=" CB PRO E 293 " pdb=" CG PRO E 293 " pdb=" CD PRO E 293 " ideal model delta sigma weight residual 106.10 9.00 97.10 3.20e+00 9.77e-02 9.21e+02 angle pdb=" CA PRO D 320 " pdb=" N PRO D 320 " pdb=" CD PRO D 320 " ideal model delta sigma weight residual 112.00 94.05 17.95 1.40e+00 5.10e-01 1.64e+02 angle pdb=" CA PRO E 293 " pdb=" N PRO E 293 " pdb=" CD PRO E 293 " ideal model delta sigma weight residual 112.00 94.43 17.57 1.40e+00 5.10e-01 1.57e+02 angle pdb=" N PRO E 293 " pdb=" CA PRO E 293 " pdb=" CB PRO E 293 " ideal model delta sigma weight residual 103.15 87.99 15.16 1.29e+00 6.01e-01 1.38e+02 angle pdb=" CA PRO E 293 " pdb=" CB PRO E 293 " pdb=" CG PRO E 293 " ideal model delta sigma weight residual 104.50 84.38 20.12 1.90e+00 2.77e-01 1.12e+02 ... (remaining 35480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.89: 14887 26.89 - 53.77: 970 53.77 - 80.66: 114 80.66 - 107.55: 16 107.55 - 134.44: 2 Dihedral angle restraints: 15989 sinusoidal: 6640 harmonic: 9349 Sorted by residual: dihedral pdb=" CA ILE D 681 " pdb=" C ILE D 681 " pdb=" N PRO D 682 " pdb=" CA PRO D 682 " ideal model delta harmonic sigma weight residual -180.00 -145.78 -34.22 0 5.00e+00 4.00e-02 4.68e+01 dihedral pdb=" CA PRO E 293 " pdb=" CB PRO E 293 " pdb=" CG PRO E 293 " pdb=" CD PRO E 293 " ideal model delta sinusoidal sigma weight residual -38.00 -172.44 134.44 1 2.00e+01 2.50e-03 4.08e+01 dihedral pdb=" N PRO E 293 " pdb=" C PRO E 293 " pdb=" CA PRO E 293 " pdb=" CB PRO E 293 " ideal model delta harmonic sigma weight residual 115.10 99.56 15.54 0 2.50e+00 1.60e-01 3.86e+01 ... (remaining 15986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3526 0.068 - 0.135: 439 0.135 - 0.203: 14 0.203 - 0.270: 4 0.270 - 0.338: 4 Chirality restraints: 3987 Sorted by residual: chirality pdb=" CA PRO D 320 " pdb=" N PRO D 320 " pdb=" C PRO D 320 " pdb=" CB PRO D 320 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C3' ANP F 801 " pdb=" C2' ANP F 801 " pdb=" C4' ANP F 801 " pdb=" O3' ANP F 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 3984 not shown) Planarity restraints: 4508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 272 " -0.086 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO D 273 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 455 " -0.090 5.00e-02 4.00e+02 1.26e-01 2.53e+01 pdb=" N PRO C 456 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO C 456 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO C 456 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 319 " 0.078 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO D 320 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO D 320 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 320 " 0.056 5.00e-02 4.00e+02 ... (remaining 4505 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 147 2.53 - 3.12: 18813 3.12 - 3.71: 38413 3.71 - 4.31: 55358 4.31 - 4.90: 92189 Nonbonded interactions: 204920 Sorted by model distance: nonbonded pdb=" OG SER C 510 " pdb="MG MG C 802 " model vdw 1.936 2.170 nonbonded pdb=" OG SER E 510 " pdb="MG MG E 803 " model vdw 1.954 2.170 nonbonded pdb=" O3G ANP C 801 " pdb="MG MG C 802 " model vdw 1.960 2.170 nonbonded pdb=" O2G ANP B 801 " pdb="MG MG B 802 " model vdw 1.970 2.170 nonbonded pdb=" OG SER B 510 " pdb="MG MG B 802 " model vdw 1.974 2.170 ... (remaining 204915 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 323 through 785 or resid 801)) selection = (chain 'B' and (resid 323 through 785 or resid 801)) selection = (chain 'C' and (resid 323 through 785 or resid 801)) selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.820 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: 1.030 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 59.940 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.009 1.054 26209 Z= 0.280 Angle : 0.896 97.096 35491 Z= 0.413 Chirality : 0.045 0.338 3987 Planarity : 0.006 0.127 4508 Dihedral : 16.946 134.435 9919 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.97 % Favored : 94.87 % Rotamer: Outliers : 1.34 % Allowed : 17.57 % Favored : 81.09 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3157 helix: 0.62 (0.15), residues: 1205 sheet: -0.09 (0.26), residues: 454 loop : -0.82 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 675 HIS 0.003 0.001 HIS E 109 PHE 0.031 0.001 PHE A 759 TYR 0.016 0.001 TYR D 482 ARG 0.012 0.000 ARG E 570 Details of bonding type rmsd hydrogen bonds : bond 0.07392 ( 951) hydrogen bonds : angle 4.64534 ( 2676) metal coordination : bond 0.00467 ( 8) metal coordination : angle 2.05184 ( 6) covalent geometry : bond 0.00891 (26201) covalent geometry : angle 0.89566 (35485) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 474 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6856 (tp30) outliers start: 38 outliers final: 28 residues processed: 280 average time/residue: 1.1613 time to fit residues: 388.0241 Evaluate side-chains 265 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain F residue 431 ASP Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 606 TYR Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 746 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 246 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN F 324 ASN C 593 ASN C 680 HIS A 324 ASN A 741 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.189435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151158 restraints weight = 30388.293| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.51 r_work: 0.3302 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 26209 Z= 0.195 Angle : 0.592 10.415 35491 Z= 0.310 Chirality : 0.046 0.223 3987 Planarity : 0.005 0.085 4508 Dihedral : 9.225 115.215 3668 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.97 % Favored : 94.81 % Rotamer: Outliers : 3.94 % Allowed : 15.99 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3157 helix: 0.47 (0.15), residues: 1200 sheet: -0.17 (0.27), residues: 424 loop : -0.95 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 675 HIS 0.006 0.001 HIS F 629 PHE 0.026 0.002 PHE D 696 TYR 0.021 0.001 TYR A 482 ARG 0.007 0.001 ARG E 570 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 951) hydrogen bonds : angle 4.57383 ( 2676) metal coordination : bond 0.00487 ( 8) metal coordination : angle 2.22003 ( 6) covalent geometry : bond 0.00481 (26201) covalent geometry : angle 0.59184 (35485) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 260 time to evaluate : 2.851 Fit side-chains revert: symmetry clash REVERT: B 591 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7991 (mttt) REVERT: B 603 ASP cc_start: 0.8935 (p0) cc_final: 0.8717 (p0) REVERT: E 52 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5462 (mt) REVERT: E 151 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7976 (ttmm) REVERT: D 320 PRO cc_start: 0.7851 (Cg_endo) cc_final: 0.7599 (Cg_exo) REVERT: D 504 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: F 428 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.6969 (p90) REVERT: F 457 GLU cc_start: 0.6866 (mp0) cc_final: 0.6461 (mt-10) REVERT: F 507 THR cc_start: 0.6043 (OUTLIER) cc_final: 0.5831 (m) REVERT: C 382 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8399 (mt-10) REVERT: C 387 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7683 (mtm110) REVERT: C 448 ASP cc_start: 0.7653 (t0) cc_final: 0.7425 (t0) REVERT: C 595 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8271 (mmp-170) REVERT: C 602 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9181 (mm) REVERT: C 653 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: A 477 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7973 (mmpt) outliers start: 112 outliers final: 45 residues processed: 343 average time/residue: 1.1969 time to fit residues: 485.9190 Evaluate side-chains 296 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 239 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 605 ASN Chi-restraints excluded: chain E residue 628 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 619 ARG Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 387 ARG Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 477 LYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 746 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 218 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 291 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 281 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 248 optimal weight: 0.0570 chunk 21 optimal weight: 4.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN E 195 HIS D 573 ASN F 324 ASN F 594 ASN C 593 ASN C 680 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.191631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138970 restraints weight = 30514.658| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.54 r_work: 0.3361 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26209 Z= 0.111 Angle : 0.494 6.413 35491 Z= 0.263 Chirality : 0.042 0.199 3987 Planarity : 0.004 0.070 4508 Dihedral : 7.914 107.954 3644 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.18 % Favored : 95.63 % Rotamer: Outliers : 3.66 % Allowed : 17.43 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3157 helix: 0.72 (0.15), residues: 1201 sheet: -0.28 (0.26), residues: 442 loop : -0.83 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 675 HIS 0.005 0.001 HIS F 629 PHE 0.024 0.001 PHE A 759 TYR 0.014 0.001 TYR D 482 ARG 0.008 0.000 ARG C 636 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 951) hydrogen bonds : angle 4.32842 ( 2676) metal coordination : bond 0.00321 ( 8) metal coordination : angle 1.94093 ( 6) covalent geometry : bond 0.00260 (26201) covalent geometry : angle 0.49371 (35485) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 267 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 603 ASP cc_start: 0.8983 (p0) cc_final: 0.8669 (p0) REVERT: E 52 LEU cc_start: 0.5917 (OUTLIER) cc_final: 0.5406 (mt) REVERT: E 69 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7907 (mtm) REVERT: E 151 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7776 (ttmm) REVERT: E 416 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8010 (tmmm) REVERT: E 604 THR cc_start: 0.7268 (OUTLIER) cc_final: 0.7047 (p) REVERT: E 670 TYR cc_start: 0.7692 (t80) cc_final: 0.7068 (t80) REVERT: D 262 ASN cc_start: 0.6718 (OUTLIER) cc_final: 0.6462 (t0) REVERT: D 319 VAL cc_start: 0.7752 (t) cc_final: 0.7519 (p) REVERT: D 504 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: F 428 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.6924 (p90) REVERT: F 457 GLU cc_start: 0.6824 (mp0) cc_final: 0.6424 (mt-10) REVERT: F 507 THR cc_start: 0.5718 (OUTLIER) cc_final: 0.5403 (m) REVERT: C 343 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: C 387 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7560 (mtm110) REVERT: C 448 ASP cc_start: 0.7539 (t0) cc_final: 0.7293 (t0) REVERT: C 602 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9172 (mm) REVERT: C 653 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: C 733 THR cc_start: 0.5620 (OUTLIER) cc_final: 0.5287 (p) REVERT: A 605 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8102 (p0) outliers start: 104 outliers final: 36 residues processed: 346 average time/residue: 1.1154 time to fit residues: 457.8602 Evaluate side-chains 289 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 683 ILE Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 576 LYS Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 387 ARG Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 751 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 141 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 170 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN F 324 ASN F 594 ASN C 324 ASN C 593 ASN C 680 HIS A 660 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.189139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122898 restraints weight = 30650.441| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.99 r_work: 0.3220 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26209 Z= 0.188 Angle : 0.564 6.668 35491 Z= 0.296 Chirality : 0.045 0.207 3987 Planarity : 0.005 0.070 4508 Dihedral : 8.076 109.921 3639 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.88 % Favored : 94.90 % Rotamer: Outliers : 4.93 % Allowed : 17.32 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3157 helix: 0.52 (0.15), residues: 1206 sheet: -0.27 (0.26), residues: 444 loop : -0.89 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 675 HIS 0.005 0.001 HIS A 548 PHE 0.024 0.002 PHE D 696 TYR 0.021 0.001 TYR A 482 ARG 0.008 0.001 ARG E 570 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 951) hydrogen bonds : angle 4.45753 ( 2676) metal coordination : bond 0.00734 ( 8) metal coordination : angle 1.90736 ( 6) covalent geometry : bond 0.00465 (26201) covalent geometry : angle 0.56368 (35485) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 248 time to evaluate : 3.018 Fit side-chains revert: symmetry clash REVERT: B 462 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8268 (mmp) REVERT: B 591 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7977 (mttt) REVERT: B 603 ASP cc_start: 0.9061 (p0) cc_final: 0.8699 (p0) REVERT: E 52 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5438 (mt) REVERT: E 69 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8137 (mtm) REVERT: E 128 ARG cc_start: 0.6025 (OUTLIER) cc_final: 0.5284 (ttt-90) REVERT: E 151 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7859 (ttmm) REVERT: E 411 ASP cc_start: 0.8109 (t0) cc_final: 0.7880 (t0) REVERT: E 416 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8072 (tmmm) REVERT: E 604 THR cc_start: 0.7228 (OUTLIER) cc_final: 0.7002 (p) REVERT: E 671 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8749 (tt) REVERT: D 319 VAL cc_start: 0.7688 (t) cc_final: 0.7488 (p) REVERT: D 504 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: F 428 TYR cc_start: 0.7665 (OUTLIER) cc_final: 0.6806 (p90) REVERT: F 457 GLU cc_start: 0.6805 (mp0) cc_final: 0.6382 (mt-10) REVERT: F 507 THR cc_start: 0.5775 (OUTLIER) cc_final: 0.5550 (m) REVERT: F 669 LEU cc_start: 0.6441 (OUTLIER) cc_final: 0.5776 (tm) REVERT: C 387 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7760 (mtm110) REVERT: C 448 ASP cc_start: 0.7650 (t0) cc_final: 0.7388 (t0) REVERT: C 595 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8306 (mmp-170) REVERT: C 602 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9158 (mm) REVERT: C 653 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: C 733 THR cc_start: 0.5605 (OUTLIER) cc_final: 0.5244 (p) outliers start: 140 outliers final: 66 residues processed: 356 average time/residue: 1.0799 time to fit residues: 461.3980 Evaluate side-chains 324 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 240 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 605 ASN Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 683 ILE Chi-restraints excluded: chain E residue 710 SER Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 685 LYS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 576 LYS Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 606 TYR Chi-restraints excluded: chain F residue 619 ARG Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain C residue 387 ARG Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 746 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 60 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 259 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 306 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 249 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN F 324 ASN F 594 ASN C 593 ASN C 680 HIS A 605 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.190582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153199 restraints weight = 30499.191| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.46 r_work: 0.3344 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26209 Z= 0.120 Angle : 0.504 6.364 35491 Z= 0.267 Chirality : 0.043 0.194 3987 Planarity : 0.004 0.063 4508 Dihedral : 7.666 108.644 3637 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.47 % Favored : 95.34 % Rotamer: Outliers : 4.54 % Allowed : 18.38 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3157 helix: 0.75 (0.15), residues: 1197 sheet: -0.33 (0.26), residues: 442 loop : -0.80 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 675 HIS 0.004 0.001 HIS F 629 PHE 0.023 0.001 PHE C 698 TYR 0.020 0.001 TYR E 670 ARG 0.009 0.000 ARG E 570 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 951) hydrogen bonds : angle 4.32762 ( 2676) metal coordination : bond 0.00472 ( 8) metal coordination : angle 1.84055 ( 6) covalent geometry : bond 0.00285 (26201) covalent geometry : angle 0.50300 (35485) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 262 time to evaluate : 2.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 603 ASP cc_start: 0.8908 (p0) cc_final: 0.8592 (p0) REVERT: E 69 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7872 (mtm) REVERT: E 128 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5303 (ttt-90) REVERT: E 151 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7878 (ttmm) REVERT: E 416 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7978 (tmmm) REVERT: E 674 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7621 (mmmm) REVERT: D 504 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: D 554 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8389 (t80) REVERT: F 428 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.6884 (p90) REVERT: F 457 GLU cc_start: 0.6872 (mp0) cc_final: 0.6482 (mt-10) REVERT: F 507 THR cc_start: 0.5766 (OUTLIER) cc_final: 0.5544 (m) REVERT: F 542 PRO cc_start: 0.7542 (Cg_endo) cc_final: 0.7259 (Cg_exo) REVERT: F 640 GLU cc_start: 0.2541 (OUTLIER) cc_final: 0.1942 (tp30) REVERT: F 669 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6376 (tp) REVERT: C 343 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8390 (mt-10) REVERT: C 387 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7745 (mtm110) REVERT: C 431 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: C 448 ASP cc_start: 0.7566 (t0) cc_final: 0.7311 (t0) REVERT: C 653 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: C 733 THR cc_start: 0.5709 (OUTLIER) cc_final: 0.5395 (p) REVERT: A 343 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8213 (mt-10) outliers start: 129 outliers final: 56 residues processed: 360 average time/residue: 1.0605 time to fit residues: 457.3015 Evaluate side-chains 318 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 245 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 605 ASN Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain E residue 683 ILE Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 685 LYS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 576 LYS Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 619 ARG Chi-restraints excluded: chain F residue 640 GLU Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 387 ARG Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 756 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 269 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN F 324 ASN F 594 ASN C 593 ASN C 680 HIS A 741 GLN ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.188606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124187 restraints weight = 30418.970| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.03 r_work: 0.3182 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26209 Z= 0.202 Angle : 0.585 7.667 35491 Z= 0.306 Chirality : 0.046 0.206 3987 Planarity : 0.005 0.070 4508 Dihedral : 8.063 109.088 3637 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.16 % Favored : 94.58 % Rotamer: Outliers : 4.89 % Allowed : 18.73 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 3157 helix: 0.48 (0.15), residues: 1205 sheet: -0.42 (0.25), residues: 450 loop : -0.90 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 350 HIS 0.006 0.001 HIS A 548 PHE 0.027 0.002 PHE D 696 TYR 0.023 0.002 TYR A 482 ARG 0.011 0.001 ARG E 570 Details of bonding type rmsd hydrogen bonds : bond 0.04515 ( 951) hydrogen bonds : angle 4.49120 ( 2676) metal coordination : bond 0.00839 ( 8) metal coordination : angle 1.94484 ( 6) covalent geometry : bond 0.00502 (26201) covalent geometry : angle 0.58487 (35485) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 250 time to evaluate : 2.814 Fit side-chains revert: symmetry clash REVERT: B 453 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: B 591 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7974 (mttt) REVERT: B 603 ASP cc_start: 0.9084 (p0) cc_final: 0.8746 (p0) REVERT: E 69 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8176 (mtm) REVERT: E 128 ARG cc_start: 0.6029 (OUTLIER) cc_final: 0.5290 (ttt-90) REVERT: E 151 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7849 (ttmm) REVERT: E 259 ILE cc_start: 0.7060 (mt) cc_final: 0.6649 (mm) REVERT: E 595 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.6846 (ttp-110) REVERT: E 670 TYR cc_start: 0.7708 (t80) cc_final: 0.7302 (t80) REVERT: E 674 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7550 (mmmm) REVERT: D 504 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: F 428 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.6710 (p90) REVERT: F 457 GLU cc_start: 0.6811 (mp0) cc_final: 0.6393 (mt-10) REVERT: F 507 THR cc_start: 0.5808 (OUTLIER) cc_final: 0.5601 (m) REVERT: F 572 ASP cc_start: 0.6732 (OUTLIER) cc_final: 0.6516 (m-30) REVERT: F 640 GLU cc_start: 0.2579 (OUTLIER) cc_final: 0.1936 (tp30) REVERT: F 669 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.5870 (tm) REVERT: C 324 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8425 (t0) REVERT: C 343 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8686 (mt-10) REVERT: C 387 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7720 (mtm180) REVERT: C 431 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: C 448 ASP cc_start: 0.7704 (t0) cc_final: 0.7447 (t0) REVERT: C 595 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8309 (mmp-170) REVERT: C 653 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: C 733 THR cc_start: 0.5726 (OUTLIER) cc_final: 0.5382 (p) REVERT: A 343 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8641 (mt-10) REVERT: A 477 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8019 (mmpt) outliers start: 139 outliers final: 67 residues processed: 356 average time/residue: 1.0507 time to fit residues: 448.9774 Evaluate side-chains 327 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 238 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 595 ARG Chi-restraints excluded: chain E residue 605 ASN Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain E residue 683 ILE Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 685 LYS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 572 ASP Chi-restraints excluded: chain F residue 576 LYS Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 619 ARG Chi-restraints excluded: chain F residue 640 GLU Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 387 ARG Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 477 LYS Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 756 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 52 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 713 HIS D 573 ASN F 324 ASN F 594 ASN C 593 ASN C 680 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.189778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126515 restraints weight = 30389.204| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.04 r_work: 0.3203 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26209 Z= 0.179 Angle : 0.564 13.019 35491 Z= 0.295 Chirality : 0.045 0.201 3987 Planarity : 0.005 0.063 4508 Dihedral : 7.994 107.724 3633 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.04 % Favored : 94.68 % Rotamer: Outliers : 4.72 % Allowed : 19.37 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3157 helix: 0.50 (0.15), residues: 1203 sheet: -0.42 (0.25), residues: 450 loop : -0.89 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 350 HIS 0.005 0.001 HIS F 629 PHE 0.028 0.002 PHE A 698 TYR 0.021 0.001 TYR A 482 ARG 0.010 0.000 ARG E 570 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 951) hydrogen bonds : angle 4.45465 ( 2676) metal coordination : bond 0.00765 ( 8) metal coordination : angle 1.95924 ( 6) covalent geometry : bond 0.00443 (26201) covalent geometry : angle 0.56368 (35485) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 254 time to evaluate : 3.023 Fit side-chains revert: symmetry clash REVERT: B 453 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7835 (tp30) REVERT: B 591 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7974 (mttt) REVERT: B 603 ASP cc_start: 0.9078 (p0) cc_final: 0.8737 (p0) REVERT: E 69 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8147 (mtm) REVERT: E 128 ARG cc_start: 0.6034 (OUTLIER) cc_final: 0.5323 (ttt-90) REVERT: E 151 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7854 (ttmm) REVERT: E 259 ILE cc_start: 0.7032 (mt) cc_final: 0.6621 (mm) REVERT: E 595 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6743 (ttp-110) REVERT: E 713 HIS cc_start: -0.0011 (OUTLIER) cc_final: -0.0703 (t70) REVERT: D 504 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: F 428 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.6835 (p90) REVERT: F 457 GLU cc_start: 0.6843 (mp0) cc_final: 0.6418 (mt-10) REVERT: F 474 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: F 572 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.6528 (m-30) REVERT: F 640 GLU cc_start: 0.2708 (OUTLIER) cc_final: 0.1967 (tp30) REVERT: F 669 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.5852 (tm) REVERT: C 324 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8261 (t0) REVERT: C 343 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8737 (mt-10) REVERT: C 387 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7742 (mtm110) REVERT: C 431 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: C 448 ASP cc_start: 0.7760 (t0) cc_final: 0.7526 (t0) REVERT: C 595 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8277 (mmp-170) REVERT: C 602 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9149 (mm) REVERT: C 653 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: C 733 THR cc_start: 0.5683 (OUTLIER) cc_final: 0.5310 (p) REVERT: A 343 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8618 (mt-10) REVERT: A 679 TYR cc_start: 0.8988 (m-80) cc_final: 0.8776 (m-80) outliers start: 134 outliers final: 72 residues processed: 357 average time/residue: 1.0634 time to fit residues: 455.4321 Evaluate side-chains 337 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 243 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 595 ARG Chi-restraints excluded: chain E residue 605 ASN Chi-restraints excluded: chain E residue 683 ILE Chi-restraints excluded: chain E residue 710 SER Chi-restraints excluded: chain E residue 713 HIS Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 685 LYS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 572 ASP Chi-restraints excluded: chain F residue 576 LYS Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 619 ARG Chi-restraints excluded: chain F residue 640 GLU Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 387 ARG Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 756 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 219 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 chunk 314 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 175 optimal weight: 0.0670 chunk 185 optimal weight: 3.9990 overall best weight: 1.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN F 324 ASN C 324 ASN C 593 ASN C 680 HIS A 605 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.190443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126775 restraints weight = 30390.001| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.97 r_work: 0.3275 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26209 Z= 0.124 Angle : 0.532 15.655 35491 Z= 0.278 Chirality : 0.043 0.197 3987 Planarity : 0.004 0.063 4508 Dihedral : 7.690 108.236 3633 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.69 % Favored : 95.09 % Rotamer: Outliers : 3.87 % Allowed : 20.11 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3157 helix: 0.73 (0.15), residues: 1193 sheet: -0.36 (0.26), residues: 441 loop : -0.80 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 350 HIS 0.006 0.001 HIS E 713 PHE 0.021 0.001 PHE C 698 TYR 0.023 0.001 TYR F 645 ARG 0.012 0.000 ARG E 570 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 951) hydrogen bonds : angle 4.35124 ( 2676) metal coordination : bond 0.00544 ( 8) metal coordination : angle 1.77783 ( 6) covalent geometry : bond 0.00295 (26201) covalent geometry : angle 0.53104 (35485) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 262 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 603 ASP cc_start: 0.9051 (p0) cc_final: 0.8668 (p0) REVERT: E 69 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8051 (mtm) REVERT: E 128 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.5332 (ttt-90) REVERT: E 151 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7826 (ttmm) REVERT: E 259 ILE cc_start: 0.6893 (mt) cc_final: 0.6466 (mm) REVERT: E 416 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7895 (tmmm) REVERT: E 595 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6672 (ttp-110) REVERT: E 618 MET cc_start: 0.5790 (ppp) cc_final: 0.5527 (ppp) REVERT: E 674 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7500 (mmmm) REVERT: E 713 HIS cc_start: -0.0243 (OUTLIER) cc_final: -0.0862 (t70) REVERT: D 504 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: F 428 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.6799 (p90) REVERT: F 457 GLU cc_start: 0.6873 (mp0) cc_final: 0.6434 (mt-10) REVERT: F 474 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7261 (tp30) REVERT: F 572 ASP cc_start: 0.6769 (m-30) cc_final: 0.6545 (m-30) REVERT: F 669 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6298 (tp) REVERT: C 343 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8665 (mt-10) REVERT: C 387 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7887 (mtm110) REVERT: C 431 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: C 448 ASP cc_start: 0.7714 (t0) cc_final: 0.7504 (t0) REVERT: C 595 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8282 (mmp-170) REVERT: C 602 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9166 (mm) REVERT: C 653 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: C 733 THR cc_start: 0.5839 (OUTLIER) cc_final: 0.5535 (p) REVERT: A 343 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8512 (mt-10) outliers start: 110 outliers final: 59 residues processed: 347 average time/residue: 1.0997 time to fit residues: 460.1749 Evaluate side-chains 326 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 248 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 595 ARG Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain E residue 683 ILE Chi-restraints excluded: chain E residue 713 HIS Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 685 LYS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 576 LYS Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 619 ARG Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 387 ARG Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 756 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 261 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 311 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 122 optimal weight: 0.1980 chunk 232 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 713 HIS D 573 ASN F 594 ASN C 593 ASN C 680 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.187693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125106 restraints weight = 30674.419| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.99 r_work: 0.3219 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 26209 Z= 0.223 Angle : 0.612 12.345 35491 Z= 0.319 Chirality : 0.047 0.206 3987 Planarity : 0.005 0.074 4508 Dihedral : 8.171 107.357 3633 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.32 % Favored : 94.39 % Rotamer: Outliers : 3.73 % Allowed : 20.25 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 3157 helix: 0.45 (0.15), residues: 1198 sheet: -0.44 (0.25), residues: 450 loop : -0.91 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 675 HIS 0.006 0.001 HIS E 109 PHE 0.027 0.002 PHE D 696 TYR 0.026 0.002 TYR F 645 ARG 0.014 0.001 ARG E 570 Details of bonding type rmsd hydrogen bonds : bond 0.04724 ( 951) hydrogen bonds : angle 4.53528 ( 2676) metal coordination : bond 0.01007 ( 8) metal coordination : angle 1.92468 ( 6) covalent geometry : bond 0.00557 (26201) covalent geometry : angle 0.61124 (35485) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 248 time to evaluate : 2.920 Fit side-chains revert: symmetry clash REVERT: B 591 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7998 (mttt) REVERT: B 603 ASP cc_start: 0.9046 (p0) cc_final: 0.8717 (p0) REVERT: E 69 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8199 (mtm) REVERT: E 128 ARG cc_start: 0.6081 (OUTLIER) cc_final: 0.5425 (ttt-90) REVERT: E 151 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7855 (ttmm) REVERT: E 259 ILE cc_start: 0.7007 (mt) cc_final: 0.6612 (mm) REVERT: E 595 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6800 (ttp-110) REVERT: E 618 MET cc_start: 0.5826 (ppp) cc_final: 0.5593 (ppp) REVERT: E 674 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7542 (mmmm) REVERT: E 713 HIS cc_start: -0.0110 (OUTLIER) cc_final: -0.0705 (t70) REVERT: D 504 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: F 324 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8397 (m-40) REVERT: F 387 ARG cc_start: 0.7678 (ttp-110) cc_final: 0.7298 (ttp-170) REVERT: F 428 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.6762 (p90) REVERT: F 457 GLU cc_start: 0.6822 (mp0) cc_final: 0.6411 (mt-10) REVERT: F 474 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7294 (tp30) REVERT: F 572 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.6528 (m-30) REVERT: F 640 GLU cc_start: 0.2704 (OUTLIER) cc_final: 0.1834 (tp30) REVERT: F 669 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.5907 (tm) REVERT: C 343 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8719 (mt-10) REVERT: C 387 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7719 (mtm180) REVERT: C 431 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8093 (m-30) REVERT: C 595 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8264 (mmp-170) REVERT: C 602 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9169 (mm) REVERT: C 653 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: C 733 THR cc_start: 0.6090 (OUTLIER) cc_final: 0.5864 (p) REVERT: A 343 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8590 (mt-10) outliers start: 106 outliers final: 64 residues processed: 333 average time/residue: 1.0926 time to fit residues: 434.3548 Evaluate side-chains 327 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 241 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 595 ARG Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain E residue 683 ILE Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 713 HIS Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 685 LYS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 572 ASP Chi-restraints excluded: chain F residue 576 LYS Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 640 GLU Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 698 PHE Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 387 ARG Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 751 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 6.9990 chunk 260 optimal weight: 1.9990 chunk 194 optimal weight: 0.1980 chunk 55 optimal weight: 0.9990 chunk 288 optimal weight: 0.9990 chunk 184 optimal weight: 0.3980 chunk 243 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 298 optimal weight: 0.7980 chunk 227 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN F 324 ASN F 594 ASN C 324 ASN C 593 ASN C 680 HIS A 605 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.191388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.153339 restraints weight = 30430.688| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.54 r_work: 0.3349 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26209 Z= 0.106 Angle : 0.524 19.736 35491 Z= 0.274 Chirality : 0.042 0.193 3987 Planarity : 0.004 0.063 4508 Dihedral : 7.517 106.276 3633 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.40 % Favored : 95.38 % Rotamer: Outliers : 2.75 % Allowed : 21.69 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3157 helix: 0.81 (0.15), residues: 1193 sheet: -0.39 (0.26), residues: 441 loop : -0.74 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 675 HIS 0.004 0.001 HIS E 713 PHE 0.029 0.001 PHE E 35 TYR 0.015 0.001 TYR F 645 ARG 0.015 0.000 ARG E 570 Details of bonding type rmsd hydrogen bonds : bond 0.02965 ( 951) hydrogen bonds : angle 4.30346 ( 2676) metal coordination : bond 0.00400 ( 8) metal coordination : angle 1.74907 ( 6) covalent geometry : bond 0.00236 (26201) covalent geometry : angle 0.52325 (35485) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 257 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 603 ASP cc_start: 0.8884 (p0) cc_final: 0.8580 (p0) REVERT: E 128 ARG cc_start: 0.6152 (OUTLIER) cc_final: 0.5439 (ttt-90) REVERT: E 151 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7845 (ttmm) REVERT: E 197 MET cc_start: 0.7324 (mtm) cc_final: 0.7076 (mtm) REVERT: E 259 ILE cc_start: 0.6818 (mt) cc_final: 0.6404 (mm) REVERT: E 416 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7963 (tmmm) REVERT: E 618 MET cc_start: 0.5773 (ppp) cc_final: 0.5504 (ppp) REVERT: E 713 HIS cc_start: -0.0542 (OUTLIER) cc_final: -0.1079 (t70) REVERT: D 504 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: F 428 TYR cc_start: 0.7587 (OUTLIER) cc_final: 0.6808 (p90) REVERT: F 457 GLU cc_start: 0.6958 (mp0) cc_final: 0.6515 (mt-10) REVERT: F 474 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7048 (tp30) REVERT: F 557 GLU cc_start: 0.5751 (pp20) cc_final: 0.5416 (pp20) REVERT: F 669 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6485 (tp) REVERT: C 343 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8535 (mt-10) REVERT: C 387 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7622 (mtm180) REVERT: C 431 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: C 602 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9217 (mm) REVERT: C 653 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: C 733 THR cc_start: 0.5976 (OUTLIER) cc_final: 0.5754 (p) REVERT: A 343 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8346 (mt-10) outliers start: 78 outliers final: 50 residues processed: 321 average time/residue: 1.0867 time to fit residues: 422.9048 Evaluate side-chains 312 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 247 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 683 ILE Chi-restraints excluded: chain E residue 713 HIS Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 573 ASN Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 576 LYS Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 700 LEU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 387 ARG Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 746 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 61 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 292 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 143 optimal weight: 0.0010 chunk 174 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN F 324 ASN F 594 ASN C 593 ASN C 680 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.187343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124074 restraints weight = 30435.445| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.90 r_work: 0.3207 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 26209 Z= 0.258 Angle : 0.653 17.666 35491 Z= 0.338 Chirality : 0.048 0.292 3987 Planarity : 0.005 0.086 4508 Dihedral : 8.222 108.557 3633 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.57 % Favored : 94.14 % Rotamer: Outliers : 3.20 % Allowed : 21.41 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3157 helix: 0.39 (0.15), residues: 1200 sheet: -0.50 (0.25), residues: 450 loop : -0.93 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 675 HIS 0.007 0.001 HIS A 548 PHE 0.030 0.002 PHE D 696 TYR 0.026 0.002 TYR A 482 ARG 0.015 0.001 ARG E 570 Details of bonding type rmsd hydrogen bonds : bond 0.05087 ( 951) hydrogen bonds : angle 4.59205 ( 2676) metal coordination : bond 0.01157 ( 8) metal coordination : angle 1.92060 ( 6) covalent geometry : bond 0.00644 (26201) covalent geometry : angle 0.65294 (35485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19693.52 seconds wall clock time: 339 minutes 23.04 seconds (20363.04 seconds total)