Starting phenix.real_space_refine on Mon Aug 25 05:27:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wgy_37522/08_2025/8wgy_37522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wgy_37522/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wgy_37522/08_2025/8wgy_37522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wgy_37522/08_2025/8wgy_37522.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wgy_37522/08_2025/8wgy_37522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wgy_37522/08_2025/8wgy_37522.map" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} 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: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} 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: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} 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: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} 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: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} 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: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} 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: 5.60, per 1000 atoms: 0.22 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: 2.21 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.76 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: 4.46 Time building geometry restraints manager: 3.01 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 801) selection = (chain 'B' and resid 323 through 801) selection = (chain 'C' and resid 323 through 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: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.460 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 25.690 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.120 ------------------------------------------------------------------------------- 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 : 8.27 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (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 ARG 0.012 0.000 ARG E 570 TYR 0.016 0.001 TYR D 482 PHE 0.031 0.001 PHE A 759 TRP 0.015 0.001 TRP F 675 HIS 0.003 0.001 HIS E 109 Details of bonding type rmsd covalent geometry : bond 0.00891 (26201) covalent geometry : angle 0.89566 (35485) hydrogen bonds : bond 0.07392 ( 951) hydrogen bonds : angle 4.64534 ( 2676) metal coordination : bond 0.00467 ( 8) metal coordination : angle 2.05184 ( 6) *********************** 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 : 1.046 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: 0.5358 time to fit residues: 177.8447 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 : 0.880 ------------------------------------------------------------------------------- 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 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.190982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151583 restraints weight = 30463.283| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.53 r_work: 0.3320 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.0567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 26209 Z= 0.152 Angle : 0.551 10.564 35491 Z= 0.290 Chirality : 0.044 0.222 3987 Planarity : 0.005 0.085 4508 Dihedral : 8.992 113.923 3668 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.72 % Favored : 95.09 % Rotamer: Outliers : 3.66 % Allowed : 15.77 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.15), residues: 3157 helix: 0.61 (0.15), residues: 1204 sheet: -0.14 (0.26), residues: 431 loop : -0.86 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 570 TYR 0.018 0.001 TYR A 482 PHE 0.021 0.001 PHE D 696 TRP 0.012 0.001 TRP F 675 HIS 0.006 0.001 HIS F 629 Details of bonding type rmsd covalent geometry : bond 0.00373 (26201) covalent geometry : angle 0.55072 (35485) hydrogen bonds : bond 0.03945 ( 951) hydrogen bonds : angle 4.46174 ( 2676) metal coordination : bond 0.00374 ( 8) metal coordination : angle 2.14038 ( 6) *********************** 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 368 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 264 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: B 591 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7929 (mttt) REVERT: E 52 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5425 (mt) REVERT: E 69 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8063 (mtm) REVERT: E 151 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7903 (ttmm) REVERT: D 262 ASN cc_start: 0.6757 (OUTLIER) cc_final: 0.6474 (t0) REVERT: D 320 PRO cc_start: 0.7870 (Cg_endo) cc_final: 0.7629 (Cg_exo) REVERT: D 504 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: F 428 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.7097 (p90) REVERT: F 457 GLU cc_start: 0.6830 (mp0) cc_final: 0.6435 (mt-10) REVERT: F 507 THR cc_start: 0.5930 (OUTLIER) cc_final: 0.5584 (m) REVERT: C 343 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: C 387 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7700 (mtm110) REVERT: C 448 ASP cc_start: 0.7581 (t0) cc_final: 0.7356 (t0) REVERT: C 653 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: A 477 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7945 (mmpt) outliers start: 104 outliers final: 38 residues processed: 341 average time/residue: 0.5883 time to fit residues: 236.0189 Evaluate side-chains 285 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 235 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 69 MET 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 D residue 262 ASN 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 343 GLU Chi-restraints excluded: chain C residue 387 ARG Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 599 THR 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 401 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 477 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 100 optimal weight: 0.3980 chunk 98 optimal weight: 20.0000 chunk 170 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 117 optimal weight: 0.0770 chunk 140 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 285 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 overall best weight: 0.8740 ------------------------------------------------------------------------------- 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 D 660 GLN F 324 ASN F 594 ASN C 593 ASN A 605 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.192159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140979 restraints weight = 30839.609| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.67 r_work: 0.3340 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26209 Z= 0.109 Angle : 0.491 6.498 35491 Z= 0.261 Chirality : 0.042 0.201 3987 Planarity : 0.004 0.070 4508 Dihedral : 7.847 108.644 3642 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.60 % Rotamer: Outliers : 3.38 % Allowed : 17.18 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.15), residues: 3157 helix: 0.81 (0.15), residues: 1201 sheet: -0.19 (0.26), residues: 434 loop : -0.78 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 636 TYR 0.019 0.001 TYR E 670 PHE 0.019 0.001 PHE C 698 TRP 0.011 0.001 TRP F 675 HIS 0.004 0.001 HIS F 629 Details of bonding type rmsd covalent geometry : bond 0.00252 (26201) covalent geometry : angle 0.49092 (35485) hydrogen bonds : bond 0.03149 ( 951) hydrogen bonds : angle 4.29166 ( 2676) metal coordination : bond 0.00322 ( 8) metal coordination : angle 1.89555 ( 6) *********************** 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 359 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 263 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 52 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5359 (mt) REVERT: E 69 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8044 (mtm) REVERT: E 151 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7764 (ttmm) REVERT: E 416 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8013 (tmmm) REVERT: E 683 ILE cc_start: 0.5977 (OUTLIER) cc_final: 0.5762 (pp) REVERT: D 262 ASN cc_start: 0.6750 (OUTLIER) cc_final: 0.6495 (t0) REVERT: D 504 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: D 554 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8472 (t80) REVERT: F 428 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.6985 (p90) REVERT: F 457 GLU cc_start: 0.6790 (mp0) cc_final: 0.6388 (mt-10) REVERT: C 343 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: C 387 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7633 (mtm110) REVERT: C 448 ASP cc_start: 0.7565 (t0) cc_final: 0.7304 (t0) REVERT: C 595 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8210 (mmp-170) REVERT: C 602 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9174 (mm) REVERT: C 653 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: C 733 THR cc_start: 0.5625 (OUTLIER) cc_final: 0.5257 (p) outliers start: 96 outliers final: 33 residues processed: 332 average time/residue: 0.5219 time to fit residues: 205.6954 Evaluate side-chains 290 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 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 683 ILE Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 426 MET 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 599 THR Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 428 TYR 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 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 A residue 401 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 746 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 100 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 111 optimal weight: 0.4980 chunk 27 optimal weight: 0.3980 chunk 276 optimal weight: 0.9980 chunk 157 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.192535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142834 restraints weight = 30349.799| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.57 r_work: 0.3370 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26209 Z= 0.102 Angle : 0.479 6.494 35491 Z= 0.256 Chirality : 0.042 0.197 3987 Planarity : 0.004 0.077 4508 Dihedral : 7.468 109.147 3637 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.28 % Favored : 95.53 % Rotamer: Outliers : 3.63 % Allowed : 17.71 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.15), residues: 3157 helix: 0.91 (0.15), residues: 1204 sheet: -0.24 (0.25), residues: 453 loop : -0.72 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 636 TYR 0.015 0.001 TYR A 482 PHE 0.019 0.001 PHE A 759 TRP 0.009 0.001 TRP F 675 HIS 0.003 0.001 HIS F 629 Details of bonding type rmsd covalent geometry : bond 0.00235 (26201) covalent geometry : angle 0.47850 (35485) hydrogen bonds : bond 0.02985 ( 951) hydrogen bonds : angle 4.21414 ( 2676) metal coordination : bond 0.00354 ( 8) metal coordination : angle 1.75166 ( 6) *********************** 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 359 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 256 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: B 554 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8291 (m-80) REVERT: B 603 ASP cc_start: 0.8975 (p0) cc_final: 0.8680 (p0) REVERT: B 684 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6931 (ttm) REVERT: E 52 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5465 (mt) REVERT: E 69 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7960 (mtm) REVERT: E 128 ARG cc_start: 0.5979 (OUTLIER) cc_final: 0.5498 (tmt170) REVERT: E 151 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7739 (ttmm) REVERT: E 252 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7729 (ttmt) REVERT: E 416 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7935 (tmmm) REVERT: E 516 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6793 (tp) REVERT: E 604 THR cc_start: 0.7152 (OUTLIER) cc_final: 0.6918 (p) REVERT: E 683 ILE cc_start: 0.5915 (OUTLIER) cc_final: 0.5683 (pp) REVERT: D 262 ASN cc_start: 0.6749 (OUTLIER) cc_final: 0.6485 (t0) REVERT: D 504 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: F 428 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.6823 (p90) REVERT: F 457 GLU cc_start: 0.6804 (mp0) cc_final: 0.6403 (mt-10) REVERT: F 542 PRO cc_start: 0.7550 (Cg_endo) cc_final: 0.7316 (Cg_exo) REVERT: F 669 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.6159 (tp) REVERT: C 382 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8356 (mt-10) REVERT: C 387 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7598 (mtm110) REVERT: C 448 ASP cc_start: 0.7528 (t0) cc_final: 0.7260 (t0) REVERT: C 595 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8226 (mmp-170) REVERT: C 602 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9185 (mm) REVERT: C 653 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: C 733 THR cc_start: 0.5667 (OUTLIER) cc_final: 0.5251 (p) outliers start: 103 outliers final: 43 residues processed: 337 average time/residue: 0.5479 time to fit residues: 220.1633 Evaluate side-chains 305 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 554 PHE Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 684 MET 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 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 449 THR Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 516 LEU 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 276 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 318 ILE 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 516 LEU 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 619 ARG Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 680 HIS 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 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 A residue 401 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 525 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 98 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 310 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 594 ASN F 763 HIS C 593 ASN C 680 HIS A 741 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.187082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122670 restraints weight = 30370.313| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.98 r_work: 0.3193 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 26209 Z= 0.290 Angle : 0.671 7.959 35491 Z= 0.349 Chirality : 0.049 0.215 3987 Planarity : 0.006 0.101 4508 Dihedral : 8.574 110.796 3637 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.45 % Favored : 94.30 % Rotamer: Outliers : 5.28 % Allowed : 17.22 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.15), residues: 3157 helix: 0.25 (0.15), residues: 1212 sheet: -0.40 (0.25), residues: 449 loop : -0.99 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 570 TYR 0.028 0.002 TYR A 482 PHE 0.034 0.002 PHE D 696 TRP 0.013 0.002 TRP C 350 HIS 0.007 0.001 HIS E 109 Details of bonding type rmsd covalent geometry : bond 0.00726 (26201) covalent geometry : angle 0.67028 (35485) hydrogen bonds : bond 0.05533 ( 951) hydrogen bonds : angle 4.66740 ( 2676) metal coordination : bond 0.01204 ( 8) metal coordination : angle 2.12001 ( 6) *********************** 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 398 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 248 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: B 603 ASP cc_start: 0.9112 (p0) cc_final: 0.8768 (p0) REVERT: E 128 ARG cc_start: 0.5996 (OUTLIER) cc_final: 0.5565 (tmt170) REVERT: E 151 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7957 (ttmm) REVERT: E 259 ILE cc_start: 0.7183 (mt) cc_final: 0.6773 (mm) REVERT: E 674 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7415 (mmmm) REVERT: D 504 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: F 324 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8494 (m-40) REVERT: F 387 ARG cc_start: 0.7820 (ttp-110) cc_final: 0.7398 (ttp-170) REVERT: F 457 GLU cc_start: 0.6850 (mp0) cc_final: 0.6405 (mt-10) REVERT: F 553 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8100 (p) REVERT: F 640 GLU cc_start: 0.2296 (OUTLIER) cc_final: 0.1831 (tp30) REVERT: F 669 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.5862 (tm) REVERT: F 751 LEU cc_start: 0.3088 (OUTLIER) cc_final: 0.2548 (mt) REVERT: C 387 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7701 (mtm180) REVERT: C 431 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: C 448 ASP cc_start: 0.7726 (t0) cc_final: 0.7451 (t0) REVERT: C 595 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8269 (mmp-170) REVERT: C 602 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9180 (mm) REVERT: C 653 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: C 733 THR cc_start: 0.5711 (OUTLIER) cc_final: 0.5399 (p) REVERT: C 734 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.6118 (mp) outliers start: 150 outliers final: 64 residues processed: 366 average time/residue: 0.5279 time to fit residues: 228.3603 Evaluate side-chains 321 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 241 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 599 THR 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 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 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 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 516 LEU 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 E residue 710 SER Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 318 ILE 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 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 428 TYR 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 640 GLU Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 751 LEU 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 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 653 GLU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 734 LEU 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 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 525 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 49 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 255 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 291 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 73 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 A 660 GLN ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.190860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149866 restraints weight = 30347.847| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.62 r_work: 0.3322 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26209 Z= 0.113 Angle : 0.517 16.593 35491 Z= 0.272 Chirality : 0.043 0.193 3987 Planarity : 0.004 0.075 4508 Dihedral : 7.751 107.577 3637 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.18 % Favored : 95.57 % Rotamer: Outliers : 3.66 % Allowed : 19.68 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.15), residues: 3157 helix: 0.68 (0.15), residues: 1192 sheet: -0.42 (0.25), residues: 456 loop : -0.78 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 570 TYR 0.015 0.001 TYR A 482 PHE 0.025 0.001 PHE A 698 TRP 0.009 0.001 TRP F 675 HIS 0.004 0.001 HIS F 629 Details of bonding type rmsd covalent geometry : bond 0.00266 (26201) covalent geometry : angle 0.51668 (35485) hydrogen bonds : bond 0.03239 ( 951) hydrogen bonds : angle 4.35497 ( 2676) metal coordination : bond 0.00452 ( 8) metal coordination : angle 1.78667 ( 6) *********************** 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 363 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 259 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: B 603 ASP cc_start: 0.8960 (p0) cc_final: 0.8600 (p0) REVERT: E 128 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.5494 (tmt170) REVERT: E 151 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7885 (ttmm) REVERT: E 259 ILE cc_start: 0.6924 (mt) cc_final: 0.6487 (mm) REVERT: E 416 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7990 (tmmm) REVERT: E 516 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.7004 (tp) REVERT: D 360 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6916 (tp30) REVERT: D 504 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: D 743 ILE cc_start: 0.5347 (OUTLIER) cc_final: 0.5109 (mm) REVERT: F 428 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.6982 (p90) REVERT: F 457 GLU cc_start: 0.6869 (mp0) cc_final: 0.6478 (mt-10) REVERT: F 542 PRO cc_start: 0.7551 (Cg_endo) cc_final: 0.7284 (Cg_exo) REVERT: F 669 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6381 (tp) REVERT: C 343 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8501 (mt-10) REVERT: C 387 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7714 (mtm110) REVERT: C 448 ASP cc_start: 0.7648 (t0) cc_final: 0.7371 (t0) REVERT: C 595 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8263 (mmp-170) REVERT: C 653 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: C 733 THR cc_start: 0.5816 (OUTLIER) cc_final: 0.5502 (p) outliers start: 104 outliers final: 49 residues processed: 341 average time/residue: 0.5199 time to fit residues: 211.2379 Evaluate side-chains 303 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 240 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 604 THR Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 779 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 516 LEU 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 D residue 276 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 360 GLU 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 582 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 743 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 428 TYR 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 669 LEU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 387 ARG 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 595 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain C residue 655 LEU 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 774 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 239 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.189959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124284 restraints weight = 30106.041| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.09 r_work: 0.3196 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26209 Z= 0.192 Angle : 0.575 7.353 35491 Z= 0.302 Chirality : 0.045 0.203 3987 Planarity : 0.005 0.068 4508 Dihedral : 7.949 109.032 3631 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.16 % Favored : 94.58 % Rotamer: Outliers : 3.91 % Allowed : 19.68 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.15), residues: 3157 helix: 0.52 (0.15), residues: 1203 sheet: -0.40 (0.25), residues: 451 loop : -0.84 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 570 TYR 0.022 0.001 TYR E 670 PHE 0.025 0.002 PHE D 696 TRP 0.011 0.002 TRP F 675 HIS 0.005 0.001 HIS E 109 Details of bonding type rmsd covalent geometry : bond 0.00477 (26201) covalent geometry : angle 0.57492 (35485) hydrogen bonds : bond 0.04357 ( 951) hydrogen bonds : angle 4.46650 ( 2676) metal coordination : bond 0.00796 ( 8) metal coordination : angle 1.83057 ( 6) *********************** 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 354 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 243 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: B 453 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: B 591 LYS cc_start: 0.8216 (mttt) cc_final: 0.7571 (mmtt) REVERT: B 603 ASP cc_start: 0.9100 (p0) cc_final: 0.8701 (p0) REVERT: E 128 ARG cc_start: 0.6008 (OUTLIER) cc_final: 0.5574 (tmt170) REVERT: E 151 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7862 (ttmm) REVERT: E 259 ILE cc_start: 0.7040 (mt) cc_final: 0.6655 (mm) REVERT: D 504 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: F 428 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.6767 (p90) REVERT: F 457 GLU cc_start: 0.6795 (mp0) cc_final: 0.6383 (mt-10) REVERT: F 640 GLU cc_start: 0.2616 (OUTLIER) cc_final: 0.1946 (tp30) REVERT: F 669 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.5811 (tm) REVERT: C 324 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.8271 (t0) REVERT: C 343 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8689 (mt-10) REVERT: C 382 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8598 (mt-10) REVERT: C 387 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7753 (mtm110) REVERT: C 448 ASP cc_start: 0.7746 (t0) cc_final: 0.7492 (t0) REVERT: C 595 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8241 (mmp-170) REVERT: C 653 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: C 733 THR cc_start: 0.5761 (OUTLIER) cc_final: 0.5464 (p) REVERT: A 477 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8046 (mmpt) outliers start: 111 outliers final: 56 residues processed: 329 average time/residue: 0.4949 time to fit residues: 195.1706 Evaluate side-chains 310 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 239 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 702 ILE Chi-restraints excluded: chain B residue 779 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 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 516 LEU 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 D residue 276 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 318 ILE 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 582 VAL 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 357 PHE Chi-restraints excluded: chain F residue 428 TYR 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 324 ASN Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 387 ARG 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 653 GLU Chi-restraints excluded: chain C residue 655 LEU 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 774 LEU 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 554 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 163 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 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** 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 = 0.4144 r_free = 0.4144 target = 0.189031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125411 restraints weight = 30370.069| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.09 r_work: 0.3201 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26209 Z= 0.180 Angle : 0.577 16.577 35491 Z= 0.301 Chirality : 0.045 0.201 3987 Planarity : 0.005 0.077 4508 Dihedral : 7.954 107.151 3631 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.97 % Favored : 94.74 % Rotamer: Outliers : 3.84 % Allowed : 19.96 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.15), residues: 3157 helix: 0.51 (0.15), residues: 1198 sheet: -0.42 (0.25), residues: 450 loop : -0.86 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 570 TYR 0.021 0.001 TYR A 482 PHE 0.022 0.002 PHE C 698 TRP 0.010 0.001 TRP F 675 HIS 0.005 0.001 HIS F 629 Details of bonding type rmsd covalent geometry : bond 0.00443 (26201) covalent geometry : angle 0.57641 (35485) hydrogen bonds : bond 0.04161 ( 951) hydrogen bonds : angle 4.46315 ( 2676) metal coordination : bond 0.00750 ( 8) metal coordination : angle 1.84452 ( 6) *********************** 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 353 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 244 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: B 453 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7844 (tp30) REVERT: B 591 LYS cc_start: 0.8202 (mttt) cc_final: 0.7594 (mmtt) REVERT: B 603 ASP cc_start: 0.9093 (p0) cc_final: 0.8704 (p0) REVERT: E 128 ARG cc_start: 0.6003 (OUTLIER) cc_final: 0.5552 (tmt170) REVERT: E 151 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7844 (ttmm) REVERT: E 259 ILE cc_start: 0.6991 (mt) cc_final: 0.6606 (mm) REVERT: E 595 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6706 (ttp-110) REVERT: E 618 MET cc_start: 0.5804 (ppp) cc_final: 0.5537 (ppp) REVERT: D 504 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: F 428 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.6851 (p90) REVERT: F 457 GLU cc_start: 0.6818 (mp0) cc_final: 0.6402 (mt-10) REVERT: F 474 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: F 640 GLU cc_start: 0.2590 (OUTLIER) cc_final: 0.1912 (tp30) REVERT: F 669 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.5867 (tm) REVERT: C 343 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8746 (mt-10) REVERT: C 387 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7736 (mtm110) REVERT: C 448 ASP cc_start: 0.7734 (t0) cc_final: 0.7492 (t0) REVERT: C 595 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8266 (mmp-170) REVERT: C 602 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9142 (mm) REVERT: C 653 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: C 733 THR cc_start: 0.5818 (OUTLIER) cc_final: 0.5465 (p) outliers start: 109 outliers final: 63 residues processed: 326 average time/residue: 0.5159 time to fit residues: 201.0866 Evaluate side-chains 315 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 237 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 702 ILE Chi-restraints excluded: chain B residue 779 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 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 516 LEU 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 628 THR 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 318 ILE 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 732 VAL Chi-restraints excluded: chain F residue 334 LEU 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 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 387 ARG 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 706 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 339 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 35 optimal weight: 0.7980 chunk 116 optimal weight: 30.0000 chunk 146 optimal weight: 0.3980 chunk 238 optimal weight: 0.9990 chunk 312 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 159 optimal weight: 0.1980 chunk 282 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 713 HIS D 573 ASN F 324 ASN C 324 ASN C 593 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.192132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.154765 restraints weight = 30535.580| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.47 r_work: 0.3375 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26209 Z= 0.099 Angle : 0.492 7.555 35491 Z= 0.261 Chirality : 0.042 0.189 3987 Planarity : 0.004 0.071 4508 Dihedral : 7.283 106.160 3631 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.05 % Favored : 95.72 % Rotamer: Outliers : 2.92 % Allowed : 20.74 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.15), residues: 3157 helix: 0.86 (0.15), residues: 1202 sheet: -0.44 (0.25), residues: 449 loop : -0.68 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 570 TYR 0.014 0.001 TYR D 482 PHE 0.023 0.001 PHE A 759 TRP 0.010 0.001 TRP F 675 HIS 0.004 0.001 HIS D 680 Details of bonding type rmsd covalent geometry : bond 0.00225 (26201) covalent geometry : angle 0.49171 (35485) hydrogen bonds : bond 0.02798 ( 951) hydrogen bonds : angle 4.21500 ( 2676) metal coordination : bond 0.00394 ( 8) metal coordination : angle 1.72986 ( 6) *********************** 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 335 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 252 time to evaluate : 1.061 Fit side-chains REVERT: B 591 LYS cc_start: 0.8105 (mttt) cc_final: 0.7741 (mmtt) REVERT: B 603 ASP cc_start: 0.8885 (p0) cc_final: 0.8538 (p0) REVERT: E 128 ARG cc_start: 0.6022 (OUTLIER) cc_final: 0.5514 (tmt170) REVERT: E 151 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7812 (ttmm) REVERT: E 197 MET cc_start: 0.7290 (mtm) cc_final: 0.7023 (mtm) REVERT: E 259 ILE cc_start: 0.6761 (mt) cc_final: 0.6365 (mm) REVERT: E 516 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6989 (tp) REVERT: E 595 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6494 (ttp-110) REVERT: E 713 HIS cc_start: -0.0219 (OUTLIER) cc_final: -0.0753 (t-90) REVERT: D 504 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: F 428 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.6685 (p90) REVERT: F 457 GLU cc_start: 0.6896 (mp0) cc_final: 0.6452 (mt-10) REVERT: F 474 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7079 (tp30) REVERT: F 542 PRO cc_start: 0.7537 (Cg_endo) cc_final: 0.7305 (Cg_exo) REVERT: C 343 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8431 (mt-10) REVERT: C 387 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7508 (mtm180) REVERT: C 595 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8230 (mmp-170) REVERT: C 602 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9187 (mm) REVERT: C 636 ARG cc_start: 0.7294 (mtp-110) cc_final: 0.7016 (mtp-110) REVERT: C 733 THR cc_start: 0.5901 (OUTLIER) cc_final: 0.5659 (p) outliers start: 83 outliers final: 49 residues processed: 318 average time/residue: 0.4951 time to fit residues: 188.5574 Evaluate side-chains 301 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 239 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 702 ILE Chi-restraints excluded: chain B residue 779 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 423 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 595 ARG 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 316 VAL Chi-restraints excluded: chain D residue 318 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 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 498 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 387 ARG 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 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 655 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 774 LEU 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 613 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 671 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 13 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 312 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.189802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.152304 restraints weight = 30482.670| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.49 r_work: 0.3333 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26209 Z= 0.142 Angle : 0.544 11.468 35491 Z= 0.285 Chirality : 0.043 0.198 3987 Planarity : 0.004 0.067 4508 Dihedral : 7.422 107.315 3629 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.78 % Favored : 95.00 % Rotamer: Outliers : 2.54 % Allowed : 21.69 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.15), residues: 3157 helix: 0.80 (0.15), residues: 1198 sheet: -0.38 (0.25), residues: 446 loop : -0.71 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 570 TYR 0.022 0.001 TYR E 670 PHE 0.030 0.001 PHE E 35 TRP 0.014 0.001 TRP F 675 HIS 0.004 0.001 HIS A 680 Details of bonding type rmsd covalent geometry : bond 0.00346 (26201) covalent geometry : angle 0.54328 (35485) hydrogen bonds : bond 0.03653 ( 951) hydrogen bonds : angle 4.30281 ( 2676) metal coordination : bond 0.00576 ( 8) metal coordination : angle 1.66291 ( 6) ********************** 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 320 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 248 time to evaluate : 1.110 Fit side-chains REVERT: B 591 LYS cc_start: 0.8119 (mttt) cc_final: 0.7730 (mmtt) REVERT: B 603 ASP cc_start: 0.8917 (p0) cc_final: 0.8583 (p0) REVERT: E 128 ARG cc_start: 0.6026 (OUTLIER) cc_final: 0.5512 (tmt170) REVERT: E 151 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7880 (ttmm) REVERT: E 259 ILE cc_start: 0.6644 (mt) cc_final: 0.6255 (mm) REVERT: E 416 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7899 (tmmm) REVERT: E 516 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7093 (tp) REVERT: E 595 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6658 (ttp-110) REVERT: D 504 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: F 428 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.6868 (p90) REVERT: F 457 GLU cc_start: 0.6969 (mp0) cc_final: 0.6512 (mt-10) REVERT: F 474 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7078 (tp30) REVERT: F 542 PRO cc_start: 0.7553 (Cg_endo) cc_final: 0.7318 (Cg_exo) REVERT: F 640 GLU cc_start: 0.2758 (OUTLIER) cc_final: 0.1834 (tp30) REVERT: C 343 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8459 (mt-10) REVERT: C 387 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7735 (mtm110) REVERT: C 595 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8220 (mmp-170) REVERT: C 602 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9204 (mm) REVERT: C 636 ARG cc_start: 0.7366 (mtp-110) cc_final: 0.7109 (mtp-110) REVERT: C 653 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: C 733 THR cc_start: 0.6067 (OUTLIER) cc_final: 0.5855 (p) outliers start: 72 outliers final: 46 residues processed: 304 average time/residue: 0.5677 time to fit residues: 205.1766 Evaluate side-chains 303 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 242 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 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 516 LEU Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 595 ARG 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 318 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 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 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 581 CYS Chi-restraints excluded: chain F residue 640 GLU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 387 ARG 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 401 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 554 PHE 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 259 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 222 optimal weight: 20.0000 chunk 171 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 281 optimal weight: 0.0570 chunk 251 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.190170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.152568 restraints weight = 30331.233| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.50 r_work: 0.3337 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26209 Z= 0.135 Angle : 0.540 14.384 35491 Z= 0.282 Chirality : 0.043 0.195 3987 Planarity : 0.004 0.067 4508 Dihedral : 7.418 106.670 3629 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.59 % Favored : 95.19 % Rotamer: Outliers : 2.82 % Allowed : 21.51 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.15), residues: 3157 helix: 0.78 (0.15), residues: 1198 sheet: -0.40 (0.25), residues: 446 loop : -0.71 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 570 TYR 0.018 0.001 TYR A 482 PHE 0.026 0.001 PHE A 759 TRP 0.014 0.001 TRP F 675 HIS 0.004 0.001 HIS A 680 Details of bonding type rmsd covalent geometry : bond 0.00327 (26201) covalent geometry : angle 0.53992 (35485) hydrogen bonds : bond 0.03540 ( 951) hydrogen bonds : angle 4.30901 ( 2676) metal coordination : bond 0.00543 ( 8) metal coordination : angle 1.64408 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9574.68 seconds wall clock time: 163 minutes 47.92 seconds (9827.92 seconds total)