Starting phenix.real_space_refine on Thu Mar 5 05:44:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jsn_22458/03_2026/7jsn_22458.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jsn_22458/03_2026/7jsn_22458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jsn_22458/03_2026/7jsn_22458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jsn_22458/03_2026/7jsn_22458.map" model { file = "/net/cci-nas-00/data/ceres_data/7jsn_22458/03_2026/7jsn_22458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jsn_22458/03_2026/7jsn_22458.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 8 5.49 5 Mg 2 5.21 5 S 141 5.16 5 C 12382 2.51 5 N 3258 2.21 5 O 3645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19438 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6707 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 820, 6703 Classifications: {'peptide': 820} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 788} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 820, 6703 Classifications: {'peptide': 820} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 788} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 6851 Chain: "B" Number of atoms: 6532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6532 Classifications: {'peptide': 806} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 774} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2464 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 310} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "F" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2451 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 310} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 551 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 551 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 1, ' ZN': 1, '35G%rna3p': 1, 'VDN': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 1, ' ZN': 1, '35G%rna3p': 1, 'VDN': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A 345 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 345 " occ=0.50 Time building chain proxies: 5.05, per 1000 atoms: 0.26 Number of scatterers: 19438 At special positions: 0 Unit cell: (165.75, 149.6, 146.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 141 16.00 P 8 15.00 Mg 2 11.99 O 3645 8.00 N 3258 7.00 C 12382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 867.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 599 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 563 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 561 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 597 " 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4562 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 7 sheets defined 47.5% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 56 through 68 removed outlier: 6.596A pdb=" N ILE A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N PHE A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.627A pdb=" N LYS A 84 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'A' and resid 205 through 222 removed outlier: 4.939A pdb=" N ASN A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 249 removed outlier: 3.931A pdb=" N ARG A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 241 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 247 " --> pdb=" O TRP A 243 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 removed outlier: 4.109A pdb=" N TYR A 264 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.790A pdb=" N ALA A 351 " --> pdb=" O PRO A 347 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN A 352 " --> pdb=" O THR A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 4.143A pdb=" N LEU A 419 " --> pdb=" O MET A 415 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 458 removed outlier: 4.132A pdb=" N ASN A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N HIS A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 494 removed outlier: 4.174A pdb=" N GLY A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.508A pdb=" N GLN A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 526 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 535 No H-bonds generated for 'chain 'A' and resid 532 through 535' Processing helix chain 'A' and resid 539 through 552 Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.631A pdb=" N ASN A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 567 " --> pdb=" O HIS A 563 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY A 568 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 586 through 597 removed outlier: 3.792A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 removed outlier: 3.644A pdb=" N MET A 612 " --> pdb=" O ASN A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 626 through 639 removed outlier: 3.591A pdb=" N HIS A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 668 removed outlier: 3.562A pdb=" N ILE A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 690 removed outlier: 6.154A pdb=" N THR A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N MET A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 688 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS A 689 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 702 Processing helix chain 'A' and resid 706 through 720 removed outlier: 3.966A pdb=" N MET A 712 " --> pdb=" O LYS A 708 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 714 " --> pdb=" O ILE A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 728 through 752 removed outlier: 4.512A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 737 " --> pdb=" O LYS A 733 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU A 741 " --> pdb=" O LEU A 737 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE A 742 " --> pdb=" O VAL A 738 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP A 747 " --> pdb=" O TRP A 743 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 748 " --> pdb=" O GLU A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 791 removed outlier: 5.122A pdb=" N ASP A 767 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 769 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Proline residue: A 770 - end of helix removed outlier: 4.335A pdb=" N PHE A 776 " --> pdb=" O GLN A 773 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE A 777 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL A 780 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N CYS A 781 " --> pdb=" O ASP A 778 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THR A 782 " --> pdb=" O PHE A 779 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A 783 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL A 784 " --> pdb=" O CYS A 781 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR A 785 " --> pdb=" O THR A 782 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 788 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 821 Proline residue: A 797 - end of helix removed outlier: 3.840A pdb=" N ASP A 800 " --> pdb=" O PRO A 797 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A 802 " --> pdb=" O LEU A 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 86 removed outlier: 3.561A pdb=" N ARG B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 163 through 166 No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 205 through 227 removed outlier: 3.773A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N PHE B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 218 " --> pdb=" O ASN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 247 removed outlier: 3.953A pdb=" N LYS B 245 " --> pdb=" O TRP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 264 removed outlier: 3.704A pdb=" N PHE B 261 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 291 No H-bonds generated for 'chain 'B' and resid 288 through 291' Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 413 through 455 removed outlier: 3.906A pdb=" N LEU B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR B 422 " --> pdb=" O MET B 418 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU B 430 " --> pdb=" O GLY B 426 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ASN B 431 " --> pdb=" O TRP B 427 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP B 436 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS B 455 " --> pdb=" O MET B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 468 Proline residue: B 468 - end of helix No H-bonds generated for 'chain 'B' and resid 464 through 468' Processing helix chain 'B' and resid 484 through 491 removed outlier: 3.688A pdb=" N ILE B 488 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 526 removed outlier: 3.517A pdb=" N TYR B 524 " --> pdb=" O GLY B 520 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 525 " --> pdb=" O ILE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 533 No H-bonds generated for 'chain 'B' and resid 530 through 533' Processing helix chain 'B' and resid 537 through 550 removed outlier: 3.778A pdb=" N VAL B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 574 removed outlier: 3.638A pdb=" N ALA B 566 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 584 through 594 removed outlier: 3.644A pdb=" N ALA B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 612 removed outlier: 3.556A pdb=" N MET B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.557A pdb=" N GLY B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 666 removed outlier: 3.836A pdb=" N ASP B 661 " --> pdb=" O ILE B 657 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 662 " --> pdb=" O HIS B 658 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 673 No H-bonds generated for 'chain 'B' and resid 670 through 673' Processing helix chain 'B' and resid 676 through 688 removed outlier: 3.925A pdb=" N GLN B 680 " --> pdb=" O ARG B 676 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 682 " --> pdb=" O MET B 678 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 687 " --> pdb=" O VAL B 683 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN B 688 " --> pdb=" O ASP B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'B' and resid 706 through 718 removed outlier: 3.633A pdb=" N MET B 712 " --> pdb=" O ILE B 708 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR B 715 " --> pdb=" O ALA B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 723 Processing helix chain 'B' and resid 726 through 750 removed outlier: 4.522A pdb=" N SER B 730 " --> pdb=" O TRP B 726 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS B 731 " --> pdb=" O GLU B 727 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU B 734 " --> pdb=" O SER B 730 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 739 " --> pdb=" O LEU B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 763 No H-bonds generated for 'chain 'B' and resid 761 through 763' Processing helix chain 'B' and resid 765 through 778 Proline residue: B 768 - end of helix removed outlier: 4.119A pdb=" N GLN B 771 " --> pdb=" O PRO B 768 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL B 778 " --> pdb=" O ILE B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 789 Processing helix chain 'B' and resid 794 through 821 Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.777A pdb=" N ALA C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'D' and resid 69 through 73 removed outlier: 3.838A pdb=" N PHE D 73 " --> pdb=" O TRP D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 59 through 87 removed outlier: 6.833A pdb=" N LEU E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ALA E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE E 69 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 78 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 85 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 107 removed outlier: 4.512A pdb=" N ASP E 98 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET E 106 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA E 107 " --> pdb=" O MET E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 128 removed outlier: 3.854A pdb=" N GLN E 124 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS E 128 " --> pdb=" O GLN E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 141 removed outlier: 5.793A pdb=" N SER E 140 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU E 141 " --> pdb=" O ASP E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 159 removed outlier: 4.307A pdb=" N GLY E 149 " --> pdb=" O ASP E 146 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR E 151 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU E 152 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASP E 154 " --> pdb=" O TYR E 151 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU E 155 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU E 156 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL E 159 " --> pdb=" O GLU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 5.286A pdb=" N LEU E 171 " --> pdb=" O GLU E 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 167 through 171' Processing helix chain 'E' and resid 201 through 210 removed outlier: 4.451A pdb=" N LYS E 205 " --> pdb=" O ARG E 201 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LYS E 206 " --> pdb=" O SER E 202 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TRP E 207 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE E 208 " --> pdb=" O ARG E 204 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N HIS E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N CYS E 210 " --> pdb=" O LYS E 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 201 through 210' Processing helix chain 'E' and resid 223 through 227 removed outlier: 4.335A pdb=" N TYR E 226 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP E 227 " --> pdb=" O SER E 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 223 through 227' Processing helix chain 'E' and resid 238 through 250 removed outlier: 3.653A pdb=" N MET E 243 " --> pdb=" O MET E 239 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS E 244 " --> pdb=" O HIS E 240 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 276 removed outlier: 4.569A pdb=" N LYS E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LYS E 276 " --> pdb=" O GLU E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 281 No H-bonds generated for 'chain 'E' and resid 279 through 281' Processing helix chain 'E' and resid 292 through 306 removed outlier: 4.733A pdb=" N LEU E 306 " --> pdb=" O GLN E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 311 removed outlier: 5.050A pdb=" N ASP E 311 " --> pdb=" O MET E 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 308 through 311' Processing helix chain 'E' and resid 325 through 341 Processing helix chain 'F' and resid 42 through 53 removed outlier: 3.599A pdb=" N VAL F 46 " --> pdb=" O LYS F 42 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 87 removed outlier: 6.975A pdb=" N LEU F 63 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL F 81 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR F 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR F 86 " --> pdb=" O ARG F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 107 removed outlier: 4.185A pdb=" N ALA F 100 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA F 107 " --> pdb=" O MET F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 128 removed outlier: 3.640A pdb=" N ILE F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 141 removed outlier: 3.776A pdb=" N ARG F 138 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA F 139 " --> pdb=" O CYS F 135 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER F 140 " --> pdb=" O PHE F 136 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLU F 141 " --> pdb=" O ASP F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 159 removed outlier: 3.690A pdb=" N GLY F 149 " --> pdb=" O ASP F 146 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU F 152 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER F 153 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU F 156 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 201 through 210 removed outlier: 4.392A pdb=" N LYS F 205 " --> pdb=" O ARG F 201 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LYS F 206 " --> pdb=" O SER F 202 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TRP F 207 " --> pdb=" O GLU F 203 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE F 208 " --> pdb=" O ARG F 204 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N HIS F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N CYS F 210 " --> pdb=" O LYS F 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 201 through 210' Processing helix chain 'F' and resid 223 through 227 removed outlier: 4.659A pdb=" N TYR F 226 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP F 227 " --> pdb=" O SER F 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 223 through 227' Processing helix chain 'F' and resid 238 through 250 removed outlier: 3.575A pdb=" N SER F 248 " --> pdb=" O HIS F 244 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE F 249 " --> pdb=" O LEU F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 276 removed outlier: 4.560A pdb=" N LYS F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS F 276 " --> pdb=" O GLU F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 281 No H-bonds generated for 'chain 'F' and resid 279 through 281' Processing helix chain 'F' and resid 292 through 306 removed outlier: 4.644A pdb=" N GLY F 296 " --> pdb=" O TYR F 292 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN F 297 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR F 298 " --> pdb=" O GLU F 294 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU F 306 " --> pdb=" O GLN F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 311 removed outlier: 5.765A pdb=" N ASP F 311 " --> pdb=" O MET F 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 308 through 311' Processing helix chain 'F' and resid 325 through 341 removed outlier: 3.995A pdb=" N ASP F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA F 334 " --> pdb=" O PHE F 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 39 removed outlier: 4.008A pdb=" N GLN A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LYS A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 32 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 37 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'B' and resid 47 through 67 removed outlier: 3.778A pdb=" N GLU B 55 " --> pdb=" O CYS B 51 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 110 through 113 removed outlier: 6.788A pdb=" N LEU A 96 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N PHE A 113 " --> pdb=" O MET A 94 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N MET A 94 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ASP A 187 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE A 182 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ILE A 191 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER A 180 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N MET A 193 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU A 178 " --> pdb=" O MET A 193 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 177 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=C, first strand: chain 'A' and resid 275 through 279 removed outlier: 6.256A pdb=" N ALA A 401 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE A 403 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER A 387 " --> pdb=" O PHE A 403 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 105 through 107 removed outlier: 5.669A pdb=" N CYS B 92 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 193 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU B 94 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N MET B 191 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N MET B 96 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 189 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 98 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N VAL B 187 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 180 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL B 189 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR B 178 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET B 191 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 176 " --> pdb=" O MET B 191 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.226A pdb=" N ALA B 399 " --> pdb=" O PRO B 387 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE B 401 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N SER B 385 " --> pdb=" O PHE B 401 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'E' and resid 317 through 320 removed outlier: 9.127A pdb=" N HIS E 318 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU E 262 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR E 320 " --> pdb=" O LEU E 262 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU E 264 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA E 216 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN E 191 " --> pdb=" O ARG E 28 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL E 30 " --> pdb=" O ASN E 191 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL E 197 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY E 36 " --> pdb=" O VAL E 197 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'F' and resid 317 through 320 removed outlier: 8.897A pdb=" N HIS F 318 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU F 262 " --> pdb=" O HIS F 318 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR F 320 " --> pdb=" O LEU F 262 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU F 264 " --> pdb=" O THR F 320 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA F 216 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU F 33 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASN F 191 " --> pdb=" O ARG F 28 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL F 197 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY F 36 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE F 192 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE F 185 " --> pdb=" O PHE F 192 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP F 196 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE F 181 " --> pdb=" O ASP F 196 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1614 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3288 1.30 - 1.43: 5098 1.43 - 1.56: 11230 1.56 - 1.68: 17 1.68 - 1.81: 232 Bond restraints: 19865 Sorted by residual: bond pdb=" O1P 35G B 905 " pdb=" P 35G B 905 " ideal model delta sigma weight residual 1.462 1.644 -0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" O1P 35G A 905 " pdb=" P 35G A 905 " ideal model delta sigma weight residual 1.462 1.642 -0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" C4 35G A 905 " pdb=" N3 35G A 905 " ideal model delta sigma weight residual 1.343 1.488 -0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" C4 35G B 905 " pdb=" N3 35G B 905 " ideal model delta sigma weight residual 1.343 1.487 -0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C2 35G B 905 " pdb=" N3 35G B 905 " ideal model delta sigma weight residual 1.319 1.458 -0.139 2.00e-02 2.50e+03 4.85e+01 ... (remaining 19860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 26307 1.93 - 3.86: 476 3.86 - 5.79: 72 5.79 - 7.72: 21 7.72 - 9.66: 12 Bond angle restraints: 26888 Sorted by residual: angle pdb=" N ASN A 462 " pdb=" CA ASN A 462 " pdb=" C ASN A 462 " ideal model delta sigma weight residual 111.28 119.55 -8.27 1.09e+00 8.42e-01 5.76e+01 angle pdb=" N MET B 712 " pdb=" CA MET B 712 " pdb=" C MET B 712 " ideal model delta sigma weight residual 113.43 106.61 6.82 1.26e+00 6.30e-01 2.93e+01 angle pdb=" N VAL A 195 " pdb=" CA VAL A 195 " pdb=" C VAL A 195 " ideal model delta sigma weight residual 108.11 115.62 -7.51 1.40e+00 5.10e-01 2.88e+01 angle pdb=" CA CYS B 92 " pdb=" C CYS B 92 " pdb=" O CYS B 92 " ideal model delta sigma weight residual 121.45 116.34 5.11 1.07e+00 8.73e-01 2.28e+01 angle pdb=" CA ASP A 461 " pdb=" CB ASP A 461 " pdb=" CG ASP A 461 " ideal model delta sigma weight residual 112.60 117.10 -4.50 1.00e+00 1.00e+00 2.03e+01 ... (remaining 26883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 11845 35.59 - 71.19: 137 71.19 - 106.78: 17 106.78 - 142.38: 3 142.38 - 177.97: 4 Dihedral angle restraints: 12006 sinusoidal: 4965 harmonic: 7041 Sorted by residual: dihedral pdb=" C4' GTP E 351 " pdb=" C5' GTP E 351 " pdb=" O5' GTP E 351 " pdb=" PA GTP E 351 " ideal model delta sinusoidal sigma weight residual 260.87 119.01 141.86 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" C4' GTP F 351 " pdb=" C5' GTP F 351 " pdb=" O5' GTP F 351 " pdb=" PA GTP F 351 " ideal model delta sinusoidal sigma weight residual 260.87 131.97 128.90 1 2.00e+01 2.50e-03 3.91e+01 dihedral pdb=" C8 GTP F 351 " pdb=" C1' GTP F 351 " pdb=" N9 GTP F 351 " pdb=" O4' GTP F 351 " ideal model delta sinusoidal sigma weight residual 104.59 -3.40 107.99 1 2.00e+01 2.50e-03 3.14e+01 ... (remaining 12003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2808 0.096 - 0.193: 135 0.193 - 0.289: 3 0.289 - 0.385: 1 0.385 - 0.482: 2 Chirality restraints: 2949 Sorted by residual: chirality pdb=" P 35G A 905 " pdb=" O2P 35G A 905 " pdb=" O3' 35G A 905 " pdb=" O5' 35G A 905 " both_signs ideal model delta sigma weight residual True 3.54 -3.06 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" P 35G B 905 " pdb=" O2P 35G B 905 " pdb=" O3' 35G B 905 " pdb=" O5' 35G B 905 " both_signs ideal model delta sigma weight residual True 3.54 -3.07 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA ARG B 676 " pdb=" N ARG B 676 " pdb=" C ARG B 676 " pdb=" CB ARG B 676 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 2946 not shown) Planarity restraints: 3440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 21 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C LYS A 21 " 0.059 2.00e-02 2.50e+03 pdb=" O LYS A 21 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN A 22 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 28 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO B 29 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 29 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 29 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 62 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C CYS F 62 " 0.033 2.00e-02 2.50e+03 pdb=" O CYS F 62 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU F 63 " -0.011 2.00e-02 2.50e+03 ... (remaining 3437 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 118 2.57 - 3.16: 15948 3.16 - 3.74: 26965 3.74 - 4.32: 36994 4.32 - 4.90: 62455 Nonbonded interactions: 142480 Sorted by model distance: nonbonded pdb=" OD2 ASP B 598 " pdb="ZN ZN B 902 " model vdw 1.992 2.230 nonbonded pdb=" OD2 ASP A 600 " pdb="ZN ZN A 902 " model vdw 2.007 2.230 nonbonded pdb=" NZ LYS A 223 " pdb=" O GLN B 67 " model vdw 2.214 3.120 nonbonded pdb=" OD1 ASP A 600 " pdb="MG MG A 903 " model vdw 2.220 2.170 nonbonded pdb=" O GLU A 642 " pdb=" OG SER A 643 " model vdw 2.235 3.040 ... (remaining 142475 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 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and ((resid 27 through 29 and (name N or name CA or name C or name O \ or name CB )) or resid 30 through 256 or (resid 257 and (name N or name CA or na \ me C or name O or name CB )) or resid 258 through 259 or (resid 260 and (name N \ or name CA or name C or name O or name CB )) or resid 261 through 266 or (resid \ 267 and (name N or name CA or name C or name O or name CB )) or resid 268 throug \ h 288 or (resid 289 and (name N or name CA or name C or name O or name CB )) or \ resid 290 through 351)) selection = (chain 'F' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 351)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.270 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.006 0.182 19869 Z= 0.289 Angle : 0.683 9.656 26888 Z= 0.392 Chirality : 0.047 0.482 2949 Planarity : 0.004 0.048 3440 Dihedral : 13.196 177.973 7444 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.05 % Allowed : 6.21 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.16), residues: 2391 helix: -0.84 (0.16), residues: 1069 sheet: -0.05 (0.36), residues: 202 loop : -1.68 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 28 TYR 0.024 0.001 TYR B 672 PHE 0.014 0.001 PHE B 215 TRP 0.007 0.001 TRP A 697 HIS 0.004 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00589 (19865) covalent geometry : angle 0.68300 (26888) hydrogen bonds : bond 0.09563 ( 616) hydrogen bonds : angle 4.95743 ( 1614) metal coordination : bond 0.00283 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ASN cc_start: 0.8602 (m-40) cc_final: 0.8378 (m-40) REVERT: A 444 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7134 (tm-30) REVERT: A 464 GLU cc_start: 0.7922 (tt0) cc_final: 0.7622 (tt0) REVERT: A 820 MET cc_start: 0.7783 (tmm) cc_final: 0.7567 (tmm) REVERT: E 119 MET cc_start: 0.7495 (ttm) cc_final: 0.7267 (ttm) REVERT: E 146 ASP cc_start: 0.7332 (t0) cc_final: 0.7122 (t70) REVERT: E 182 GLU cc_start: 0.7509 (mp0) cc_final: 0.7137 (mp0) REVERT: E 210 CYS cc_start: 0.7375 (m) cc_final: 0.6935 (p) REVERT: F 106 MET cc_start: 0.7976 (ppp) cc_final: 0.7581 (ppp) REVERT: F 308 MET cc_start: 0.7931 (tmm) cc_final: 0.7724 (tmm) REVERT: C 74 ASN cc_start: 0.8565 (t0) cc_final: 0.8120 (m-40) REVERT: D 24 ARG cc_start: 0.8432 (ptt180) cc_final: 0.8229 (ptt180) REVERT: D 29 LYS cc_start: 0.8591 (tttp) cc_final: 0.8352 (tttm) REVERT: D 37 GLN cc_start: 0.8197 (mm110) cc_final: 0.7917 (mm110) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.1349 time to fit residues: 52.3848 Evaluate side-chains 200 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 232 ASN A 258 GLN A 384 ASN ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 145 ASN F 90 GLN F 168 GLN C 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.103156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.069434 restraints weight = 42124.212| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.09 r_work: 0.2860 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19869 Z= 0.111 Angle : 0.542 11.030 26888 Z= 0.283 Chirality : 0.042 0.195 2949 Planarity : 0.004 0.054 3440 Dihedral : 10.320 178.584 2707 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.64 % Rotamer: Outliers : 1.10 % Allowed : 8.74 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.17), residues: 2391 helix: -0.57 (0.16), residues: 1095 sheet: 0.26 (0.37), residues: 204 loop : -1.51 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 460 TYR 0.015 0.001 TYR F 151 PHE 0.026 0.001 PHE A 19 TRP 0.016 0.001 TRP A 480 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00236 (19865) covalent geometry : angle 0.54153 (26888) hydrogen bonds : bond 0.04966 ( 616) hydrogen bonds : angle 4.18928 ( 1614) metal coordination : bond 0.00142 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 464 GLU cc_start: 0.8410 (tt0) cc_final: 0.8080 (tt0) REVERT: A 820 MET cc_start: 0.7688 (tmm) cc_final: 0.7416 (tmm) REVERT: B 574 MET cc_start: 0.8349 (mmm) cc_final: 0.8060 (mmm) REVERT: E 146 ASP cc_start: 0.7195 (t0) cc_final: 0.6930 (t70) REVERT: E 210 CYS cc_start: 0.7357 (m) cc_final: 0.6801 (p) REVERT: F 119 MET cc_start: 0.6272 (mmt) cc_final: 0.5571 (mmt) REVERT: F 168 GLN cc_start: 0.7164 (tt0) cc_final: 0.6954 (tp40) REVERT: F 308 MET cc_start: 0.8182 (tmm) cc_final: 0.7887 (tmm) REVERT: C 15 ARG cc_start: 0.8865 (mmt90) cc_final: 0.8635 (mmt90) REVERT: C 74 ASN cc_start: 0.8564 (t0) cc_final: 0.8062 (m-40) outliers start: 23 outliers final: 10 residues processed: 237 average time/residue: 0.1336 time to fit residues: 49.7645 Evaluate side-chains 207 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 69 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 GLN ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** 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 = 0.3604 r_free = 0.3604 target = 0.100659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.066612 restraints weight = 42798.062| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.11 r_work: 0.2803 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19869 Z= 0.187 Angle : 0.584 9.374 26888 Z= 0.307 Chirality : 0.044 0.156 2949 Planarity : 0.004 0.054 3440 Dihedral : 10.314 178.421 2707 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.62 % Allowed : 10.21 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.17), residues: 2391 helix: -0.53 (0.16), residues: 1096 sheet: 0.17 (0.37), residues: 205 loop : -1.52 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 460 TYR 0.020 0.002 TYR B 273 PHE 0.022 0.001 PHE A 19 TRP 0.017 0.001 TRP A 480 HIS 0.004 0.001 HIS B 561 Details of bonding type rmsd covalent geometry : bond 0.00448 (19865) covalent geometry : angle 0.58365 (26888) hydrogen bonds : bond 0.06132 ( 616) hydrogen bonds : angle 4.31816 ( 1614) metal coordination : bond 0.00348 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.7972 (pm20) cc_final: 0.7742 (pm20) REVERT: A 444 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7522 (tm-30) REVERT: A 571 MET cc_start: 0.8695 (tpp) cc_final: 0.8473 (tpp) REVERT: B 574 MET cc_start: 0.8548 (mmm) cc_final: 0.8300 (mmm) REVERT: E 84 MET cc_start: 0.7639 (ttm) cc_final: 0.7394 (tpp) REVERT: E 210 CYS cc_start: 0.7385 (m) cc_final: 0.6827 (p) REVERT: F 97 GLN cc_start: 0.8578 (mt0) cc_final: 0.8099 (tp40) REVERT: F 119 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5429 (mmt) REVERT: F 168 GLN cc_start: 0.7245 (tt0) cc_final: 0.7029 (tp40) REVERT: C 15 ARG cc_start: 0.8915 (mmt90) cc_final: 0.8628 (mmt90) REVERT: D 24 ARG cc_start: 0.8690 (ptt180) cc_final: 0.8357 (ttp-170) outliers start: 34 outliers final: 21 residues processed: 226 average time/residue: 0.1333 time to fit residues: 47.0474 Evaluate side-chains 217 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 210 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 167 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 52 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 230 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 75 optimal weight: 0.1980 chunk 191 optimal weight: 30.0000 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 GLN B 771 GLN F 97 GLN ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.104471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.070746 restraints weight = 42380.062| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.11 r_work: 0.2885 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19869 Z= 0.099 Angle : 0.508 8.605 26888 Z= 0.263 Chirality : 0.040 0.147 2949 Planarity : 0.004 0.054 3440 Dihedral : 10.006 178.909 2707 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.58 % Allowed : 11.46 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.17), residues: 2391 helix: -0.16 (0.16), residues: 1084 sheet: 0.46 (0.37), residues: 203 loop : -1.39 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 309 TYR 0.011 0.001 TYR F 298 PHE 0.009 0.001 PHE E 185 TRP 0.018 0.001 TRP A 480 HIS 0.003 0.000 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00199 (19865) covalent geometry : angle 0.50775 (26888) hydrogen bonds : bond 0.04153 ( 616) hydrogen bonds : angle 3.84858 ( 1614) metal coordination : bond 0.00112 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.8046 (pm20) cc_final: 0.7746 (pm20) REVERT: A 416 ASP cc_start: 0.8810 (m-30) cc_final: 0.8540 (m-30) REVERT: A 444 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7313 (tm-30) REVERT: E 115 MET cc_start: 0.6153 (pmm) cc_final: 0.4629 (ptt) REVERT: E 210 CYS cc_start: 0.7390 (m) cc_final: 0.6792 (p) REVERT: F 97 GLN cc_start: 0.8535 (mt0) cc_final: 0.8105 (tp40) REVERT: F 106 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7497 (ppp) REVERT: C 74 ASN cc_start: 0.8582 (t0) cc_final: 0.8090 (m-40) REVERT: C 77 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6993 (tm-30) REVERT: D 24 ARG cc_start: 0.8671 (ptt180) cc_final: 0.8413 (ttp-170) outliers start: 33 outliers final: 16 residues processed: 244 average time/residue: 0.1295 time to fit residues: 48.4809 Evaluate side-chains 227 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 210 CYS Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 231 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 49 optimal weight: 0.0670 chunk 127 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 687 GLN B 88 HIS E 53 HIS ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.104524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.070637 restraints weight = 42455.705| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.13 r_work: 0.2884 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19869 Z= 0.100 Angle : 0.511 9.078 26888 Z= 0.263 Chirality : 0.040 0.141 2949 Planarity : 0.004 0.052 3440 Dihedral : 9.884 176.375 2707 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.53 % Allowed : 12.03 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.17), residues: 2391 helix: -0.02 (0.16), residues: 1087 sheet: 0.55 (0.37), residues: 203 loop : -1.32 (0.17), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 460 TYR 0.012 0.001 TYR B 273 PHE 0.010 0.001 PHE E 185 TRP 0.012 0.001 TRP A 480 HIS 0.003 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00212 (19865) covalent geometry : angle 0.51132 (26888) hydrogen bonds : bond 0.04219 ( 616) hydrogen bonds : angle 3.73930 ( 1614) metal coordination : bond 0.00102 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.8089 (pm20) cc_final: 0.7753 (pm20) REVERT: A 416 ASP cc_start: 0.8793 (m-30) cc_final: 0.8420 (m-30) REVERT: A 444 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7368 (tm-30) REVERT: B 169 ASP cc_start: 0.8612 (t0) cc_final: 0.8389 (t0) REVERT: B 197 ASP cc_start: 0.8047 (m-30) cc_final: 0.7485 (p0) REVERT: B 574 MET cc_start: 0.8390 (mmm) cc_final: 0.7912 (mmm) REVERT: E 101 ARG cc_start: 0.8400 (tmm160) cc_final: 0.7541 (mtm-85) REVERT: E 115 MET cc_start: 0.6264 (pmm) cc_final: 0.4746 (ptt) REVERT: E 121 ASP cc_start: 0.8312 (t70) cc_final: 0.7920 (m-30) REVERT: E 210 CYS cc_start: 0.7384 (m) cc_final: 0.6791 (p) REVERT: F 97 GLN cc_start: 0.8520 (mt0) cc_final: 0.8084 (tp40) REVERT: C 77 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: D 24 ARG cc_start: 0.8671 (ptt180) cc_final: 0.8363 (ttp-170) outliers start: 32 outliers final: 20 residues processed: 235 average time/residue: 0.1319 time to fit residues: 48.2127 Evaluate side-chains 224 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 165 optimal weight: 4.9990 chunk 77 optimal weight: 0.0980 chunk 144 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 220 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 GLN B 88 HIS ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.104217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.070251 restraints weight = 42279.794| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.12 r_work: 0.2882 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19869 Z= 0.104 Angle : 0.516 10.690 26888 Z= 0.263 Chirality : 0.041 0.139 2949 Planarity : 0.004 0.052 3440 Dihedral : 9.787 174.300 2707 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.58 % Allowed : 12.12 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.17), residues: 2391 helix: 0.12 (0.16), residues: 1077 sheet: 0.60 (0.38), residues: 203 loop : -1.23 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 460 TYR 0.013 0.001 TYR B 97 PHE 0.009 0.001 PHE E 185 TRP 0.016 0.001 TRP A 480 HIS 0.003 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00231 (19865) covalent geometry : angle 0.51633 (26888) hydrogen bonds : bond 0.04331 ( 616) hydrogen bonds : angle 3.72688 ( 1614) metal coordination : bond 0.00154 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.8156 (pm20) cc_final: 0.7787 (pm20) REVERT: A 416 ASP cc_start: 0.8797 (m-30) cc_final: 0.8427 (m-30) REVERT: A 444 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7400 (tm-30) REVERT: B 197 ASP cc_start: 0.8020 (m-30) cc_final: 0.7496 (p0) REVERT: B 282 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7619 (ttmm) REVERT: B 574 MET cc_start: 0.8413 (mmm) cc_final: 0.7965 (mmm) REVERT: E 101 ARG cc_start: 0.8444 (tmm160) cc_final: 0.8188 (tmm160) REVERT: E 102 LYS cc_start: 0.8901 (tttm) cc_final: 0.8566 (tttm) REVERT: E 121 ASP cc_start: 0.8300 (t70) cc_final: 0.7983 (m-30) REVERT: E 210 CYS cc_start: 0.7386 (m) cc_final: 0.6837 (p) REVERT: E 241 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8662 (tm-30) REVERT: F 97 GLN cc_start: 0.8530 (mt0) cc_final: 0.8077 (tp40) REVERT: C 77 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6876 (tm-30) REVERT: D 24 ARG cc_start: 0.8654 (ptt180) cc_final: 0.8303 (ttp-170) outliers start: 33 outliers final: 26 residues processed: 232 average time/residue: 0.1363 time to fit residues: 49.0778 Evaluate side-chains 235 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 318 HIS Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 210 CYS Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 223 optimal weight: 8.9990 chunk 158 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 205 optimal weight: 8.9990 chunk 49 optimal weight: 0.0870 chunk 170 optimal weight: 40.0000 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS C 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.103954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.069923 restraints weight = 42295.733| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.12 r_work: 0.2876 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19869 Z= 0.110 Angle : 0.522 10.445 26888 Z= 0.267 Chirality : 0.041 0.139 2949 Planarity : 0.004 0.052 3440 Dihedral : 9.714 172.550 2707 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.62 % Allowed : 12.41 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2391 helix: 0.18 (0.17), residues: 1077 sheet: 0.63 (0.37), residues: 204 loop : -1.20 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 460 TYR 0.014 0.001 TYR B 97 PHE 0.022 0.001 PHE F 65 TRP 0.014 0.001 TRP A 480 HIS 0.003 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00249 (19865) covalent geometry : angle 0.52156 (26888) hydrogen bonds : bond 0.04441 ( 616) hydrogen bonds : angle 3.74492 ( 1614) metal coordination : bond 0.00165 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.8205 (pm20) cc_final: 0.7817 (pm20) REVERT: A 444 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7455 (tm-30) REVERT: B 197 ASP cc_start: 0.8034 (m-30) cc_final: 0.7507 (p0) REVERT: B 282 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7650 (ttmm) REVERT: B 574 MET cc_start: 0.8501 (mmm) cc_final: 0.8050 (mmm) REVERT: E 101 ARG cc_start: 0.8372 (tmm160) cc_final: 0.8143 (tmm160) REVERT: E 121 ASP cc_start: 0.8246 (t70) cc_final: 0.7986 (m-30) REVERT: E 210 CYS cc_start: 0.7397 (m) cc_final: 0.6858 (p) REVERT: E 241 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8677 (tm-30) REVERT: F 97 GLN cc_start: 0.8542 (mt0) cc_final: 0.8118 (tp40) REVERT: C 34 GLN cc_start: 0.8553 (pp30) cc_final: 0.8337 (pp30) REVERT: C 77 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: D 24 ARG cc_start: 0.8649 (ptt180) cc_final: 0.8434 (ttp-170) outliers start: 34 outliers final: 29 residues processed: 226 average time/residue: 0.1359 time to fit residues: 48.0614 Evaluate side-chains 232 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 318 HIS Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 44 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 19 optimal weight: 0.9990 chunk 201 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 237 optimal weight: 0.0000 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.104321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.070296 restraints weight = 42302.052| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.12 r_work: 0.2879 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19869 Z= 0.103 Angle : 0.516 11.034 26888 Z= 0.263 Chirality : 0.040 0.137 2949 Planarity : 0.004 0.052 3440 Dihedral : 9.609 170.142 2707 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.62 % Allowed : 12.74 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2391 helix: 0.25 (0.17), residues: 1076 sheet: 0.63 (0.37), residues: 205 loop : -1.14 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 460 TYR 0.013 0.001 TYR B 97 PHE 0.017 0.001 PHE F 65 TRP 0.014 0.001 TRP A 480 HIS 0.005 0.000 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00230 (19865) covalent geometry : angle 0.51605 (26888) hydrogen bonds : bond 0.04262 ( 616) hydrogen bonds : angle 3.69476 ( 1614) metal coordination : bond 0.00140 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8985 (mmm) cc_final: 0.8689 (mmt) REVERT: A 285 GLN cc_start: 0.8177 (pm20) cc_final: 0.7804 (pm20) REVERT: A 444 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7420 (tm-30) REVERT: B 197 ASP cc_start: 0.7926 (m-30) cc_final: 0.7402 (p0) REVERT: B 282 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7658 (ttmm) REVERT: B 574 MET cc_start: 0.8456 (mmm) cc_final: 0.8162 (mmm) REVERT: E 121 ASP cc_start: 0.8202 (t70) cc_final: 0.7963 (m-30) REVERT: E 210 CYS cc_start: 0.7388 (m) cc_final: 0.6843 (p) REVERT: E 241 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8629 (tm-30) REVERT: F 97 GLN cc_start: 0.8527 (mt0) cc_final: 0.8074 (tp40) REVERT: C 15 ARG cc_start: 0.8907 (mmt90) cc_final: 0.8595 (mmt90) REVERT: C 34 GLN cc_start: 0.8484 (pp30) cc_final: 0.8223 (pp30) REVERT: C 77 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6784 (tm-30) REVERT: D 24 ARG cc_start: 0.8656 (ptt180) cc_final: 0.8281 (ttp-170) outliers start: 34 outliers final: 27 residues processed: 232 average time/residue: 0.1342 time to fit residues: 48.7673 Evaluate side-chains 230 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 318 HIS Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 174 CYS Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 219 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 145 optimal weight: 0.2980 chunk 170 optimal weight: 0.5980 chunk 164 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS B 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.103404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.070054 restraints weight = 42145.750| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.96 r_work: 0.2878 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19869 Z= 0.117 Angle : 0.533 11.216 26888 Z= 0.272 Chirality : 0.041 0.143 2949 Planarity : 0.004 0.052 3440 Dihedral : 9.584 169.319 2707 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.43 % Allowed : 12.98 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.17), residues: 2391 helix: 0.26 (0.17), residues: 1076 sheet: 0.56 (0.37), residues: 205 loop : -1.12 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 101 TYR 0.014 0.001 TYR B 97 PHE 0.017 0.001 PHE F 65 TRP 0.019 0.001 TRP A 480 HIS 0.003 0.001 HIS B 561 Details of bonding type rmsd covalent geometry : bond 0.00268 (19865) covalent geometry : angle 0.53317 (26888) hydrogen bonds : bond 0.04498 ( 616) hydrogen bonds : angle 3.72778 ( 1614) metal coordination : bond 0.00181 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8961 (mmm) cc_final: 0.8666 (mmt) REVERT: A 285 GLN cc_start: 0.8192 (pm20) cc_final: 0.7842 (pm20) REVERT: A 444 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7480 (tm-30) REVERT: B 282 LYS cc_start: 0.8095 (mtpp) cc_final: 0.7688 (ttmm) REVERT: B 574 MET cc_start: 0.8506 (mmm) cc_final: 0.8215 (mmm) REVERT: E 101 ARG cc_start: 0.7807 (tmm160) cc_final: 0.7266 (mtm-85) REVERT: E 121 ASP cc_start: 0.8131 (t70) cc_final: 0.7915 (m-30) REVERT: E 210 CYS cc_start: 0.7417 (m) cc_final: 0.6881 (p) REVERT: E 241 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8654 (tm-30) REVERT: F 97 GLN cc_start: 0.8534 (mt0) cc_final: 0.8079 (tp40) REVERT: C 15 ARG cc_start: 0.8861 (mmt90) cc_final: 0.8530 (mmt90) REVERT: C 34 GLN cc_start: 0.8488 (pp30) cc_final: 0.8229 (pp30) REVERT: C 77 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6804 (tm-30) REVERT: D 24 ARG cc_start: 0.8691 (ptt180) cc_final: 0.8304 (ttp-170) outliers start: 30 outliers final: 27 residues processed: 224 average time/residue: 0.1353 time to fit residues: 47.5282 Evaluate side-chains 229 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 318 HIS Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 227 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 133 optimal weight: 0.0470 chunk 220 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.102413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.068652 restraints weight = 42318.454| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.06 r_work: 0.2845 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19869 Z= 0.142 Angle : 0.556 11.370 26888 Z= 0.286 Chirality : 0.042 0.140 2949 Planarity : 0.004 0.052 3440 Dihedral : 9.622 170.091 2707 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.38 % Allowed : 13.03 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.17), residues: 2391 helix: 0.20 (0.16), residues: 1075 sheet: 0.47 (0.37), residues: 205 loop : -1.15 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 101 TYR 0.016 0.001 TYR B 273 PHE 0.017 0.001 PHE F 65 TRP 0.018 0.001 TRP A 480 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00335 (19865) covalent geometry : angle 0.55616 (26888) hydrogen bonds : bond 0.05069 ( 616) hydrogen bonds : angle 3.86196 ( 1614) metal coordination : bond 0.00243 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8978 (mmm) cc_final: 0.8684 (mmt) REVERT: A 285 GLN cc_start: 0.8263 (pm20) cc_final: 0.7881 (pm20) REVERT: A 444 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7538 (tm-30) REVERT: B 282 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7713 (ttmm) REVERT: B 574 MET cc_start: 0.8552 (mmm) cc_final: 0.8118 (mmm) REVERT: E 121 ASP cc_start: 0.8278 (t70) cc_final: 0.8056 (m-30) REVERT: E 210 CYS cc_start: 0.7419 (m) cc_final: 0.6883 (p) REVERT: E 241 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8658 (tm-30) REVERT: F 97 GLN cc_start: 0.8516 (mt0) cc_final: 0.8104 (tp40) REVERT: C 15 ARG cc_start: 0.8843 (mmt90) cc_final: 0.8495 (mmt90) REVERT: C 34 GLN cc_start: 0.8471 (pp30) cc_final: 0.8207 (pp30) REVERT: C 77 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6775 (tm-30) REVERT: D 24 ARG cc_start: 0.8674 (ptt180) cc_final: 0.8438 (ttp-170) outliers start: 29 outliers final: 27 residues processed: 219 average time/residue: 0.1365 time to fit residues: 47.2431 Evaluate side-chains 225 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 318 HIS Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 113 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 127 optimal weight: 0.0000 chunk 50 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.103550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.069465 restraints weight = 42274.666| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.10 r_work: 0.2854 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19869 Z= 0.113 Angle : 0.537 11.544 26888 Z= 0.274 Chirality : 0.041 0.140 2949 Planarity : 0.004 0.052 3440 Dihedral : 9.532 169.034 2707 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.34 % Allowed : 13.08 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.17), residues: 2391 helix: 0.31 (0.17), residues: 1069 sheet: 0.50 (0.37), residues: 205 loop : -1.10 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 101 TYR 0.014 0.001 TYR B 97 PHE 0.016 0.001 PHE F 65 TRP 0.018 0.001 TRP A 480 HIS 0.003 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00254 (19865) covalent geometry : angle 0.53692 (26888) hydrogen bonds : bond 0.04588 ( 616) hydrogen bonds : angle 3.76368 ( 1614) metal coordination : bond 0.00144 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5301.13 seconds wall clock time: 91 minutes 57.78 seconds (5517.78 seconds total)