Starting phenix.real_space_refine on Wed May 21 21:40:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh6_37530/05_2025/8wh6_37530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh6_37530/05_2025/8wh6_37530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wh6_37530/05_2025/8wh6_37530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh6_37530/05_2025/8wh6_37530.map" model { file = "/net/cci-nas-00/data/ceres_data/8wh6_37530/05_2025/8wh6_37530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh6_37530/05_2025/8wh6_37530.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 11 5.49 5 S 94 5.16 5 C 13946 2.51 5 N 3898 2.21 5 O 4136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22087 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3346 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 418 Unresolved non-hydrogen angles: 530 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 13, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 235 Chain: "B" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3313 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 452 Unresolved non-hydrogen angles: 571 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 15, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 232 Chain: "C" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3285 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 483 Unresolved non-hydrogen angles: 609 Unresolved non-hydrogen dihedrals: 399 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 8, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 237 Chain: "D" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 3722 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 211} Link IDs: {'PTRANS': 27, 'TRANS': 522} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 752 Unresolved non-hydrogen angles: 944 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 11, 'TYR:plan': 8, 'ASN:plan1': 18, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 17, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 399 Chain: "E" Number of atoms: 5142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5142 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 274} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 718} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 973 Unresolved non-hydrogen angles: 1217 Unresolved non-hydrogen dihedrals: 788 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 29, 'TYR:plan': 7, 'ASN:plan1': 20, 'HIS:plan': 5, 'PHE:plan': 12, 'GLU:plan': 26, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 521 Chain: "F" Number of atoms: 3112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3112 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 441} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 662 Unresolved non-hydrogen angles: 839 Unresolved non-hydrogen dihedrals: 544 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 12, 'ASP:plan': 16, 'PHE:plan': 9, 'GLU:plan': 17, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 363 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: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10236 SG CYS D 282 89.434 87.170 119.618 1.00 38.71 S ATOM 10255 SG CYS D 285 87.887 90.513 120.688 1.00 37.84 S ATOM 10449 SG CYS D 314 88.020 87.610 123.188 1.00 36.71 S ATOM 15490 SG CYS E 282 71.721 66.908 136.632 1.00 31.63 S ATOM 15506 SG CYS E 285 74.256 68.425 138.230 1.00 33.51 S ATOM 15710 SG CYS E 314 72.102 70.855 138.795 1.00 32.65 S Residues with excluded nonbonded symmetry interactions: 524 residue: pdb=" N PHE A 698 " occ=0.57 ... (9 atoms not shown) pdb=" CZ PHE A 698 " occ=0.57 residue: pdb=" N TYR A 699 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR A 699 " occ=0.50 residue: pdb=" N LEU A 700 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU A 700 " occ=0.97 residue: pdb=" N LYS A 701 " occ=0.47 ... (7 atoms not shown) pdb=" NZ LYS A 701 " occ=0.47 residue: pdb=" N ILE A 702 " occ=0.80 ... (6 atoms not shown) pdb=" CD1 ILE A 702 " occ=0.80 residue: pdb=" N GLY A 703 " occ=0.54 ... (2 atoms not shown) pdb=" O GLY A 703 " occ=0.54 residue: pdb=" N THR A 704 " occ=0.32 ... (3 atoms not shown) pdb=" CB THR A 704 " occ=0.32 residue: pdb=" N LEU A 705 " occ=0.39 ... (3 atoms not shown) pdb=" CB LEU A 705 " occ=0.39 residue: pdb=" N LEU A 706 " occ=0.45 ... (3 atoms not shown) pdb=" CB LEU A 706 " occ=0.45 residue: pdb=" N VAL A 707 " occ=0.29 ... (3 atoms not shown) pdb=" CB VAL A 707 " occ=0.29 residue: pdb=" N SER A 708 " occ=0.39 ... (3 atoms not shown) pdb=" CB SER A 708 " occ=0.39 residue: pdb=" N SER A 709 " occ=0.25 ... (3 atoms not shown) pdb=" CB SER A 709 " occ=0.25 ... (remaining 512 not shown) Time building chain proxies: 14.02, per 1000 atoms: 0.63 Number of scatterers: 22087 At special positions: 0 Unit cell: (127.68, 130.2, 156.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 94 16.00 P 11 15.00 O 4136 8.00 N 3898 7.00 C 13946 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.69 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 802 " pdb="ZN ZN D 802 " - pdb=" NE2 HIS D 290 " pdb="ZN ZN D 802 " - pdb=" SG CYS D 285 " pdb="ZN ZN D 802 " - pdb=" SG CYS D 282 " pdb="ZN ZN D 802 " - pdb=" SG CYS D 314 " pdb=" ZN E 801 " pdb="ZN ZN E 801 " - pdb=" SG CYS E 285 " pdb="ZN ZN E 801 " - pdb=" SG CYS E 282 " pdb="ZN ZN E 801 " - pdb=" SG CYS E 314 " Number of angles added : 3 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6036 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 47 sheets defined 43.2% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.929A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 399 removed outlier: 3.732A pdb=" N THR A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 removed outlier: 3.672A pdb=" N ASP A 432 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 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 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.562A pdb=" N THR A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.507A pdb=" N ILE A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 635 through 641 removed outlier: 3.519A pdb=" N ASN A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) 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 692 removed outlier: 3.793A pdb=" N GLU A 692 " --> pdb=" O THR A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 693 through 704 removed outlier: 3.696A pdb=" N ALA A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE A 698 " --> pdb=" O PRO A 694 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 703 " --> pdb=" O TYR A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 715 Proline residue: A 715 - end of helix Processing helix chain 'A' and resid 716 through 724 Processing helix chain 'A' and resid 735 through 745 Processing helix chain 'A' and resid 752 through 763 Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.743A pdb=" N THR B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.895A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 400 removed outlier: 3.790A pdb=" N THR B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 475 through 488 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 removed outlier: 3.568A pdb=" N ALA B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 578 Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 665 through 680 Processing helix chain 'B' and resid 693 through 695 No H-bonds generated for 'chain 'B' and resid 693 through 695' Processing helix chain 'B' and resid 696 through 705 removed outlier: 3.506A pdb=" N GLY B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 724 Processing helix chain 'B' and resid 735 through 747 Processing helix chain 'B' and resid 748 through 764 removed outlier: 5.523A pdb=" N HIS B 754 " --> pdb=" O ARG B 750 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASP B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.773A 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 381 removed outlier: 3.816A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 398 Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 528 through 533 removed outlier: 3.771A pdb=" N ILE C 531 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 577 Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'C' and resid 696 through 705 removed outlier: 4.536A pdb=" N THR C 704 " --> pdb=" O LEU C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 715 No H-bonds generated for 'chain 'C' and resid 713 through 715' Processing helix chain 'C' and resid 716 through 724 removed outlier: 3.671A pdb=" N LYS C 722 " --> pdb=" O THR C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 745 removed outlier: 3.801A pdb=" N LYS C 745 " --> pdb=" O GLN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 removed outlier: 6.334A pdb=" N HIS C 754 " --> pdb=" O ARG C 750 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ASP C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 784 Processing helix chain 'D' and resid 242 through 255 removed outlier: 3.666A pdb=" N ILE D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 336 Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 376 through 381 removed outlier: 4.356A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 399 removed outlier: 3.799A pdb=" N THR D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 435 removed outlier: 3.504A pdb=" N LYS D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 4.154A 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: 3.602A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU D 460 " --> pdb=" O PRO D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 570 through 578 removed outlier: 3.530A pdb=" N ILE D 574 " --> pdb=" O ARG D 570 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 619 Processing helix chain 'D' and resid 632 through 636 removed outlier: 3.533A pdb=" N ARG D 636 " --> pdb=" O PRO D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 642 removed outlier: 4.076A pdb=" N ASN D 641 " --> pdb=" O ALA D 638 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN D 642 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 4.352A pdb=" N GLY D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 680 Processing helix chain 'D' and resid 697 through 703 removed outlier: 4.272A pdb=" N GLY D 703 " --> pdb=" O TYR D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 722 removed outlier: 3.850A pdb=" N THR D 718 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP D 719 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS D 722 " --> pdb=" O THR D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 731 removed outlier: 3.996A pdb=" N ASN D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 747 Processing helix chain 'D' and resid 753 through 763 removed outlier: 4.125A pdb=" N GLU D 757 " --> pdb=" O GLY D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 783 removed outlier: 3.569A pdb=" N SER D 783 " --> pdb=" O ILE D 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 779 through 783' Processing helix chain 'E' and resid 36 through 47 Processing helix chain 'E' and resid 78 through 104 Processing helix chain 'E' and resid 108 through 119 removed outlier: 4.169A pdb=" N ASN E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 150 through 160 Processing helix chain 'E' and resid 163 through 168 Processing helix chain 'E' and resid 203 through 208 removed outlier: 3.769A pdb=" N TYR E 207 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 4.075A 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 310 through 314 removed outlier: 3.593A pdb=" N SER E 313 " --> pdb=" O ASN E 310 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS E 314 " --> pdb=" O PRO E 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 310 through 314' Processing helix chain 'E' and resid 325 through 335 removed outlier: 3.512A pdb=" N ILE E 329 " --> pdb=" O LYS E 325 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 Processing helix chain 'E' and resid 372 through 375 Processing helix chain 'E' and resid 381 through 385 removed outlier: 3.759A pdb=" N LEU E 384 " --> pdb=" O SER E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 400 removed outlier: 3.735A pdb=" N THR E 391 " --> pdb=" O ARG E 387 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE E 396 " --> pdb=" O VAL E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 436 Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 475 through 488 Processing helix chain 'E' and resid 508 through 521 removed outlier: 3.600A pdb=" N THR E 512 " --> pdb=" O GLY E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.576A pdb=" N THR E 533 " --> pdb=" O GLN E 529 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP E 534 " --> pdb=" O THR E 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 529 through 534' Processing helix chain 'E' and resid 541 through 547 Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'E' and resid 614 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 641 removed outlier: 3.738A pdb=" N ASN E 641 " --> pdb=" O GLU E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 Processing helix chain 'E' and resid 664 through 680 Processing helix chain 'E' and resid 693 through 705 removed outlier: 3.932A pdb=" N PHE E 698 " --> pdb=" O PRO E 694 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR E 699 " --> pdb=" O ASP E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 716 through 724 removed outlier: 3.502A pdb=" N LEU E 720 " --> pdb=" O LEU E 716 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 747 removed outlier: 4.312A pdb=" N LYS E 745 " --> pdb=" O GLN E 741 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR E 746 " --> pdb=" O LYS E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 763 Processing helix chain 'E' and resid 779 through 784 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.625A pdb=" N ALA F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) removed outlier: 3.731A 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: 3.628A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 401 removed outlier: 3.629A pdb=" N THR F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL F 401 " --> pdb=" O ARG F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 434 removed outlier: 3.890A pdb=" N ASP F 432 " --> pdb=" O SER F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 469 removed outlier: 3.905A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 488 Processing helix chain 'F' and resid 508 through 520 Processing helix chain 'F' and resid 529 through 533 Processing helix chain 'F' and resid 541 through 547 removed outlier: 4.256A pdb=" N ALA F 545 " --> pdb=" O ASN F 541 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET F 547 " --> pdb=" O PHE F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 578 Processing helix chain 'F' and resid 616 through 619 Processing helix chain 'F' and resid 632 through 634 No H-bonds generated for 'chain 'F' and resid 632 through 634' Processing helix chain 'F' and resid 635 through 641 Processing helix chain 'F' and resid 653 through 662 removed outlier: 4.044A pdb=" N GLY F 657 " --> pdb=" O GLU F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'F' and resid 693 through 705 removed outlier: 3.633A pdb=" N ALA F 697 " --> pdb=" O ILE F 693 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE F 698 " --> pdb=" O PRO F 694 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR F 699 " --> pdb=" O ASP F 695 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU F 700 " --> pdb=" O PHE F 696 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY F 703 " --> pdb=" O TYR F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 713 through 716 Processing helix chain 'F' and resid 717 through 722 removed outlier: 3.640A pdb=" N SER F 721 " --> pdb=" O MET F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 735 through 745 Processing helix chain 'F' and resid 752 through 763 Processing helix chain 'F' and resid 779 through 784 Processing sheet with id=AA1, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 415 Processing sheet with id=AA3, first strand: chain 'A' and resid 525 through 526 removed outlier: 6.476A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASP A 603 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N CYS A 555 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N THR A 604 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N PHE A 501 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 582 Processing sheet with id=AA5, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.409A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 706 through 708 Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 728 Processing sheet with id=AA8, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA9, first strand: chain 'B' and resid 412 through 415 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 603 removed outlier: 6.890A pdb=" N THR B 499 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB3, first strand: chain 'B' and resid 629 through 631 removed outlier: 6.283A pdb=" N HIS B 629 " --> pdb=" O LYS B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 706 through 708 Processing sheet with id=AB5, first strand: chain 'B' and resid 726 through 728 Processing sheet with id=AB6, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB7, first strand: chain 'C' and resid 412 through 415 Processing sheet with id=AB8, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.522A pdb=" N THR C 499 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR C 604 " --> pdb=" O THR C 499 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N PHE C 501 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AC1, first strand: chain 'C' and resid 629 through 631 removed outlier: 6.556A pdb=" N HIS C 629 " --> pdb=" O LYS C 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 706 through 708 Processing sheet with id=AC3, first strand: chain 'C' and resid 726 through 728 Processing sheet with id=AC4, first strand: chain 'D' and resid 294 through 299 Processing sheet with id=AC5, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC6, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.652A pdb=" N VAL D 419 " --> pdb=" O TYR D 428 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 524 through 526 removed outlier: 6.221A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N THR D 604 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N PHE D 501 " --> pdb=" O THR D 604 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AC9, first strand: chain 'D' and resid 629 through 631 Processing sheet with id=AD1, first strand: chain 'D' and resid 706 through 707 removed outlier: 3.768A pdb=" N ILE D 777 " --> pdb=" O VAL D 707 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 734 through 735 Processing sheet with id=AD3, first strand: chain 'E' and resid 33 through 35 removed outlier: 4.264A pdb=" N PHE E 12 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 64 through 73 removed outlier: 3.653A pdb=" N ILE E 67 " --> pdb=" O THR E 140 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR E 140 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 11.809A pdb=" N MET E 69 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N LEU E 138 " --> pdb=" O MET E 69 " (cutoff:3.500A) removed outlier: 12.032A pdb=" N VAL E 71 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 10.995A pdb=" N ILE E 136 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 12.509A pdb=" N LEU E 73 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 11.571A pdb=" N HIS E 134 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 64 through 73 removed outlier: 3.653A pdb=" N ILE E 67 " --> pdb=" O THR E 140 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR E 140 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 11.809A pdb=" N MET E 69 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N LEU E 138 " --> pdb=" O MET E 69 " (cutoff:3.500A) removed outlier: 12.032A pdb=" N VAL E 71 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 10.995A pdb=" N ILE E 136 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 12.509A pdb=" N LEU E 73 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 11.571A pdb=" N HIS E 134 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR E 143 " --> pdb=" O PHE E 221 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 294 through 299 Processing sheet with id=AD7, first strand: chain 'E' and resid 349 through 350 Processing sheet with id=AD8, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AD9, first strand: chain 'E' and resid 524 through 526 removed outlier: 3.695A pdb=" N THR E 499 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AE2, first strand: chain 'E' and resid 629 through 631 Processing sheet with id=AE3, first strand: chain 'E' and resid 706 through 707 removed outlier: 3.533A pdb=" N VAL E 707 " --> pdb=" O ILE E 777 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 726 through 728 removed outlier: 3.839A pdb=" N ILE E 726 " --> pdb=" O THR E 733 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AE6, first strand: chain 'F' and resid 412 through 415 Processing sheet with id=AE7, first strand: chain 'F' and resid 524 through 527 removed outlier: 6.048A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 581 through 583 Processing sheet with id=AE9, first strand: chain 'F' and resid 628 through 631 removed outlier: 3.789A pdb=" N LYS F 649 " --> pdb=" O HIS F 629 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 706 through 708 Processing sheet with id=AF2, first strand: chain 'F' and resid 726 through 728 920 hydrogen bonds defined for protein. 2583 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: 7.86 Time building geometry restraints manager: 6.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7427 1.34 - 1.46: 3672 1.46 - 1.58: 11260 1.58 - 1.69: 21 1.69 - 1.81: 131 Bond restraints: 22511 Sorted by residual: bond pdb=" C4 ADP F 801 " pdb=" C5 ADP F 801 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C4 ADP D 801 " pdb=" C5 ADP D 801 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" O3B ADP F 801 " pdb=" PB ADP F 801 " ideal model delta sigma weight residual 1.510 1.603 -0.093 2.00e-02 2.50e+03 2.15e+01 ... (remaining 22506 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 30503 2.52 - 5.03: 222 5.03 - 7.55: 21 7.55 - 10.06: 12 10.06 - 12.58: 18 Bond angle restraints: 30776 Sorted by residual: angle pdb=" C VAL E 401 " pdb=" N ASP E 402 " pdb=" CA ASP E 402 " ideal model delta sigma weight residual 121.54 129.61 -8.07 1.91e+00 2.74e-01 1.79e+01 angle pdb=" PA ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PB ADP F 801 " ideal model delta sigma weight residual 120.50 133.08 -12.58 3.00e+00 1.11e-01 1.76e+01 angle pdb=" O1B ADP B 801 " pdb=" PB ADP B 801 " pdb=" O3B ADP B 801 " ideal model delta sigma weight residual 119.90 108.07 11.83 3.00e+00 1.11e-01 1.55e+01 angle pdb=" PA ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sigma weight residual 120.50 132.13 -11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" C1' ADP D 801 " pdb=" C2' ADP D 801 " pdb=" C3' ADP D 801 " ideal model delta sigma weight residual 111.00 99.45 11.55 3.00e+00 1.11e-01 1.48e+01 ... (remaining 30771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.87: 12978 25.87 - 51.75: 440 51.75 - 77.62: 18 77.62 - 103.50: 5 103.50 - 129.37: 7 Dihedral angle restraints: 13448 sinusoidal: 4186 harmonic: 9262 Sorted by residual: dihedral pdb=" O1B ADP D 801 " pdb=" O3A ADP D 801 " pdb=" PB ADP D 801 " pdb=" PA ADP D 801 " ideal model delta sinusoidal sigma weight residual 300.00 170.63 129.37 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" O1B ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PB ADP B 801 " pdb=" PA ADP B 801 " ideal model delta sinusoidal sigma weight residual 300.00 172.91 127.08 1 2.00e+01 2.50e-03 3.85e+01 dihedral pdb=" C5' ADP B 801 " pdb=" O5' ADP B 801 " pdb=" PA ADP B 801 " pdb=" O2A ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 62.52 -122.52 1 2.00e+01 2.50e-03 3.69e+01 ... (remaining 13445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2998 0.056 - 0.112: 590 0.112 - 0.167: 56 0.167 - 0.223: 2 0.223 - 0.279: 4 Chirality restraints: 3650 Sorted by residual: chirality pdb=" C3' ADP B 801 " pdb=" C2' ADP B 801 " pdb=" C4' ADP B 801 " pdb=" O3' ADP B 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.79 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' ADP D 801 " pdb=" C2' ADP D 801 " pdb=" C4' ADP D 801 " pdb=" O3' ADP D 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C3' ADP F 801 " pdb=" C2' ADP F 801 " pdb=" C4' ADP F 801 " pdb=" O3' ADP F 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3647 not shown) Planarity restraints: 4021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 681 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO D 682 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 682 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 682 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 375 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 376 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 376 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 376 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 681 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO B 682 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 682 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 682 " -0.023 5.00e-02 4.00e+02 ... (remaining 4018 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4046 2.77 - 3.30: 20808 3.30 - 3.83: 34123 3.83 - 4.37: 37310 4.37 - 4.90: 67430 Nonbonded interactions: 163717 Sorted by model distance: nonbonded pdb=" OG1 THR C 342 " pdb=" O ASP C 346 " model vdw 2.234 3.040 nonbonded pdb=" O LEU F 490 " pdb=" NH1 ARG F 551 " model vdw 2.268 3.120 nonbonded pdb=" CE2 PHE C 630 " pdb=" N7 ADP F 801 " model vdw 2.288 2.736 nonbonded pdb=" O LEU C 490 " pdb=" NH1 ARG C 551 " model vdw 2.303 3.120 nonbonded pdb=" O ASP F 473 " pdb=" NZ LYS F 476 " model vdw 2.304 3.120 ... (remaining 163712 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 345 or (resid 346 and (name N or name CA or na \ me C or name O or name CB )) or resid 347 through 350 or (resid 351 and (name N \ or name CA or name C or name O or name CB )) or resid 352 through 353 or (resid \ 354 and (name N or name CA or name C or name O or name CB )) or resid 355 throug \ h 357 or (resid 358 and (name N or name CA or name C or name O or name CB )) or \ resid 359 or (resid 360 through 361 and (name N or name CA or name C or name O o \ r name CB )) or resid 362 through 376 or (resid 377 through 378 and (name N or n \ ame CA or name C or name O or name CB )) or resid 379 through 386 or (resid 387 \ and (name N or name CA or name C or name O or name CB )) or resid 388 through 40 \ 0 or (resid 401 and (name N or name CA or name C or name O or name CB )) or resi \ d 402 through 404 or (resid 405 through 407 and (name N or name CA or name C or \ name O or name CB )) or resid 408 through 416 or (resid 417 and (name N or name \ CA or name C or name O or name CB )) or resid 418 through 420 or (resid 421 and \ (name N or name CA or name C or name O or name CB )) or resid 422 or (resid 423 \ through 424 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 5 through 436 or (resid 437 and (name N or name CA or name C or name O or name C \ B )) or resid 438 through 444 or (resid 445 and (name N or name CA or name C or \ name O or name CB )) or resid 446 or (resid 447 through 450 and (name N or name \ CA or name C or name O or name CB )) or resid 451 or (resid 452 through 454 and \ (name N or name CA or name C or name O or name CB )) or resid 455 through 456 or \ (resid 457 through 465 and (name N or name CA or name C or name O or name CB )) \ or resid 466 through 479 or (resid 480 and (name N or name CA or name C or name \ O or name CB )) or resid 481 through 482 or (resid 483 and (name N or name CA o \ r name C or name O or name CB )) or resid 484 or (resid 485 and (name N or name \ CA or name C or name O or name CB )) or resid 486 through 493 or (resid 494 and \ (name N or name CA or name C or name O or name CB )) or resid 495 through 497 or \ (resid 498 through 499 and (name N or name CA or name C or name O or name CB )) \ or resid 500 through 504 or (resid 505 through 507 and (name N or name CA or na \ me C or name O or name CB )) or resid 508 or (resid 509 through 510 and (name N \ or name CA or name C or name O or name CB )) or resid 511 through 512 or (resid \ 513 through 514 and (name N or name CA or name C or name O or name CB )) or resi \ d 515 through 516 or (resid 517 and (name N or name CA or name C or name O or na \ me CB )) or resid 518 through 519 or (resid 520 and (name N or name CA or name C \ or name O or name CB )) or resid 521 or (resid 522 and (name N or name CA or na \ me C or name O or name CB )) or resid 523 through 525 or (resid 526 and (name N \ or name CA or name C or name O or name CB )) or resid 527 through 529 or (resid \ 530 through 532 and (name N or name CA or name C or name O or name CB )) or resi \ d 533 or (resid 534 through 538 and (name N or name CA or name C or name O or na \ me CB )) or resid 539 through 540 or (resid 541 and (name N or name CA or name C \ or name O or name CB )) or resid 542 or (resid 543 and (name N or name CA or na \ me C or name O or name CB )) or resid 544 through 547 or (resid 548 and (name N \ or name CA or name C or name O or name CB )) or resid 549 through 555 or (resid \ 556 through 562 and (name N or name CA or name C or name O or name CB )) or resi \ d 563 through 566 or (resid 567 through 573 and (name N or name CA or name C or \ name O or name CB )) or resid 574 or (resid 575 through 579 and (name N or name \ CA or name C or name O or name CB )) or resid 580 through 581 or (resid 582 and \ (name N or name CA or name C or name O or name CB )) or resid 583 through 586 or \ (resid 587 and (name N or name CA or name C or name O or name CB )) or resid 58 \ 8 through 590 or (resid 591 through 592 and (name N or name CA or name C or name \ O or name CB )) or resid 593 or (resid 594 and (name N or name CA or name C or \ name O or name CB )) or resid 595 or (resid 596 and (name N or name CA or name C \ or name O or name CB )) or resid 597 through 599 or (resid 600 and (name N or n \ ame CA or name C or name O or name CB )) or resid 601 or (resid 602 through 604 \ and (name N or name CA or name C or name O or name CB )) or resid 605 or (resid \ 606 through 607 and (name N or name CA or name C or name O or name CB )) or resi \ d 608 through 610 or (resid 611 through 613 and (name N or name CA or name C or \ name O or name CB )) or resid 614 through 616 or (resid 617 and (name N or name \ CA or name C or name O or name CB )) or resid 618 through 620 or (resid 621 thro \ ugh 623 and (name N or name CA or name C or name O or name CB )) or resid 624 th \ rough 627 or (resid 628 through 634 and (name N or name CA or name C or name O o \ r name CB )) or (resid 635 through 647 and (name N or name CA or name C or name \ O or name CB )) or resid 648 or (resid 649 through 650 and (name N or name CA or \ name C or name O or name CB )) or resid 651 through 657 or (resid 658 through 6 \ 60 and (name N or name CA or name C or name O or name CB )) or resid 661 through \ 662 or (resid 663 through 664 and (name N or name CA or name C or name O or nam \ e CB )) or resid 665 through 672 or (resid 673 and (name N or name CA or name C \ or name O or name CB )) or resid 674 through 676 or (resid 677 through 678 and ( \ name N or name CA or name C or name O or name CB )) or resid 679 through 682 or \ (resid 683 through 684 and (name N or name CA or name C or name O or name CB )) \ or resid 685 through 692 or (resid 693 and (name N or name CA or name C or name \ O or name CB )) or resid 694 through 697 or (resid 698 through 702 and (name N o \ r name CA or name C or name O or name CB )) or resid 703 through 785)) selection = (chain 'B' and (resid 323 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB )) or resid 347 through 350 or (resid \ 351 and (name N or name CA or name C or name O or name CB )) or resid 352 or (re \ sid 353 through 354 and (name N or name CA or name C or name O or name CB )) or \ resid 355 through 357 or (resid 358 and (name N or name CA or name C or name O o \ r name CB )) or resid 359 or (resid 360 through 361 and (name N or name CA or na \ me C or name O or name CB )) or resid 362 through 367 or (resid 368 and (name N \ or name CA or name C or name O or name CB )) or resid 369 through 370 or (resid \ 371 and (name N or name CA or name C or name O or name CB )) or resid 372 throug \ h 376 or (resid 377 through 378 and (name N or name CA or name C or name O or na \ me CB )) or resid 379 through 386 or (resid 387 and (name N or name CA or name C \ or name O or name CB )) or resid 388 or (resid 389 and (name N or name CA or na \ me C or name O or name CB )) or resid 390 through 397 or (resid 398 through 399 \ and (name N or name CA or name C or name O or name CB )) or resid 400 through 41 \ 6 or (resid 417 and (name N or name CA or name C or name O or name CB )) or resi \ d 418 through 422 or (resid 423 through 424 and (name N or name CA or name C or \ name O or name CB )) or resid 425 through 444 or (resid 445 and (name N or name \ CA or name C or name O or name CB )) or resid 446 or (resid 447 through 450 and \ (name N or name CA or name C or name O or name CB )) or resid 451 or (resid 452 \ through 454 and (name N or name CA or name C or name O or name CB )) or resid 45 \ 5 through 456 or (resid 457 through 465 and (name N or name CA or name C or name \ O or name CB )) or resid 466 through 472 or (resid 473 through 474 and (name N \ or name CA or name C or name O or name CB )) or resid 475 through 482 or (resid \ 483 and (name N or name CA or name C or name O or name CB )) or resid 484 throug \ h 493 or (resid 494 and (name N or name CA or name C or name O or name CB )) or \ resid 495 through 497 or (resid 498 through 499 and (name N or name CA or name C \ or name O or name CB )) or resid 500 through 504 or (resid 505 through 507 and \ (name N or name CA or name C or name O or name CB )) or resid 508 or (resid 509 \ through 510 and (name N or name CA or name C or name O or name CB )) or resid 51 \ 1 through 513 or (resid 514 and (name N or name CA or name C or name O or name C \ B )) or resid 515 through 516 or (resid 517 and (name N or name CA or name C or \ name O or name CB )) or resid 518 through 525 or (resid 526 and (name N or name \ CA or name C or name O or name CB )) or resid 527 through 529 or (resid 530 thro \ ugh 532 and (name N or name CA or name C or name O or name CB )) or resid 533 or \ (resid 534 through 538 and (name N or name CA or name C or name O or name CB )) \ or resid 539 through 540 or (resid 541 and (name N or name CA or name C or name \ O or name CB )) or resid 542 or (resid 543 and (name N or name CA or name C or \ name O or name CB )) or resid 544 through 547 or (resid 548 and (name N or name \ CA or name C or name O or name CB )) or resid 549 or (resid 550 and (name N or n \ ame CA or name C or name O or name CB )) or resid 551 through 552 or (resid 553 \ and (name N or name CA or name C or name O or name CB )) or resid 554 or (resid \ 555 through 562 and (name N or name CA or name C or name O or name CB )) or resi \ d 563 through 566 or (resid 567 through 573 and (name N or name CA or name C or \ name O or name CB )) or resid 574 or (resid 575 through 579 and (name N or name \ CA or name C or name O or name CB )) or resid 580 or (resid 581 through 582 and \ (name N or name CA or name C or name O or name CB )) or resid 583 through 591 or \ (resid 592 and (name N or name CA or name C or name O or name CB )) or resid 59 \ 3 or (resid 594 and (name N or name CA or name C or name O or name CB )) or resi \ d 595 through 599 or (resid 600 and (name N or name CA or name C or name O or na \ me CB )) or resid 601 through 605 or (resid 606 through 607 and (name N or name \ CA or name C or name O or name CB )) or resid 608 through 612 or (resid 613 and \ (name N or name CA or name C or name O or name CB )) or resid 614 through 620 or \ (resid 621 through 623 and (name N or name CA or name C or name O or name CB )) \ or resid 624 through 627 or (resid 628 through 634 and (name N or name CA or na \ me C or name O or name CB )) or (resid 635 through 647 and (name N or name CA or \ name C or name O or name CB )) or resid 648 through 652 or (resid 653 and (name \ N or name CA or name C or name O or name CB )) or resid 654 through 655 or (res \ id 656 and (name N or name CA or name C or name O or name CB )) or resid 657 or \ (resid 658 through 660 and (name N or name CA or name C or name O or name CB )) \ or resid 661 through 662 or (resid 663 through 664 and (name N or name CA or nam \ e C or name O or name CB )) or resid 665 through 672 or (resid 673 and (name N o \ r name CA or name C or name O or name CB )) or resid 674 through 677 or (resid 6 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 679 through \ 682 or (resid 683 through 684 and (name N or name CA or name C or name O or nam \ e CB )) or resid 685 through 688 or (resid 689 and (name N or name CA or name C \ or name O or name CB )) or resid 690 through 691 or (resid 692 through 693 and ( \ name N or name CA or name C or name O or name CB )) or resid 694 through 698 or \ (resid 699 through 702 and (name N or name CA or name C or name O or name CB )) \ or resid 703 or (resid 704 through 723 and (name N or name CA or name C or name \ O or name CB )) or resid 724 through 785)) selection = (chain 'C' and (resid 323 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 through 350 or (resid 351 and (name N \ or name CA or name C or name O or name CB )) or resid 352 or (resid 353 through \ 354 and (name N or name CA or name C or name O or name CB )) or resid 355 throug \ h 360 or (resid 361 and (name N or name CA or name C or name O or name CB )) or \ resid 362 through 367 or (resid 368 and (name N or name CA or name C or name O o \ r name CB )) or resid 369 through 370 or (resid 371 and (name N or name CA or na \ me C or name O or name CB )) or resid 372 through 386 or (resid 387 and (name N \ or name CA or name C or name O or name CB )) or resid 388 or (resid 389 and (nam \ e N or name CA or name C or name O or name CB )) or resid 390 through 397 or (re \ sid 398 through 399 and (name N or name CA or name C or name O or name CB )) or \ resid 400 or (resid 401 and (name N or name CA or name C or name O or name CB )) \ or resid 402 through 404 or (resid 405 through 407 and (name N or name CA or na \ me C or name O or name CB )) or resid 408 through 415 or (resid 416 through 417 \ and (name N or name CA or name C or name O or name CB )) or resid 418 through 42 \ 0 or (resid 421 and (name N or name CA or name C or name O or name CB )) or resi \ d 422 through 436 or (resid 437 and (name N or name CA or name C or name O or na \ me CB )) or resid 438 through 444 or (resid 445 and (name N or name CA or name C \ or name O or name CB )) or resid 446 or (resid 447 through 450 and (name N or n \ ame CA or name C or name O or name CB )) or resid 451 or (resid 452 through 454 \ and (name N or name CA or name C or name O or name CB )) or resid 455 through 45 \ 6 or (resid 457 through 465 and (name N or name CA or name C or name O or name C \ B )) or resid 466 through 472 or (resid 473 through 474 and (name N or name CA o \ r name C or name O or name CB )) or resid 475 through 479 or (resid 480 and (nam \ e N or name CA or name C or name O or name CB )) or resid 481 through 482 or (re \ sid 483 and (name N or name CA or name C or name O or name CB )) or resid 484 or \ (resid 485 and (name N or name CA or name C or name O or name CB )) or resid 48 \ 6 through 493 or (resid 494 and (name N or name CA or name C or name O or name C \ B )) or resid 495 through 497 or (resid 498 through 499 and (name N or name CA o \ r name C or name O or name CB )) or resid 500 through 504 or (resid 505 through \ 507 and (name N or name CA or name C or name O or name CB )) or resid 508 throug \ h 512 or (resid 513 through 514 and (name N or name CA or name C or name O or na \ me CB )) or resid 515 through 521 or (resid 522 and (name N or name CA or name C \ or name O or name CB )) or resid 523 through 529 or (resid 530 through 532 and \ (name N or name CA or name C or name O or name CB )) or resid 533 or (resid 534 \ through 538 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 9 through 540 or (resid 541 and (name N or name CA or name C or name O or name C \ B )) or resid 542 or (resid 543 and (name N or name CA or name C or name O or na \ me CB )) or resid 544 through 547 or (resid 548 and (name N or name CA or name C \ or name O or name CB )) or resid 549 or (resid 550 and (name N or name CA or na \ me C or name O or name CB )) or resid 551 through 552 or (resid 553 and (name N \ or name CA or name C or name O or name CB )) or resid 554 or (resid 555 through \ 562 and (name N or name CA or name C or name O or name CB )) or resid 563 throug \ h 566 or (resid 567 through 573 and (name N or name CA or name C or name O or na \ me CB )) or resid 574 through 577 or (resid 578 through 579 and (name N or name \ CA or name C or name O or name CB )) or resid 580 or (resid 581 through 582 and \ (name N or name CA or name C or name O or name CB )) or resid 583 through 593 or \ (resid 594 and (name N or name CA or name C or name O or name CB )) or resid 59 \ 5 or (resid 596 and (name N or name CA or name C or name O or name CB )) or resi \ d 597 through 605 or (resid 606 through 607 and (name N or name CA or name C or \ name O or name CB )) or resid 608 through 610 or (resid 611 through 613 and (nam \ e N or name CA or name C or name O or name CB )) or resid 614 through 616 or (re \ sid 617 and (name N or name CA or name C or name O or name CB )) or resid 618 th \ rough 622 or (resid 623 and (name N or name CA or name C or name O or name CB )) \ or resid 624 through 627 or (resid 628 through 634 and (name N or name CA or na \ me C or name O or name CB )) or (resid 635 through 647 and (name N or name CA or \ name C or name O or name CB )) or resid 648 through 655 or (resid 656 and (name \ N or name CA or name C or name O or name CB )) or resid 657 or (resid 658 throu \ gh 660 and (name N or name CA or name C or name O or name CB )) or resid 661 thr \ ough 662 or (resid 663 through 664 and (name N or name CA or name C or name O or \ name CB )) or resid 665 through 672 or (resid 673 and (name N or name CA or nam \ e C or name O or name CB )) or resid 674 through 676 or (resid 677 through 678 a \ nd (name N or name CA or name C or name O or name CB )) or resid 679 through 682 \ or (resid 683 through 684 and (name N or name CA or name C or name O or name CB \ )) or resid 685 through 688 or (resid 689 and (name N or name CA or name C or n \ ame O or name CB )) or resid 690 through 692 or (resid 693 and (name N or name C \ A or name C or name O or name CB )) or resid 694 through 698 or (resid 699 throu \ gh 702 and (name N or name CA or name C or name O or name CB )) or resid 703 thr \ ough 785)) selection = (chain 'F' and (resid 323 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB )) or resid 347 through 352 or (resid \ 353 through 354 and (name N or name CA or name C or name O or name CB )) or resi \ d 355 through 367 or (resid 368 and (name N or name CA or name C or name O or na \ me CB )) or resid 369 through 376 or (resid 377 through 378 and (name N or name \ CA or name C or name O or name CB )) or resid 379 through 397 or (resid 398 thro \ ugh 399 and (name N or name CA or name C or name O or name CB )) or resid 400 or \ (resid 401 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 2 through 420 or (resid 421 and (name N or name CA or name C or name O or name C \ B )) or resid 422 through 423 or (resid 424 and (name N or name CA or name C or \ name O or name CB )) or resid 425 through 436 or (resid 437 and (name N or name \ CA or name C or name O or name CB )) or resid 438 through 464 or (resid 465 and \ (name N or name CA or name C or name O or name CB )) or resid 466 through 472 or \ (resid 473 through 474 and (name N or name CA or name C or name O or name CB )) \ or resid 475 through 479 or (resid 480 and (name N or name CA or name C or name \ O or name CB )) or resid 481 through 498 or (resid 499 and (name N or name CA o \ r name C or name O or name CB )) or resid 500 through 506 or (resid 507 and (nam \ e N or name CA or name C or name O or name CB )) or resid 508 or (resid 509 thro \ ugh 510 and (name N or name CA or name C or name O or name CB )) or resid 511 th \ rough 512 or (resid 513 through 514 and (name N or name CA or name C or name O o \ r name CB )) or resid 515 through 516 or (resid 517 and (name N or name CA or na \ me C or name O or name CB )) or resid 518 through 519 or (resid 520 and (name N \ or name CA or name C or name O or name CB )) or resid 521 through 525 or (resid \ 526 and (name N or name CA or name C or name O or name CB )) or resid 527 throug \ h 534 or (resid 535 through 538 and (name N or name CA or name C or name O or na \ me CB )) or resid 539 through 552 or (resid 553 and (name N or name CA or name C \ or name O or name CB )) or resid 554 or (resid 555 through 562 and (name N or n \ ame CA or name C or name O or name CB )) or resid 563 through 570 or (resid 571 \ through 573 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 4 through 575 or (resid 576 through 579 and (name N or name CA or name C or name \ O or name CB )) or resid 580 or (resid 581 through 582 and (name N or name CA o \ r name C or name O or name CB )) or resid 583 through 591 or (resid 592 and (nam \ e N or name CA or name C or name O or name CB )) or resid 593 through 595 or (re \ sid 596 and (name N or name CA or name C or name O or name CB )) or resid 597 th \ rough 603 or (resid 604 and (name N or name CA or name C or name O or name CB )) \ or resid 605 through 610 or (resid 611 through 613 and (name N or name CA or na \ me C or name O or name CB )) or resid 614 through 616 or (resid 617 and (name N \ or name CA or name C or name O or name CB )) or resid 618 through 620 or (resid \ 621 through 623 and (name N or name CA or name C or name O or name CB )) or resi \ d 624 through 645 or (resid 646 through 647 and (name N or name CA or name C or \ name O or name CB )) or resid 648 or (resid 649 through 650 and (name N or name \ CA or name C or name O or name CB )) or resid 651 through 668 or (resid 669 and \ (name N or name CA or name C or name O or name CB )) or resid 670 through 676 or \ (resid 677 through 678 and (name N or name CA or name C or name O or name CB )) \ or resid 679 through 680 or (resid 681 and (name N or name CA or name C or name \ O or name CB )) or resid 682 through 688 or (resid 689 and (name N or name CA o \ r name C or name O or name CB )) or resid 690 through 699 or (resid 700 through \ 702 and (name N or name CA or name C or name O or name CB )) or resid 703 throug \ h 785)) } 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=0.00 max=1.00 mean=0.93 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: 11.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 54.580 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 : 0.005 0.114 22521 Z= 0.220 Angle : 0.646 12.576 30779 Z= 0.310 Chirality : 0.044 0.279 3650 Planarity : 0.004 0.050 4021 Dihedral : 13.220 129.372 7412 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.38 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 3135 helix: 1.04 (0.16), residues: 1188 sheet: -0.55 (0.28), residues: 384 loop : -0.85 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 350 HIS 0.004 0.001 HIS F 680 PHE 0.024 0.001 PHE E 668 TYR 0.018 0.001 TYR A 482 ARG 0.005 0.000 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.15083 ( 918) hydrogen bonds : angle 5.63015 ( 2583) metal coordination : bond 0.00201 ( 7) metal coordination : angle 0.60522 ( 3) covalent geometry : bond 0.00499 (22511) covalent geometry : angle 0.64609 (30776) Misc. bond : bond 0.00199 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 397 ARG cc_start: 0.8671 (mtp85) cc_final: 0.8376 (mtt180) REVERT: E 434 LYS cc_start: 0.8041 (tttt) cc_final: 0.7691 (ttmt) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.3414 time to fit residues: 163.4345 Evaluate side-chains 227 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 8.9990 chunk 237 optimal weight: 3.9990 chunk 132 optimal weight: 50.0000 chunk 81 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 246 optimal weight: 50.0000 chunk 95 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 285 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN B 324 ASN B 573 ASN ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 ASN E 198 GLN ** F 324 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 = 0.4120 r_free = 0.4120 target = 0.176865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.135338 restraints weight = 30520.085| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.07 r_work: 0.3337 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 244 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 214 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 22521 Z= 0.286 Angle : 0.643 7.609 30779 Z= 0.327 Chirality : 0.047 0.201 3650 Planarity : 0.004 0.051 4021 Dihedral : 7.666 124.022 3395 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.83 % Favored : 93.05 % Rotamer: Outliers : 1.63 % Allowed : 8.03 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 3135 helix: 0.88 (0.16), residues: 1179 sheet: -0.79 (0.26), residues: 426 loop : -0.96 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 350 HIS 0.007 0.001 HIS C 680 PHE 0.028 0.002 PHE E 668 TYR 0.030 0.002 TYR E 211 ARG 0.004 0.000 ARG F 372 Details of bonding type rmsd hydrogen bonds : bond 0.04688 ( 918) hydrogen bonds : angle 4.73552 ( 2583) metal coordination : bond 0.00348 ( 7) metal coordination : angle 0.78755 ( 3) covalent geometry : bond 0.00705 (22511) covalent geometry : angle 0.64304 (30776) Misc. bond : bond 0.00197 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 186 ARG cc_start: 0.3522 (mtp180) cc_final: 0.3280 (mtp180) REVERT: E 434 LYS cc_start: 0.8595 (tttt) cc_final: 0.8266 (tttt) REVERT: F 343 GLU cc_start: 0.8327 (mp0) cc_final: 0.8074 (mp0) REVERT: F 486 LEU cc_start: 0.8148 (mm) cc_final: 0.7877 (mm) outliers start: 30 outliers final: 22 residues processed: 252 average time/residue: 0.3281 time to fit residues: 129.2966 Evaluate side-chains 237 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 680 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 163 optimal weight: 6.9990 chunk 185 optimal weight: 0.0020 chunk 173 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 295 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 136 optimal weight: 40.0000 chunk 151 optimal weight: 0.7980 chunk 260 optimal weight: 20.0000 overall best weight: 1.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 594 ASN ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 ASN ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.183268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.147733 restraints weight = 30313.897| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.91 r_work: 0.3378 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 214 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 209 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22521 Z= 0.176 Angle : 0.551 7.458 30779 Z= 0.279 Chirality : 0.044 0.186 3650 Planarity : 0.004 0.050 4021 Dihedral : 7.129 122.587 3395 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.71 % Favored : 94.16 % Rotamer: Outliers : 1.57 % Allowed : 11.45 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 3135 helix: 1.00 (0.16), residues: 1194 sheet: -0.73 (0.26), residues: 415 loop : -0.95 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 350 HIS 0.006 0.001 HIS C 680 PHE 0.016 0.001 PHE E 668 TYR 0.020 0.001 TYR E 211 ARG 0.003 0.000 ARG E 175 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 918) hydrogen bonds : angle 4.36128 ( 2583) metal coordination : bond 0.00235 ( 7) metal coordination : angle 0.51122 ( 3) covalent geometry : bond 0.00433 (22511) covalent geometry : angle 0.55094 (30776) Misc. bond : bond 0.00215 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 343 GLU cc_start: 0.8620 (tp30) cc_final: 0.8346 (tt0) REVERT: D 374 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7348 (mp10) REVERT: E 180 LEU cc_start: 0.8720 (tt) cc_final: 0.8506 (tt) REVERT: E 434 LYS cc_start: 0.8496 (tttt) cc_final: 0.8166 (tttt) REVERT: E 447 ASP cc_start: 0.8070 (t70) cc_final: 0.7857 (t0) REVERT: F 554 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.5981 (m-80) outliers start: 29 outliers final: 22 residues processed: 256 average time/residue: 0.3247 time to fit residues: 130.8927 Evaluate side-chains 242 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 344 ARG Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 581 CYS Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 680 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 14 optimal weight: 1.9990 chunk 272 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 299 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 282 optimal weight: 2.9990 chunk 249 optimal weight: 20.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 GLN E 475 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.183038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150701 restraints weight = 30729.965| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.83 r_work: 0.3375 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 209 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 214 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22521 Z= 0.180 Angle : 0.553 7.139 30779 Z= 0.280 Chirality : 0.044 0.190 3650 Planarity : 0.004 0.050 4021 Dihedral : 7.012 121.510 3395 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.19 % Favored : 93.68 % Rotamer: Outliers : 2.06 % Allowed : 12.76 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3135 helix: 1.00 (0.16), residues: 1201 sheet: -0.83 (0.27), residues: 407 loop : -0.94 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 350 HIS 0.004 0.001 HIS C 680 PHE 0.014 0.001 PHE E 668 TYR 0.020 0.001 TYR A 482 ARG 0.004 0.000 ARG C 663 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 918) hydrogen bonds : angle 4.30826 ( 2583) metal coordination : bond 0.00219 ( 7) metal coordination : angle 0.42320 ( 3) covalent geometry : bond 0.00443 (22511) covalent geometry : angle 0.55345 (30776) Misc. bond : bond 0.00187 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 343 GLU cc_start: 0.8635 (tp30) cc_final: 0.8345 (tt0) REVERT: C 606 TYR cc_start: 0.6843 (m-80) cc_final: 0.6521 (m-80) REVERT: D 374 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7344 (mp10) REVERT: E 180 LEU cc_start: 0.8648 (tt) cc_final: 0.8421 (tt) REVERT: E 186 ARG cc_start: 0.3116 (mtp180) cc_final: 0.2829 (mtp180) REVERT: E 447 ASP cc_start: 0.8052 (t70) cc_final: 0.7807 (t0) REVERT: F 474 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7189 (tm-30) REVERT: F 554 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.5954 (m-80) outliers start: 38 outliers final: 27 residues processed: 257 average time/residue: 0.3139 time to fit residues: 128.8691 Evaluate side-chains 251 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 581 CYS Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 680 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 232 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 130 optimal weight: 50.0000 chunk 54 optimal weight: 0.6980 chunk 200 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN B 573 ASN ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.187339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.151315 restraints weight = 30085.313| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.95 r_work: 0.3442 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 214 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 214 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22521 Z= 0.097 Angle : 0.492 7.115 30779 Z= 0.250 Chirality : 0.042 0.193 3650 Planarity : 0.003 0.051 4021 Dihedral : 6.529 121.881 3395 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.40 % Favored : 95.47 % Rotamer: Outliers : 1.47 % Allowed : 13.84 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 3135 helix: 1.33 (0.16), residues: 1200 sheet: -0.70 (0.27), residues: 405 loop : -0.83 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 350 HIS 0.003 0.001 HIS C 680 PHE 0.012 0.001 PHE F 446 TYR 0.017 0.001 TYR C 645 ARG 0.004 0.000 ARG E 175 Details of bonding type rmsd hydrogen bonds : bond 0.02625 ( 918) hydrogen bonds : angle 3.97383 ( 2583) metal coordination : bond 0.00205 ( 7) metal coordination : angle 0.27903 ( 3) covalent geometry : bond 0.00225 (22511) covalent geometry : angle 0.49188 (30776) Misc. bond : bond 0.00165 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 685 LYS cc_start: 0.8345 (tttm) cc_final: 0.7917 (tttm) REVERT: C 343 GLU cc_start: 0.8539 (tp30) cc_final: 0.8321 (tt0) REVERT: C 462 MET cc_start: 0.7690 (tpp) cc_final: 0.7407 (tpp) REVERT: C 606 TYR cc_start: 0.6780 (m-80) cc_final: 0.6451 (m-80) REVERT: E 180 LEU cc_start: 0.8693 (tt) cc_final: 0.8455 (tt) REVERT: E 186 ARG cc_start: 0.3023 (mtp180) cc_final: 0.2776 (mtp180) REVERT: E 249 ARG cc_start: 0.7890 (ttm170) cc_final: 0.7670 (ttm170) REVERT: E 447 ASP cc_start: 0.8067 (t70) cc_final: 0.7859 (t0) REVERT: E 543 PHE cc_start: 0.6433 (m-80) cc_final: 0.6146 (m-80) REVERT: F 428 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7384 (p90) REVERT: F 480 GLU cc_start: 0.8672 (tm-30) cc_final: 0.7505 (mm-30) REVERT: F 554 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.5979 (m-80) outliers start: 27 outliers final: 17 residues processed: 265 average time/residue: 0.3222 time to fit residues: 133.1844 Evaluate side-chains 241 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 680 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 263 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 297 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 chunk 210 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 107 optimal weight: 0.4980 chunk 167 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.185199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.149000 restraints weight = 29931.215| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.94 r_work: 0.3401 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 214 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 219 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22521 Z= 0.158 Angle : 0.531 6.982 30779 Z= 0.268 Chirality : 0.043 0.185 3650 Planarity : 0.004 0.050 4021 Dihedral : 6.560 118.010 3395 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.74 % Favored : 94.13 % Rotamer: Outliers : 1.68 % Allowed : 15.15 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 3135 helix: 1.26 (0.16), residues: 1204 sheet: -0.82 (0.26), residues: 425 loop : -0.84 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 350 HIS 0.005 0.001 HIS D 629 PHE 0.013 0.001 PHE A 502 TYR 0.020 0.001 TYR A 482 ARG 0.004 0.000 ARG E 175 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 918) hydrogen bonds : angle 4.09590 ( 2583) metal coordination : bond 0.00193 ( 7) metal coordination : angle 0.30978 ( 3) covalent geometry : bond 0.00385 (22511) covalent geometry : angle 0.53072 (30776) Misc. bond : bond 0.00167 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 343 GLU cc_start: 0.8541 (tp30) cc_final: 0.8258 (tt0) REVERT: C 351 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8355 (mt) REVERT: C 462 MET cc_start: 0.7763 (tpp) cc_final: 0.7472 (tpp) REVERT: D 374 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7325 (mp10) REVERT: E 180 LEU cc_start: 0.8713 (tt) cc_final: 0.8475 (tt) REVERT: E 186 ARG cc_start: 0.3125 (mtp180) cc_final: 0.2874 (mtp180) REVERT: E 447 ASP cc_start: 0.8061 (t70) cc_final: 0.7847 (t0) REVERT: F 554 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6119 (m-80) outliers start: 31 outliers final: 25 residues processed: 257 average time/residue: 0.3290 time to fit residues: 132.7213 Evaluate side-chains 250 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 344 ARG Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 680 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 180 optimal weight: 0.0770 chunk 242 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 289 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 261 optimal weight: 0.3980 chunk 174 optimal weight: 8.9990 chunk 313 optimal weight: 50.0000 overall best weight: 0.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.188013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.152840 restraints weight = 30100.284| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.93 r_work: 0.3436 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 219 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 214 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22521 Z= 0.108 Angle : 0.500 8.481 30779 Z= 0.253 Chirality : 0.042 0.177 3650 Planarity : 0.003 0.052 4021 Dihedral : 6.317 115.538 3395 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.47 % Favored : 95.41 % Rotamer: Outliers : 1.90 % Allowed : 15.53 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 3135 helix: 1.38 (0.16), residues: 1210 sheet: -0.62 (0.27), residues: 405 loop : -0.79 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 350 HIS 0.005 0.001 HIS D 629 PHE 0.014 0.001 PHE A 502 TYR 0.015 0.001 TYR A 482 ARG 0.004 0.000 ARG E 175 Details of bonding type rmsd hydrogen bonds : bond 0.02738 ( 918) hydrogen bonds : angle 3.93850 ( 2583) metal coordination : bond 0.00159 ( 7) metal coordination : angle 0.17315 ( 3) covalent geometry : bond 0.00257 (22511) covalent geometry : angle 0.49992 (30776) Misc. bond : bond 0.00132 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 685 LYS cc_start: 0.8299 (tttm) cc_final: 0.7890 (tttm) REVERT: C 343 GLU cc_start: 0.8540 (tp30) cc_final: 0.8222 (tt0) REVERT: C 351 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8325 (mt) REVERT: C 462 MET cc_start: 0.7733 (tpp) cc_final: 0.7447 (tpp) REVERT: D 374 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: E 180 LEU cc_start: 0.8710 (tt) cc_final: 0.8467 (tt) REVERT: E 186 ARG cc_start: 0.3118 (mtp180) cc_final: 0.2774 (mtp180) REVERT: E 447 ASP cc_start: 0.8077 (t70) cc_final: 0.7877 (t0) REVERT: F 428 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.6861 (p90) REVERT: F 480 GLU cc_start: 0.8701 (tm-30) cc_final: 0.7547 (mm-30) REVERT: F 554 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6049 (m-80) outliers start: 35 outliers final: 25 residues processed: 255 average time/residue: 0.3234 time to fit residues: 130.5586 Evaluate side-chains 248 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 344 ARG Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 680 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 172 optimal weight: 1.9990 chunk 191 optimal weight: 50.0000 chunk 185 optimal weight: 0.0270 chunk 121 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 0.0980 chunk 300 optimal weight: 20.0000 chunk 298 optimal weight: 9.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.187997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151185 restraints weight = 30209.456| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.05 r_work: 0.3430 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 214 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 209 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22521 Z= 0.114 Angle : 0.502 8.049 30779 Z= 0.253 Chirality : 0.042 0.179 3650 Planarity : 0.003 0.052 4021 Dihedral : 6.160 111.791 3395 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.63 % Favored : 95.25 % Rotamer: Outliers : 1.63 % Allowed : 16.02 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 3135 helix: 1.45 (0.16), residues: 1205 sheet: -0.63 (0.26), residues: 420 loop : -0.79 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 350 HIS 0.004 0.001 HIS D 629 PHE 0.015 0.001 PHE A 502 TYR 0.015 0.001 TYR A 482 ARG 0.004 0.000 ARG E 175 Details of bonding type rmsd hydrogen bonds : bond 0.02792 ( 918) hydrogen bonds : angle 3.90060 ( 2583) metal coordination : bond 0.00135 ( 7) metal coordination : angle 0.15887 ( 3) covalent geometry : bond 0.00273 (22511) covalent geometry : angle 0.50237 (30776) Misc. bond : bond 0.00160 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 685 LYS cc_start: 0.8288 (tttm) cc_final: 0.7883 (tttm) REVERT: C 343 GLU cc_start: 0.8625 (tp30) cc_final: 0.8265 (tt0) REVERT: C 351 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8345 (mt) REVERT: C 462 MET cc_start: 0.7791 (tpp) cc_final: 0.7511 (tpp) REVERT: D 374 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: E 186 ARG cc_start: 0.3149 (mtp180) cc_final: 0.2818 (mtp180) REVERT: E 447 ASP cc_start: 0.8147 (t70) cc_final: 0.7932 (t0) REVERT: F 428 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.6705 (p90) REVERT: F 554 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6238 (m-80) outliers start: 30 outliers final: 21 residues processed: 253 average time/residue: 0.3317 time to fit residues: 132.3428 Evaluate side-chains 249 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 680 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 223 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 194 optimal weight: 20.0000 chunk 207 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 275 optimal weight: 0.9980 chunk 306 optimal weight: 5.9990 chunk 61 optimal weight: 0.0030 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 ASN ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.189233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.154889 restraints weight = 29996.202| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.09 r_work: 0.3437 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 209 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 209 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22521 Z= 0.100 Angle : 0.495 9.729 30779 Z= 0.250 Chirality : 0.042 0.203 3650 Planarity : 0.003 0.053 4021 Dihedral : 5.772 103.430 3395 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.18 % Favored : 95.69 % Rotamer: Outliers : 1.52 % Allowed : 16.34 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 3135 helix: 1.54 (0.16), residues: 1212 sheet: -0.56 (0.26), residues: 421 loop : -0.75 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 350 HIS 0.003 0.001 HIS C 680 PHE 0.016 0.001 PHE A 502 TYR 0.019 0.001 TYR E 211 ARG 0.004 0.000 ARG E 175 Details of bonding type rmsd hydrogen bonds : bond 0.02516 ( 918) hydrogen bonds : angle 3.79234 ( 2583) metal coordination : bond 0.00119 ( 7) metal coordination : angle 0.13173 ( 3) covalent geometry : bond 0.00236 (22511) covalent geometry : angle 0.49529 (30776) Misc. bond : bond 0.00142 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 685 LYS cc_start: 0.8217 (tttm) cc_final: 0.7893 (tttm) REVERT: C 359 SER cc_start: 0.8328 (m) cc_final: 0.8035 (p) REVERT: C 462 MET cc_start: 0.7591 (tpp) cc_final: 0.7294 (tpp) REVERT: D 374 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7115 (mp10) REVERT: E 186 ARG cc_start: 0.3135 (mtp180) cc_final: 0.2806 (mtp180) REVERT: F 428 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7116 (p90) REVERT: F 480 GLU cc_start: 0.8682 (tm-30) cc_final: 0.7552 (mm-30) REVERT: F 554 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6245 (m-80) outliers start: 28 outliers final: 21 residues processed: 252 average time/residue: 0.3349 time to fit residues: 132.1910 Evaluate side-chains 241 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 680 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 56 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 272 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 chunk 262 optimal weight: 50.0000 chunk 129 optimal weight: 3.9990 chunk 70 optimal weight: 0.0050 chunk 110 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 192 optimal weight: 30.0000 chunk 103 optimal weight: 4.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.186642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.150363 restraints weight = 30201.864| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.00 r_work: 0.3409 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 209 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 209 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22521 Z= 0.143 Angle : 0.531 10.435 30779 Z= 0.267 Chirality : 0.043 0.196 3650 Planarity : 0.004 0.053 4021 Dihedral : 5.803 95.285 3395 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.20 % Favored : 94.67 % Rotamer: Outliers : 1.41 % Allowed : 16.78 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 3135 helix: 1.46 (0.16), residues: 1210 sheet: -0.56 (0.27), residues: 413 loop : -0.76 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 350 HIS 0.003 0.001 HIS D 629 PHE 0.017 0.001 PHE A 502 TYR 0.019 0.001 TYR A 482 ARG 0.007 0.000 ARG F 619 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 918) hydrogen bonds : angle 3.92217 ( 2583) metal coordination : bond 0.00186 ( 7) metal coordination : angle 0.38813 ( 3) covalent geometry : bond 0.00349 (22511) covalent geometry : angle 0.53144 (30776) Misc. bond : bond 0.00117 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 402 ASP cc_start: 0.8229 (p0) cc_final: 0.7698 (m-30) REVERT: B 685 LYS cc_start: 0.8365 (tttm) cc_final: 0.7983 (tttm) REVERT: D 374 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: E 186 ARG cc_start: 0.3197 (mtp180) cc_final: 0.2896 (mtp180) REVERT: F 480 GLU cc_start: 0.8738 (tm-30) cc_final: 0.7529 (mm-30) REVERT: F 554 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.6404 (m-80) outliers start: 26 outliers final: 23 residues processed: 241 average time/residue: 0.3235 time to fit residues: 123.1969 Evaluate side-chains 240 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 680 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 105 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 271 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 299 optimal weight: 9.9990 chunk 55 optimal weight: 0.0970 chunk 242 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.188454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.152118 restraints weight = 30231.312| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.01 r_work: 0.3429 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 209 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 209 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22521 Z= 0.105 Angle : 0.504 10.269 30779 Z= 0.253 Chirality : 0.042 0.198 3650 Planarity : 0.003 0.061 4021 Dihedral : 5.480 83.537 3395 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.02 % Favored : 95.85 % Rotamer: Outliers : 1.41 % Allowed : 16.88 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 3135 helix: 1.59 (0.16), residues: 1212 sheet: -0.50 (0.27), residues: 413 loop : -0.74 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 350 HIS 0.003 0.001 HIS D 629 PHE 0.017 0.001 PHE A 502 TYR 0.018 0.001 TYR E 211 ARG 0.005 0.000 ARG E 175 Details of bonding type rmsd hydrogen bonds : bond 0.02555 ( 918) hydrogen bonds : angle 3.79021 ( 2583) metal coordination : bond 0.00131 ( 7) metal coordination : angle 0.26011 ( 3) covalent geometry : bond 0.00250 (22511) covalent geometry : angle 0.50391 (30776) Misc. bond : bond 0.00157 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12588.87 seconds wall clock time: 218 minutes 5.82 seconds (13085.82 seconds total)