Starting phenix.real_space_refine on Thu Mar 5 21:51:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ok0_12960/03_2026/7ok0_12960.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ok0_12960/03_2026/7ok0_12960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ok0_12960/03_2026/7ok0_12960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ok0_12960/03_2026/7ok0_12960.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ok0_12960/03_2026/7ok0_12960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ok0_12960/03_2026/7ok0_12960.map" } resolution = 2.9 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= 1.000 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 Fe 3 7.16 5 Zn 6 6.06 5 Mg 1 5.21 5 S 122 5.16 5 C 16294 2.51 5 N 4427 2.21 5 O 4783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s 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: 25636 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 7023 Classifications: {'peptide': 880} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 48, 'TRANS': 827} 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: "B" Number of atoms: 8725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8725 Classifications: {'peptide': 1109} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1055} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3087 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 384} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2057 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 246} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 402 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "G" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 991 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 617 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 690 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "L" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 707 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "N" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 534 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "P" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 376 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 357 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'F3S': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 435 SG CYS A 58 18.367 75.532 45.318 1.00124.98 S ATOM 455 SG CYS A 61 18.421 71.740 44.766 1.00122.81 S ATOM 497 SG CYS A 68 20.583 73.306 47.472 1.00117.60 S ATOM 744 SG CYS A 98 54.448 82.125 12.433 1.00133.82 S ATOM 775 SG CYS A 101 52.641 79.333 10.773 1.00135.01 S ATOM 1162 SG CYS A 146 56.435 79.218 10.850 1.00135.96 S ATOM 1185 SG CYS A 149 54.749 81.813 8.683 1.00138.63 S ATOM 4568 SG CYS A 575 83.314 38.808 91.778 1.00101.43 S ATOM 4608 SG CYS A 580 81.407 37.971 92.061 1.00 95.71 S ATOM 15263 SG CYS B1060 26.489 62.648 33.979 1.00106.21 S ATOM 15286 SG CYS B1063 28.705 65.672 34.066 1.00104.50 S ATOM 15417 SG CYS B1078 24.964 66.062 34.528 1.00114.57 S ATOM 20467 SG CYS D 209 72.142 53.258 122.116 1.00 73.26 S ATOM 20421 SG CYS D 203 66.228 53.698 123.074 1.00 61.07 S ATOM 20443 SG CYS D 206 67.977 56.107 119.534 1.00 62.13 S ATOM 20268 SG CYS D 183 68.476 58.536 124.159 1.00 67.39 S ATOM 24411 SG CYS N 7 49.304 70.647 113.304 1.00 45.72 S ATOM 24435 SG CYS N 10 48.935 67.656 115.689 1.00 49.44 S ATOM 24698 SG CYS N 44 52.354 68.655 114.415 1.00 48.19 S ATOM 24704 SG CYS N 45 50.547 70.803 116.958 1.00 48.07 S ATOM 24932 SG CYS P 6 26.195 105.880 98.468 1.00 96.89 S ATOM 25082 SG CYS P 26 23.396 107.491 97.973 1.00103.51 S ATOM 25107 SG CYS P 29 26.386 108.729 98.722 1.00109.19 S Time building chain proxies: 5.42, per 1000 atoms: 0.21 Number of scatterers: 25636 At special positions: 0 Unit cell: (126.945, 149.73, 149.73, 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 6 29.99 Fe 3 26.01 S 122 16.00 Mg 1 11.99 O 4783 8.00 N 4427 7.00 C 16294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 29 " distance=2.04 Simple disulfide: pdb=" SG CYS G 69 " - pdb=" SG CYS G 119 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S D 301 " pdb="FE4 F3S D 301 " - pdb=" SG CYS D 183 " pdb="FE1 F3S D 301 " - pdb=" SG CYS D 209 " pdb="FE3 F3S D 301 " - pdb=" SG CYS D 203 " pdb="FE3 F3S D 301 " - pdb=" SG CYS D 206 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 71 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 61 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 68 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 58 " pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 98 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 101 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 146 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 149 " pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 580 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 575 " pdb="ZN ZN A 904 " - pdb=" ND1 HIS A 582 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" ND1 HIS B1081 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1063 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1060 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1078 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 10 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 44 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 45 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 7 " pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 29 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 6 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 26 " Number of angles added : 18 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6018 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 39 sheets defined 40.6% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 15 through 23 Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 125 through 142 Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.862A pdb=" N ARG A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 203 through 206 Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 224 through 228 removed outlier: 3.924A pdb=" N SER A 227 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 228 " --> pdb=" O ILE A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 224 through 228' Processing helix chain 'A' and resid 233 through 256 removed outlier: 3.638A pdb=" N HIS A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 278 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 357 through 367 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.753A pdb=" N LEU A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.843A pdb=" N TYR A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 Processing helix chain 'A' and resid 481 through 486 removed outlier: 3.941A pdb=" N ILE A 486 " --> pdb=" O HIS A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.506A pdb=" N SER A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 599 through 604 Processing helix chain 'A' and resid 610 through 642 removed outlier: 7.037A pdb=" N THR A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N GLU A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE A 632 " --> pdb=" O MET A 628 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N MET A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 636 " --> pdb=" O PHE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 654 through 680 removed outlier: 3.557A pdb=" N GLN A 658 " --> pdb=" O PRO A 654 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 718 Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 736 through 745 Processing helix chain 'A' and resid 776 through 779 removed outlier: 3.507A pdb=" N ARG A 779 " --> pdb=" O PRO A 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 779' Processing helix chain 'A' and resid 791 through 827 removed outlier: 4.985A pdb=" N GLU A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLY A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR A 809 " --> pdb=" O GLY A 805 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ALA A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL A 811 " --> pdb=" O VAL A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 877 Processing helix chain 'A' and resid 878 through 880 No H-bonds generated for 'chain 'A' and resid 878 through 880' Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 21 through 34 Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.912A pdb=" N ILE B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.901A pdb=" N ASN B 130 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 232 through 241 removed outlier: 3.536A pdb=" N SER B 241 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 removed outlier: 3.935A pdb=" N GLU B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 256 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.541A pdb=" N PHE B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 325 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 343 through 374 Processing helix chain 'B' and resid 378 through 384 removed outlier: 4.037A pdb=" N VAL B 383 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG B 384 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 397 removed outlier: 3.750A pdb=" N THR B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 393 " --> pdb=" O THR B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 3.737A pdb=" N GLY B 404 " --> pdb=" O TRP B 401 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 405 " --> pdb=" O VAL B 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 405' Processing helix chain 'B' and resid 416 through 424 removed outlier: 3.513A pdb=" N MET B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.671A pdb=" N TRP B 448 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 removed outlier: 4.156A pdb=" N VAL B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 504 Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.661A pdb=" N SER B 514 " --> pdb=" O LYS B 511 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP B 515 " --> pdb=" O TYR B 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 511 through 515' Processing helix chain 'B' and resid 530 through 544 Processing helix chain 'B' and resid 588 through 596 Processing helix chain 'B' and resid 601 through 608 Processing helix chain 'B' and resid 617 through 622 Processing helix chain 'B' and resid 627 through 631 removed outlier: 3.654A pdb=" N LEU B 631 " --> pdb=" O PRO B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 646 removed outlier: 3.931A pdb=" N ILE B 645 " --> pdb=" O PRO B 642 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 646 " --> pdb=" O SER B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 653 removed outlier: 3.694A pdb=" N ILE B 653 " --> pdb=" O ALA B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 removed outlier: 3.710A pdb=" N ASN B 659 " --> pdb=" O PRO B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 672 removed outlier: 3.780A pdb=" N ASN B 664 " --> pdb=" O GLN B 660 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 665 " --> pdb=" O SER B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 709 removed outlier: 4.298A pdb=" N GLY B 707 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 714 Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 785 through 789 removed outlier: 4.367A pdb=" N LEU B 789 " --> pdb=" O TYR B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 911 No H-bonds generated for 'chain 'B' and resid 909 through 911' Processing helix chain 'B' and resid 912 through 917 removed outlier: 3.910A pdb=" N ARG B 916 " --> pdb=" O ALA B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 935 removed outlier: 4.239A pdb=" N ILE B 922 " --> pdb=" O THR B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 959 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1028 through 1039 Processing helix chain 'B' and resid 1040 through 1049 Processing helix chain 'B' and resid 1094 through 1106 removed outlier: 3.691A pdb=" N MET B1106 " --> pdb=" O GLU B1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 16 through 18 No H-bonds generated for 'chain 'C' and resid 16 through 18' Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 67 through 78 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.729A pdb=" N MET C 83 " --> pdb=" O GLY C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 111 Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 131 through 142 removed outlier: 3.604A pdb=" N ILE C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 149 Processing helix chain 'C' and resid 168 through 176 removed outlier: 3.614A pdb=" N GLY C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 216 through 226 Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.773A pdb=" N ILE C 270 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 282 removed outlier: 3.747A pdb=" N VAL C 278 " --> pdb=" O ASN C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 302 removed outlier: 3.543A pdb=" N ALA C 287 " --> pdb=" O GLY C 283 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN C 302 " --> pdb=" O VAL C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.819A pdb=" N ILE C 311 " --> pdb=" O ASP C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 removed outlier: 3.692A pdb=" N ARG C 342 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 346 " --> pdb=" O ARG C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 359 Processing helix chain 'C' and resid 367 through 374 Processing helix chain 'C' and resid 379 through 384 removed outlier: 3.716A pdb=" N VAL C 384 " --> pdb=" O THR C 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 35 removed outlier: 3.836A pdb=" N ILE D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 64 Processing helix chain 'D' and resid 112 through 114 No H-bonds generated for 'chain 'D' and resid 112 through 114' Processing helix chain 'D' and resid 153 through 157 Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.941A pdb=" N TYR D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 262 Processing helix chain 'E' and resid 14 through 18 Processing helix chain 'E' and resid 21 through 34 removed outlier: 4.184A pdb=" N ILE E 25 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 42 through 44 No H-bonds generated for 'chain 'G' and resid 42 through 44' Processing helix chain 'H' and resid 24 through 36 Processing helix chain 'H' and resid 38 through 42 removed outlier: 3.667A pdb=" N LEU H 42 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 55 Processing helix chain 'K' and resid 4 through 15 Processing helix chain 'K' and resid 19 through 35 Processing helix chain 'K' and resid 51 through 63 Processing helix chain 'L' and resid 21 through 33 removed outlier: 3.890A pdb=" N LEU L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 88 Processing helix chain 'N' and resid 14 through 16 No H-bonds generated for 'chain 'N' and resid 14 through 16' Processing helix chain 'N' and resid 17 through 27 removed outlier: 3.587A pdb=" N PHE N 21 " --> pdb=" O LYS N 17 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN N 23 " --> pdb=" O GLU N 19 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET N 26 " --> pdb=" O SER N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 39 removed outlier: 3.537A pdb=" N VAL N 34 " --> pdb=" O ASP N 30 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY N 39 " --> pdb=" O LEU N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 51 Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'Q' and resid 39 through 58 Processing helix chain 'Q' and resid 62 through 79 removed outlier: 3.823A pdb=" N LYS Q 79 " --> pdb=" O ARG Q 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 1111 through 1116 removed outlier: 6.270A pdb=" N ARG B1111 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A 9 " --> pdb=" O ARG B1111 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B1113 " --> pdb=" O ARG A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 82 removed outlier: 10.308A pdb=" N LEU A 77 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N LYS A 79 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL A 211 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 146 removed outlier: 3.548A pdb=" N GLU A 151 " --> pdb=" O CYS A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 159 removed outlier: 3.784A pdb=" N LYS A 157 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 165 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 316 through 318 Processing sheet with id=AA6, first strand: chain 'B' and resid 1001 through 1003 removed outlier: 3.650A pdb=" N HIS B1001 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.945A pdb=" N TYR A 377 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS A 410 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA A 375 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 515 through 516 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.736A pdb=" N CYS G 69 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS G 10 " --> pdb=" O ASP G 28 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS G 26 " --> pdb=" O SER G 12 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE G 14 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL G 24 " --> pdb=" O ILE G 14 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ILE G 95 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU G 94 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE G 86 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU G 77 " --> pdb=" O ILE G 86 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU G 88 " --> pdb=" O PHE G 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 562 through 565 removed outlier: 3.588A pdb=" N GLU A 595 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LYS A 589 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 748 through 749 Processing sheet with id=AB3, first strand: chain 'A' and resid 751 through 752 Processing sheet with id=AB4, first strand: chain 'A' and resid 830 through 832 removed outlier: 6.813A pdb=" N VAL A 838 " --> pdb=" O VAL A 846 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 45 through 46 removed outlier: 5.637A pdb=" N SER B 97 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE B 60 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE B 95 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR B 62 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SER B 92 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP B 116 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B 94 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AB7, first strand: chain 'B' and resid 150 through 152 Processing sheet with id=AB8, first strand: chain 'B' and resid 339 through 342 removed outlier: 6.468A pdb=" N ALA B 161 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 170 through 174 removed outlier: 3.847A pdb=" N HIS B 183 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC2, first strand: chain 'B' and resid 584 through 585 Processing sheet with id=AC3, first strand: chain 'B' and resid 523 through 528 removed outlier: 6.560A pdb=" N VAL B 518 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR B 527 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER B 516 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 566 " --> pdb=" O TYR B 519 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 689 through 693 removed outlier: 6.683A pdb=" N LEU B 859 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 850 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS B 861 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B 848 " --> pdb=" O LYS B 861 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG B 863 " --> pdb=" O ASP B 846 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 689 through 693 removed outlier: 6.683A pdb=" N LEU B 859 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 850 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS B 861 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B 848 " --> pdb=" O LYS B 861 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG B 863 " --> pdb=" O ASP B 846 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL B 848 " --> pdb=" O MET P 36 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET P 36 " --> pdb=" O VAL B 848 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 702 Processing sheet with id=AC7, first strand: chain 'B' and resid 718 through 719 removed outlier: 7.487A pdb=" N ILE B 736 " --> pdb=" O GLY B 887 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 889 " --> pdb=" O ILE B 736 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET B 738 " --> pdb=" O LEU B 889 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA B 723 " --> pdb=" O LEU B 908 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 983 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER B 980 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL B 969 " --> pdb=" O SER B 980 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 807 through 809 removed outlier: 6.876A pdb=" N ILE B 835 " --> pdb=" O LEU B 808 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 812 through 813 Processing sheet with id=AD1, first strand: chain 'B' and resid 1054 through 1060 Processing sheet with id=AD2, first strand: chain 'B' and resid 1068 through 1070 removed outlier: 3.611A pdb=" N ASP B1070 " --> pdb=" O ARG B1075 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG B1075 " --> pdb=" O ASP B1070 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 238 through 242 Processing sheet with id=AD4, first strand: chain 'C' and resid 151 through 157 removed outlier: 3.767A pdb=" N SER C 153 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER C 203 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N THR C 205 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP C 198 " --> pdb=" O THR C 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 57 through 59 removed outlier: 4.833A pdb=" N LEU C 386 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU C 385 " --> pdb=" O ARG K 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 3 through 8 removed outlier: 6.891A pdb=" N ARG D 14 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG D 8 " --> pdb=" O ARG D 12 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG D 12 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ILE D 219 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N VAL D 172 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N SER D 221 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N VAL D 170 " --> pdb=" O SER D 221 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLU D 223 " --> pdb=" O PRO D 168 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LYS D 225 " --> pdb=" O TYR D 166 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N TYR D 166 " --> pdb=" O LYS D 225 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE D 227 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL D 164 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU D 229 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER D 162 " --> pdb=" O GLU D 229 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLU D 231 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 115 through 116 removed outlier: 6.876A pdb=" N LYS D 138 " --> pdb=" O ASN D 49 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN D 49 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER D 140 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 43 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG D 146 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL D 41 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY D 148 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N MET D 39 " --> pdb=" O GLY D 148 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 107 through 110 removed outlier: 6.341A pdb=" N LEU D 107 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU D 132 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 109 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 188 through 189 Processing sheet with id=AE1, first strand: chain 'E' and resid 8 through 13 removed outlier: 3.522A pdb=" N GLU E 71 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS E 52 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.048A pdb=" N ILE H 45 " --> pdb=" O ILE H 82 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 2 through 8 removed outlier: 6.770A pdb=" N GLU L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU L 8 " --> pdb=" O TYR L 12 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR L 12 " --> pdb=" O GLU L 8 " (cutoff:3.500A) 1093 hydrogen bonds defined for protein. 3027 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: 5.70 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.83: 26064 1.83 - 2.43: 8 2.43 - 3.03: 0 3.03 - 3.64: 0 3.64 - 4.24: 3 Bond restraints: 26075 Sorted by residual: bond pdb=" S4 F3S D 301 " pdb="FE1 F3S D 301 " ideal model delta sigma weight residual 2.233 4.243 -2.010 2.00e-02 2.50e+03 1.01e+04 bond pdb=" S1 F3S D 301 " pdb="FE4 F3S D 301 " ideal model delta sigma weight residual 2.258 4.230 -1.972 2.00e-02 2.50e+03 9.72e+03 bond pdb=" S2 F3S D 301 " pdb="FE3 F3S D 301 " ideal model delta sigma weight residual 2.300 4.187 -1.887 2.00e-02 2.50e+03 8.90e+03 bond pdb=" S2 F3S D 301 " pdb="FE4 F3S D 301 " ideal model delta sigma weight residual 2.317 2.202 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" S3 F3S D 301 " pdb="FE1 F3S D 301 " ideal model delta sigma weight residual 2.296 2.192 0.104 2.00e-02 2.50e+03 2.68e+01 ... (remaining 26070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.04: 35192 15.04 - 30.09: 11 30.09 - 45.13: 2 45.13 - 60.17: 0 60.17 - 75.21: 2 Bond angle restraints: 35207 Sorted by residual: angle pdb=" S1 F3S D 301 " pdb="FE4 F3S D 301 " pdb=" S3 F3S D 301 " ideal model delta sigma weight residual 114.75 39.54 75.21 3.00e+00 1.11e-01 6.29e+02 angle pdb=" S3 F3S D 301 " pdb="FE1 F3S D 301 " pdb=" S4 F3S D 301 " ideal model delta sigma weight residual 112.59 39.39 73.20 3.00e+00 1.11e-01 5.95e+02 angle pdb=" S1 F3S D 301 " pdb="FE3 F3S D 301 " pdb=" S4 F3S D 301 " ideal model delta sigma weight residual 112.54 150.11 -37.57 3.00e+00 1.11e-01 1.57e+02 angle pdb="FE1 F3S D 301 " pdb=" S4 F3S D 301 " pdb="FE3 F3S D 301 " ideal model delta sigma weight residual 74.86 43.55 31.31 3.00e+00 1.11e-01 1.09e+02 angle pdb="FE3 F3S D 301 " pdb=" S1 F3S D 301 " pdb="FE4 F3S D 301 " ideal model delta sigma weight residual 73.06 43.65 29.41 3.00e+00 1.11e-01 9.61e+01 ... (remaining 35202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 14532 16.88 - 33.76: 1255 33.76 - 50.64: 223 50.64 - 67.52: 34 67.52 - 84.40: 17 Dihedral angle restraints: 16061 sinusoidal: 6697 harmonic: 9364 Sorted by residual: dihedral pdb=" CB CYS G 9 " pdb=" SG CYS G 9 " pdb=" SG CYS G 29 " pdb=" CB CYS G 29 " ideal model delta sinusoidal sigma weight residual 93.00 36.02 56.98 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CB CYS G 69 " pdb=" SG CYS G 69 " pdb=" SG CYS G 119 " pdb=" CB CYS G 119 " ideal model delta sinusoidal sigma weight residual 93.00 48.23 44.77 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CA SER B1072 " pdb=" C SER B1072 " pdb=" N LYS B1073 " pdb=" CA LYS B1073 " ideal model delta harmonic sigma weight residual 180.00 161.05 18.95 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 16058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.704: 3997 2.704 - 5.408: 0 5.408 - 8.111: 0 8.111 - 10.815: 0 10.815 - 13.519: 1 Chirality restraints: 3998 Sorted by residual: chirality pdb=" S2 F3S D 301 " pdb="FE1 F3S D 301 " pdb="FE3 F3S D 301 " pdb="FE4 F3S D 301 " both_signs ideal model delta sigma weight residual False 10.77 -2.75 13.52 2.00e-01 2.50e+01 4.57e+03 chirality pdb=" CA CYS G 69 " pdb=" N CYS G 69 " pdb=" C CYS G 69 " pdb=" CB CYS G 69 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE C 214 " pdb=" CA ILE C 214 " pdb=" CG1 ILE C 214 " pdb=" CG2 ILE C 214 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 3995 not shown) Planarity restraints: 4519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS P 39 " -0.036 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO P 40 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO P 40 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO P 40 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 38 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A 39 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1069 " -0.013 2.00e-02 2.50e+03 1.21e-02 2.92e+00 pdb=" CG TYR B1069 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B1069 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B1069 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B1069 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B1069 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B1069 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B1069 " 0.004 2.00e-02 2.50e+03 ... (remaining 4516 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 224 2.61 - 3.18: 21544 3.18 - 3.76: 37124 3.76 - 4.33: 54243 4.33 - 4.90: 92267 Nonbonded interactions: 205402 Sorted by model distance: nonbonded pdb=" OD1 ASP A 456 " pdb="MG MG A 901 " model vdw 2.038 2.170 nonbonded pdb=" OD2 ASP A 460 " pdb="MG MG A 901 " model vdw 2.056 2.170 nonbonded pdb=" OD1 ASP A 460 " pdb="MG MG A 901 " model vdw 2.063 2.170 nonbonded pdb=" OG1 THR D 171 " pdb=" OG SER D 218 " model vdw 2.067 3.040 nonbonded pdb=" OD2 ASP A 458 " pdb="MG MG A 901 " model vdw 2.076 2.170 ... (remaining 205397 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.310 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.021 2.010 26103 Z= 1.060 Angle : 1.027 75.214 35241 Z= 0.381 Chirality : 0.218 13.519 3998 Planarity : 0.004 0.056 4519 Dihedral : 12.908 84.403 10037 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.12 (0.15), residues: 3202 helix: 1.05 (0.16), residues: 1140 sheet: 0.30 (0.24), residues: 481 loop : -0.68 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 320 TYR 0.029 0.001 TYR B1069 PHE 0.024 0.001 PHE A 419 TRP 0.010 0.001 TRP B 8 HIS 0.007 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.02126 (26075) covalent geometry : angle 0.92900 (35207) SS BOND : bond 0.01312 ( 2) SS BOND : angle 4.73362 ( 4) hydrogen bonds : bond 0.16548 ( 1076) hydrogen bonds : angle 5.90070 ( 3027) metal coordination : bond 0.00869 ( 26) metal coordination : angle 14.94078 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.056 Fit side-chains REVERT: A 1 MET cc_start: 0.6106 (tmm) cc_final: 0.5661 (tmm) REVERT: A 159 GLU cc_start: 0.7795 (tp30) cc_final: 0.7586 (tp30) REVERT: B 390 GLU cc_start: 0.7894 (tp30) cc_final: 0.7683 (tp30) REVERT: C 133 ASP cc_start: 0.7233 (p0) cc_final: 0.7032 (t0) REVERT: C 252 ASP cc_start: 0.7462 (t0) cc_final: 0.7160 (t0) REVERT: C 301 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7491 (tm-30) REVERT: D 118 ASP cc_start: 0.8328 (t70) cc_final: 0.7965 (t0) REVERT: E 69 GLU cc_start: 0.7256 (tt0) cc_final: 0.7004 (tt0) REVERT: H 21 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7518 (mt-10) REVERT: L 1 MET cc_start: 0.7444 (ttt) cc_final: 0.7128 (ttt) REVERT: P 16 ASP cc_start: 0.8270 (p0) cc_final: 0.7920 (p0) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.7949 time to fit residues: 332.5146 Evaluate side-chains 281 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 272 HIS A 420 ASN A 739 ASN ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1001 HIS B1009 GLN C 199 ASN C 326 GLN D 60 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.082532 restraints weight = 35691.319| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.45 r_work: 0.2858 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.195 26103 Z= 0.160 Angle : 1.117 84.432 35241 Z= 0.372 Chirality : 0.063 2.775 3998 Planarity : 0.004 0.049 4519 Dihedral : 4.005 20.754 3559 Min Nonbonded Distance : 1.500 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.31 % Allowed : 8.24 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.22 (0.15), residues: 3202 helix: 1.17 (0.16), residues: 1164 sheet: 0.27 (0.23), residues: 502 loop : -0.65 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 25 TYR 0.019 0.001 TYR A 162 PHE 0.020 0.001 PHE A 419 TRP 0.008 0.001 TRP B 8 HIS 0.007 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00350 (26075) covalent geometry : angle 0.88438 (35207) SS BOND : bond 0.01214 ( 2) SS BOND : angle 3.76506 ( 4) hydrogen bonds : bond 0.04372 ( 1076) hydrogen bonds : angle 4.58041 ( 3027) metal coordination : bond 0.00853 ( 26) metal coordination : angle 23.34471 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 308 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7799 (pp20) REVERT: A 134 GLU cc_start: 0.8126 (tp30) cc_final: 0.7686 (pt0) REVERT: A 230 ARG cc_start: 0.7325 (mtm-85) cc_final: 0.6665 (ptp-110) REVERT: A 822 ARG cc_start: 0.7904 (mtp85) cc_final: 0.7547 (mtm110) REVERT: B 390 GLU cc_start: 0.7844 (tp30) cc_final: 0.7452 (tm-30) REVERT: B 768 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6276 (pm20) REVERT: C 133 ASP cc_start: 0.7540 (p0) cc_final: 0.7147 (t0) REVERT: C 252 ASP cc_start: 0.7794 (t0) cc_final: 0.7470 (t0) REVERT: C 280 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7930 (mm-30) REVERT: C 301 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7897 (tm-30) REVERT: D 7 GLU cc_start: 0.8980 (tt0) cc_final: 0.8457 (pt0) REVERT: D 118 ASP cc_start: 0.8592 (t70) cc_final: 0.7975 (t0) REVERT: G 106 ASN cc_start: 0.8759 (t0) cc_final: 0.8306 (t0) REVERT: H 21 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8138 (mt-10) REVERT: P 16 ASP cc_start: 0.8350 (p0) cc_final: 0.8013 (p0) REVERT: Q 48 LYS cc_start: 0.8289 (mttt) cc_final: 0.8080 (mttp) REVERT: Q 58 ARG cc_start: 0.8585 (mtp180) cc_final: 0.8259 (mtp180) outliers start: 37 outliers final: 17 residues processed: 327 average time/residue: 0.7690 time to fit residues: 285.1813 Evaluate side-chains 299 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 280 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain P residue 46 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 210 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 272 HIS B 793 ASN B 921 GLN C 226 ASN ** C 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.077347 restraints weight = 36328.481| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.43 r_work: 0.2761 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 26103 Z= 0.304 Angle : 1.069 82.617 35241 Z= 0.377 Chirality : 0.055 1.453 3998 Planarity : 0.005 0.053 4519 Dihedral : 4.436 22.999 3559 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.40 % Favored : 95.57 % Rotamer: Outliers : 1.88 % Allowed : 10.91 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: -0.08 (0.15), residues: 3202 helix: 0.98 (0.16), residues: 1164 sheet: 0.16 (0.23), residues: 488 loop : -0.90 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 75 TYR 0.025 0.002 TYR G 118 PHE 0.020 0.002 PHE A 419 TRP 0.011 0.002 TRP B 8 HIS 0.010 0.001 HIS B 993 Details of bonding type rmsd covalent geometry : bond 0.00760 (26075) covalent geometry : angle 0.81587 (35207) SS BOND : bond 0.01180 ( 2) SS BOND : angle 4.52423 ( 4) hydrogen bonds : bond 0.05673 ( 1076) hydrogen bonds : angle 4.60451 ( 3027) metal coordination : bond 0.01332 ( 26) metal coordination : angle 23.64885 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 288 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7771 (pp20) REVERT: A 134 GLU cc_start: 0.8203 (tp30) cc_final: 0.7704 (pt0) REVERT: A 822 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7811 (mtm110) REVERT: B 59 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7585 (mtpp) REVERT: B 342 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7874 (mmp80) REVERT: B 390 GLU cc_start: 0.7832 (tp30) cc_final: 0.7357 (tm-30) REVERT: B 768 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6136 (pm20) REVERT: C 44 GLU cc_start: 0.7828 (mp0) cc_final: 0.7318 (tm-30) REVERT: C 133 ASP cc_start: 0.7633 (p0) cc_final: 0.7275 (t0) REVERT: C 215 MET cc_start: 0.7526 (tpp) cc_final: 0.7298 (tpt) REVERT: C 252 ASP cc_start: 0.7914 (t0) cc_final: 0.7566 (t0) REVERT: C 280 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7934 (mm-30) REVERT: C 329 ARG cc_start: 0.6504 (tpt170) cc_final: 0.6098 (tpt170) REVERT: C 360 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: D 118 ASP cc_start: 0.8725 (t70) cc_final: 0.8140 (t0) REVERT: E 71 GLU cc_start: 0.7885 (mt-10) cc_final: 0.6765 (mp0) REVERT: G 106 ASN cc_start: 0.8744 (t0) cc_final: 0.8217 (t0) REVERT: K 12 GLU cc_start: 0.8640 (tp30) cc_final: 0.8334 (tt0) REVERT: K 46 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.7773 (t0) REVERT: L 39 LYS cc_start: 0.9199 (mtpt) cc_final: 0.8985 (mmmm) REVERT: P 16 ASP cc_start: 0.8326 (p0) cc_final: 0.8005 (p0) REVERT: Q 65 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8030 (pm20) outliers start: 53 outliers final: 25 residues processed: 315 average time/residue: 0.7745 time to fit residues: 275.5695 Evaluate side-chains 302 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain D residue 206 CYS Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 46 ASN Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 65 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 45 optimal weight: 0.2980 chunk 290 optimal weight: 2.9990 chunk 303 optimal weight: 0.9980 chunk 138 optimal weight: 0.3980 chunk 69 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 311 optimal weight: 0.1980 chunk 200 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.121414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.081091 restraints weight = 35862.926| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.46 r_work: 0.2836 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 26103 Z= 0.120 Angle : 0.959 81.388 35241 Z= 0.322 Chirality : 0.050 1.571 3998 Planarity : 0.004 0.054 4519 Dihedral : 4.093 20.754 3559 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.56 % Allowed : 12.40 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.16 (0.15), residues: 3202 helix: 1.22 (0.16), residues: 1162 sheet: 0.25 (0.23), residues: 500 loop : -0.78 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 75 TYR 0.020 0.001 TYR G 118 PHE 0.012 0.001 PHE A 419 TRP 0.010 0.001 TRP B 8 HIS 0.006 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00263 (26075) covalent geometry : angle 0.71740 (35207) SS BOND : bond 0.01208 ( 2) SS BOND : angle 3.62818 ( 4) hydrogen bonds : bond 0.03980 ( 1076) hydrogen bonds : angle 4.34024 ( 3027) metal coordination : bond 0.00677 ( 26) metal coordination : angle 21.80203 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 287 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7756 (pp20) REVERT: A 134 GLU cc_start: 0.8264 (tp30) cc_final: 0.7698 (pt0) REVERT: A 501 ASP cc_start: 0.8663 (m-30) cc_final: 0.8241 (m-30) REVERT: B 390 GLU cc_start: 0.7797 (tp30) cc_final: 0.7332 (tm-30) REVERT: B 768 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5979 (pm20) REVERT: C 133 ASP cc_start: 0.7657 (p0) cc_final: 0.7278 (t0) REVERT: C 215 MET cc_start: 0.7449 (tpp) cc_final: 0.7160 (tpt) REVERT: C 252 ASP cc_start: 0.7795 (t0) cc_final: 0.7497 (t0) REVERT: C 280 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7909 (mm-30) REVERT: C 329 ARG cc_start: 0.6840 (tpt170) cc_final: 0.6375 (tpt170) REVERT: D 7 GLU cc_start: 0.9031 (tt0) cc_final: 0.8484 (pt0) REVERT: D 118 ASP cc_start: 0.8675 (t70) cc_final: 0.8072 (t0) REVERT: E 71 GLU cc_start: 0.7839 (mt-10) cc_final: 0.6734 (mp0) REVERT: G 6 GLN cc_start: 0.7859 (tt0) cc_final: 0.7640 (tt0) REVERT: H 21 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8135 (mt-10) REVERT: L 39 LYS cc_start: 0.9184 (mtpt) cc_final: 0.8968 (mmmm) REVERT: P 16 ASP cc_start: 0.8232 (p0) cc_final: 0.7904 (p0) REVERT: Q 48 LYS cc_start: 0.8180 (mmtp) cc_final: 0.7901 (mttp) outliers start: 44 outliers final: 15 residues processed: 312 average time/residue: 0.7309 time to fit residues: 259.6161 Evaluate side-chains 296 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 279 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain P residue 46 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 101 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS B1009 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.117554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.076886 restraints weight = 36223.961| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.45 r_work: 0.2767 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 26103 Z= 0.273 Angle : 1.020 81.031 35241 Z= 0.365 Chirality : 0.055 1.605 3998 Planarity : 0.005 0.056 4519 Dihedral : 4.400 22.841 3559 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 1.99 % Allowed : 13.43 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: -0.05 (0.15), residues: 3202 helix: 1.02 (0.16), residues: 1164 sheet: 0.23 (0.23), residues: 483 loop : -0.92 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 75 TYR 0.018 0.002 TYR B 336 PHE 0.037 0.002 PHE B 438 TRP 0.010 0.001 TRP B 8 HIS 0.009 0.001 HIS B 993 Details of bonding type rmsd covalent geometry : bond 0.00682 (26075) covalent geometry : angle 0.79346 (35207) SS BOND : bond 0.01186 ( 2) SS BOND : angle 4.30931 ( 4) hydrogen bonds : bond 0.05293 ( 1076) hydrogen bonds : angle 4.45852 ( 3027) metal coordination : bond 0.01211 ( 26) metal coordination : angle 21.93583 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 292 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8272 (tp30) cc_final: 0.7706 (pt0) REVERT: A 788 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8512 (ttp80) REVERT: A 822 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7764 (mtm110) REVERT: B 59 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7944 (mtpp) REVERT: B 234 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7330 (ttp-110) REVERT: B 390 GLU cc_start: 0.7768 (tp30) cc_final: 0.7279 (tm-30) REVERT: B 768 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6011 (pm20) REVERT: C 44 GLU cc_start: 0.7766 (mp0) cc_final: 0.7079 (tp30) REVERT: C 133 ASP cc_start: 0.7572 (p0) cc_final: 0.7162 (t0) REVERT: C 215 MET cc_start: 0.7627 (tpp) cc_final: 0.7395 (tpt) REVERT: C 252 ASP cc_start: 0.7886 (t0) cc_final: 0.7561 (t0) REVERT: C 329 ARG cc_start: 0.6755 (tpt170) cc_final: 0.6194 (tpt170) REVERT: D 118 ASP cc_start: 0.8721 (t70) cc_final: 0.8072 (t0) REVERT: E 71 GLU cc_start: 0.7884 (mt-10) cc_final: 0.6769 (mp0) REVERT: G 42 GLU cc_start: 0.8241 (mp0) cc_final: 0.7969 (mp0) REVERT: G 106 ASN cc_start: 0.8773 (t0) cc_final: 0.8319 (t0) REVERT: H 15 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8003 (pp20) REVERT: K 12 GLU cc_start: 0.8635 (tp30) cc_final: 0.8311 (tt0) REVERT: P 16 ASP cc_start: 0.8243 (p0) cc_final: 0.7930 (p0) REVERT: Q 48 LYS cc_start: 0.8191 (mmtp) cc_final: 0.7988 (mttp) outliers start: 56 outliers final: 25 residues processed: 322 average time/residue: 0.7648 time to fit residues: 278.7871 Evaluate side-chains 296 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 266 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 788 ARG Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain D residue 206 CYS Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain P residue 46 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 120 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 chunk 251 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 98 optimal weight: 0.0770 chunk 317 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 272 optimal weight: 5.9990 chunk 183 optimal weight: 0.0870 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN P 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.080830 restraints weight = 36117.620| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.46 r_work: 0.2830 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 26103 Z= 0.121 Angle : 0.945 81.629 35241 Z= 0.323 Chirality : 0.051 1.571 3998 Planarity : 0.004 0.058 4519 Dihedral : 4.093 20.620 3559 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.46 % Allowed : 14.46 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.17 (0.15), residues: 3202 helix: 1.23 (0.16), residues: 1162 sheet: 0.33 (0.23), residues: 489 loop : -0.81 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 75 TYR 0.017 0.001 TYR A 818 PHE 0.011 0.001 PHE A 419 TRP 0.011 0.001 TRP B 8 HIS 0.005 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00269 (26075) covalent geometry : angle 0.72137 (35207) SS BOND : bond 0.01188 ( 2) SS BOND : angle 3.55163 ( 4) hydrogen bonds : bond 0.03889 ( 1076) hydrogen bonds : angle 4.27288 ( 3027) metal coordination : bond 0.00728 ( 26) metal coordination : angle 20.88286 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 287 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8288 (tp30) cc_final: 0.7703 (pt0) REVERT: A 536 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8622 (mt-10) REVERT: A 788 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8503 (ttp80) REVERT: B 59 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7945 (mtpp) REVERT: B 342 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7783 (mmp80) REVERT: B 390 GLU cc_start: 0.7816 (tp30) cc_final: 0.7364 (tm-30) REVERT: C 133 ASP cc_start: 0.7610 (p0) cc_final: 0.7199 (t0) REVERT: C 252 ASP cc_start: 0.7834 (t0) cc_final: 0.7547 (t0) REVERT: C 280 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7914 (mm-30) REVERT: C 329 ARG cc_start: 0.6799 (tpt170) cc_final: 0.6299 (tpt170) REVERT: D 118 ASP cc_start: 0.8703 (t70) cc_final: 0.8076 (t0) REVERT: E 71 GLU cc_start: 0.7872 (mt-10) cc_final: 0.6801 (mp0) REVERT: G 106 ASN cc_start: 0.8720 (t0) cc_final: 0.8224 (t0) REVERT: H 15 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7928 (pp20) REVERT: P 16 ASP cc_start: 0.8189 (p0) cc_final: 0.7881 (p0) REVERT: Q 58 ARG cc_start: 0.8405 (mtp180) cc_final: 0.8137 (mtp180) REVERT: Q 65 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7846 (pm20) outliers start: 41 outliers final: 18 residues processed: 310 average time/residue: 0.7603 time to fit residues: 267.4542 Evaluate side-chains 290 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 267 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 788 ARG Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain D residue 206 CYS Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 65 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 244 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 277 optimal weight: 5.9990 chunk 211 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 229 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 chunk 187 optimal weight: 0.0370 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1001 HIS B1009 GLN P 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.121344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.081132 restraints weight = 35945.535| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.46 r_work: 0.2835 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 26103 Z= 0.126 Angle : 0.931 82.019 35241 Z= 0.325 Chirality : 0.050 1.564 3998 Planarity : 0.004 0.056 4519 Dihedral : 3.976 19.654 3559 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.10 % Rotamer: Outliers : 1.74 % Allowed : 14.88 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.24 (0.15), residues: 3202 helix: 1.28 (0.16), residues: 1162 sheet: 0.38 (0.23), residues: 489 loop : -0.76 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Q 75 TYR 0.021 0.001 TYR G 118 PHE 0.035 0.001 PHE B 438 TRP 0.010 0.001 TRP B1068 HIS 0.005 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00287 (26075) covalent geometry : angle 0.72612 (35207) SS BOND : bond 0.01187 ( 2) SS BOND : angle 3.53845 ( 4) hydrogen bonds : bond 0.03804 ( 1076) hydrogen bonds : angle 4.19645 ( 3027) metal coordination : bond 0.00647 ( 26) metal coordination : angle 19.92844 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 291 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5975 (tmm) cc_final: 0.4935 (tmm) REVERT: A 134 GLU cc_start: 0.8289 (tp30) cc_final: 0.7720 (pt0) REVERT: A 536 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8661 (mt-10) REVERT: A 788 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8491 (ttp80) REVERT: B 59 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7928 (mtpp) REVERT: B 234 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7502 (ttp80) REVERT: B 342 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7814 (mmp80) REVERT: B 390 GLU cc_start: 0.7786 (tp30) cc_final: 0.7349 (tm-30) REVERT: C 133 ASP cc_start: 0.7617 (p0) cc_final: 0.7214 (t0) REVERT: C 252 ASP cc_start: 0.7822 (t0) cc_final: 0.7530 (t0) REVERT: C 329 ARG cc_start: 0.6844 (tpt170) cc_final: 0.6346 (tpt170) REVERT: D 118 ASP cc_start: 0.8689 (t70) cc_final: 0.8060 (t0) REVERT: E 29 ILE cc_start: 0.8716 (mm) cc_final: 0.8443 (mp) REVERT: E 71 GLU cc_start: 0.7868 (mt-10) cc_final: 0.6829 (mp0) REVERT: G 21 ASN cc_start: 0.8690 (p0) cc_final: 0.8406 (p0) REVERT: G 106 ASN cc_start: 0.8710 (t0) cc_final: 0.8163 (t0) REVERT: H 15 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7934 (pp20) REVERT: H 21 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8154 (mt-10) REVERT: K 8 GLU cc_start: 0.8589 (mm-30) cc_final: 0.7996 (mm-30) REVERT: K 12 GLU cc_start: 0.8665 (tp30) cc_final: 0.8196 (tp30) REVERT: K 58 GLU cc_start: 0.8939 (tp30) cc_final: 0.8735 (tp30) REVERT: P 16 ASP cc_start: 0.8172 (p0) cc_final: 0.7863 (p0) REVERT: Q 48 LYS cc_start: 0.8183 (mttp) cc_final: 0.7939 (mttp) REVERT: Q 58 ARG cc_start: 0.8401 (mtp180) cc_final: 0.8173 (mtp180) REVERT: Q 65 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7887 (pm20) outliers start: 49 outliers final: 20 residues processed: 321 average time/residue: 0.7507 time to fit residues: 273.9921 Evaluate side-chains 303 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 788 ARG Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 65 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 35 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 191 optimal weight: 0.3980 chunk 269 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 274 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS B1009 GLN B1074 ASN P 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.078817 restraints weight = 36176.601| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.45 r_work: 0.2794 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 26103 Z= 0.190 Angle : 0.952 82.297 35241 Z= 0.348 Chirality : 0.052 1.565 3998 Planarity : 0.004 0.066 4519 Dihedral : 4.156 21.006 3559 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 2.02 % Allowed : 15.24 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.13 (0.15), residues: 3202 helix: 1.17 (0.16), residues: 1167 sheet: 0.34 (0.23), residues: 501 loop : -0.84 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG P 25 TYR 0.017 0.001 TYR A 818 PHE 0.013 0.001 PHE B 212 TRP 0.010 0.001 TRP B1068 HIS 0.006 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00466 (26075) covalent geometry : angle 0.76675 (35207) SS BOND : bond 0.01169 ( 2) SS BOND : angle 3.89438 ( 4) hydrogen bonds : bond 0.04497 ( 1076) hydrogen bonds : angle 4.29634 ( 3027) metal coordination : bond 0.00909 ( 26) metal coordination : angle 19.31646 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 281 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5956 (tmm) cc_final: 0.4906 (tmm) REVERT: A 53 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7689 (pp20) REVERT: A 134 GLU cc_start: 0.8303 (tp30) cc_final: 0.7732 (pt0) REVERT: A 536 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8635 (mt-10) REVERT: A 788 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8514 (ttp80) REVERT: B 59 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7938 (mtpp) REVERT: B 234 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7535 (ttp80) REVERT: B 342 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7802 (mmp80) REVERT: B 390 GLU cc_start: 0.7741 (tp30) cc_final: 0.7310 (tm-30) REVERT: C 44 GLU cc_start: 0.7663 (mp0) cc_final: 0.7099 (tm-30) REVERT: C 133 ASP cc_start: 0.7603 (p0) cc_final: 0.7168 (t0) REVERT: C 252 ASP cc_start: 0.7903 (t0) cc_final: 0.7618 (t0) REVERT: C 329 ARG cc_start: 0.6818 (tpt170) cc_final: 0.6467 (tpt170) REVERT: D 118 ASP cc_start: 0.8720 (t70) cc_final: 0.8060 (t0) REVERT: E 71 GLU cc_start: 0.7840 (mt-10) cc_final: 0.6794 (mp0) REVERT: G 21 ASN cc_start: 0.8690 (p0) cc_final: 0.8382 (p0) REVERT: G 106 ASN cc_start: 0.8693 (t0) cc_final: 0.8134 (t0) REVERT: H 15 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7982 (pp20) REVERT: K 8 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8073 (mm-30) REVERT: L 2 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7978 (mm-30) REVERT: P 16 ASP cc_start: 0.8162 (p0) cc_final: 0.7862 (p0) REVERT: P 17 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7857 (mm-40) REVERT: Q 58 ARG cc_start: 0.8446 (mtp180) cc_final: 0.8215 (mtp180) REVERT: Q 65 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7958 (pm20) outliers start: 57 outliers final: 26 residues processed: 317 average time/residue: 0.7567 time to fit residues: 272.5642 Evaluate side-chains 306 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 272 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 788 ARG Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 206 CYS Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 65 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 117 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 266 optimal weight: 5.9990 chunk 186 optimal weight: 0.2980 chunk 258 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 256 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS A 272 HIS ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN P 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.121492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.081286 restraints weight = 36196.345| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.47 r_work: 0.2836 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 26103 Z= 0.122 Angle : 0.915 82.741 35241 Z= 0.331 Chirality : 0.050 1.527 3998 Planarity : 0.004 0.075 4519 Dihedral : 3.993 20.082 3559 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.46 % Allowed : 15.81 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.26 (0.15), residues: 3202 helix: 1.26 (0.16), residues: 1163 sheet: 0.46 (0.23), residues: 498 loop : -0.74 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG P 25 TYR 0.023 0.001 TYR G 118 PHE 0.027 0.001 PHE B 438 TRP 0.011 0.001 TRP B 8 HIS 0.006 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00273 (26075) covalent geometry : angle 0.73760 (35207) SS BOND : bond 0.01185 ( 2) SS BOND : angle 3.45988 ( 4) hydrogen bonds : bond 0.03765 ( 1076) hydrogen bonds : angle 4.21504 ( 3027) metal coordination : bond 0.00648 ( 26) metal coordination : angle 18.55224 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 282 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5865 (tmm) cc_final: 0.4859 (tmm) REVERT: A 53 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7622 (pp20) REVERT: A 134 GLU cc_start: 0.8311 (tp30) cc_final: 0.7732 (pt0) REVERT: A 536 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8647 (mt-10) REVERT: A 788 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8439 (ttp80) REVERT: B 59 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7950 (mtpp) REVERT: B 234 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7486 (ttp80) REVERT: B 342 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7784 (mmp80) REVERT: B 390 GLU cc_start: 0.7802 (tp30) cc_final: 0.7361 (tm-30) REVERT: C 119 MET cc_start: 0.8179 (mtm) cc_final: 0.7787 (mtp) REVERT: C 133 ASP cc_start: 0.7660 (p0) cc_final: 0.7239 (t0) REVERT: C 252 ASP cc_start: 0.7826 (t0) cc_final: 0.7579 (t0) REVERT: C 329 ARG cc_start: 0.6864 (tpt170) cc_final: 0.6491 (tpt170) REVERT: D 118 ASP cc_start: 0.8673 (t70) cc_final: 0.8033 (t0) REVERT: E 71 GLU cc_start: 0.7826 (mt-10) cc_final: 0.6794 (mp0) REVERT: G 21 ASN cc_start: 0.8647 (p0) cc_final: 0.8360 (p0) REVERT: H 15 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7923 (pp20) REVERT: H 21 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8125 (mt-10) REVERT: K 8 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8034 (mm-30) REVERT: K 12 GLU cc_start: 0.8663 (tp30) cc_final: 0.8192 (tp30) REVERT: L 2 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7858 (mm-30) REVERT: P 16 ASP cc_start: 0.8016 (p0) cc_final: 0.7713 (p0) REVERT: P 17 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7758 (mm-40) REVERT: Q 48 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7928 (mttp) REVERT: Q 58 ARG cc_start: 0.8439 (mtp180) cc_final: 0.8223 (mtp180) REVERT: Q 65 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.8006 (pm20) outliers start: 41 outliers final: 22 residues processed: 309 average time/residue: 0.7408 time to fit residues: 260.5504 Evaluate side-chains 311 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 788 ARG Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 48 LYS Chi-restraints excluded: chain Q residue 65 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 219 optimal weight: 0.0970 chunk 179 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 255 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 233 optimal weight: 6.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1001 HIS B1009 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.121430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.081266 restraints weight = 36066.439| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.46 r_work: 0.2835 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 26103 Z= 0.131 Angle : 0.912 82.985 35241 Z= 0.334 Chirality : 0.050 1.512 3998 Planarity : 0.004 0.072 4519 Dihedral : 3.962 19.759 3559 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 1.31 % Allowed : 16.20 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.30 (0.15), residues: 3202 helix: 1.27 (0.16), residues: 1162 sheet: 0.48 (0.23), residues: 498 loop : -0.71 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG P 25 TYR 0.017 0.001 TYR A 818 PHE 0.019 0.001 PHE A 419 TRP 0.010 0.001 TRP B 8 HIS 0.006 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00301 (26075) covalent geometry : angle 0.74491 (35207) SS BOND : bond 0.01160 ( 2) SS BOND : angle 3.42503 ( 4) hydrogen bonds : bond 0.03790 ( 1076) hydrogen bonds : angle 4.19940 ( 3027) metal coordination : bond 0.00675 ( 26) metal coordination : angle 18.02892 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 282 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5877 (tmm) cc_final: 0.4668 (tmm) REVERT: A 53 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7603 (pp20) REVERT: A 134 GLU cc_start: 0.8310 (tp30) cc_final: 0.7730 (pt0) REVERT: A 536 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8662 (mt-10) REVERT: A 788 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8440 (ttp80) REVERT: B 59 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7939 (mtpp) REVERT: B 234 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7487 (ttp80) REVERT: B 342 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7788 (mmp80) REVERT: B 390 GLU cc_start: 0.7800 (tp30) cc_final: 0.7360 (tm-30) REVERT: B 803 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7738 (ptpp) REVERT: C 119 MET cc_start: 0.8269 (mtm) cc_final: 0.7842 (mtp) REVERT: C 133 ASP cc_start: 0.7582 (p0) cc_final: 0.7137 (t0) REVERT: C 252 ASP cc_start: 0.7832 (t0) cc_final: 0.7583 (t0) REVERT: C 329 ARG cc_start: 0.6857 (tpt170) cc_final: 0.6483 (tpt170) REVERT: D 118 ASP cc_start: 0.8684 (t70) cc_final: 0.8052 (t0) REVERT: E 71 GLU cc_start: 0.7805 (mt-10) cc_final: 0.6778 (mp0) REVERT: G 21 ASN cc_start: 0.8638 (p0) cc_final: 0.8352 (p0) REVERT: G 106 ASN cc_start: 0.8721 (t0) cc_final: 0.8316 (t0) REVERT: H 15 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7945 (pp20) REVERT: H 21 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8133 (mt-10) REVERT: K 8 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8048 (mm-30) REVERT: K 12 GLU cc_start: 0.8678 (tp30) cc_final: 0.8205 (tp30) REVERT: L 2 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7858 (mm-30) REVERT: N 37 GLU cc_start: 0.9069 (pt0) cc_final: 0.8843 (pp20) REVERT: P 16 ASP cc_start: 0.8189 (p0) cc_final: 0.7856 (p0) REVERT: P 17 GLN cc_start: 0.8005 (mm110) cc_final: 0.7697 (mm-40) REVERT: Q 58 ARG cc_start: 0.8449 (mtp180) cc_final: 0.8231 (mtp180) REVERT: Q 65 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.8021 (pm20) outliers start: 37 outliers final: 23 residues processed: 305 average time/residue: 0.7505 time to fit residues: 260.5525 Evaluate side-chains 304 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 274 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 788 ARG Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 65 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 158 optimal weight: 0.9980 chunk 247 optimal weight: 2.9990 chunk 117 optimal weight: 0.2980 chunk 143 optimal weight: 4.9990 chunk 317 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 174 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS A 605 ASN ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1001 HIS B1009 GLN K 46 ASN P 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.081398 restraints weight = 35862.136| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.47 r_work: 0.2842 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 26103 Z= 0.130 Angle : 0.904 83.224 35241 Z= 0.334 Chirality : 0.050 1.497 3998 Planarity : 0.004 0.069 4519 Dihedral : 3.942 19.552 3559 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.39 % Allowed : 16.02 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.30 (0.15), residues: 3202 helix: 1.26 (0.16), residues: 1165 sheet: 0.50 (0.23), residues: 493 loop : -0.71 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG P 25 TYR 0.024 0.001 TYR G 118 PHE 0.024 0.001 PHE B 438 TRP 0.010 0.001 TRP B 8 HIS 0.006 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00301 (26075) covalent geometry : angle 0.74639 (35207) SS BOND : bond 0.01165 ( 2) SS BOND : angle 3.45998 ( 4) hydrogen bonds : bond 0.03774 ( 1076) hydrogen bonds : angle 4.18855 ( 3027) metal coordination : bond 0.00679 ( 26) metal coordination : angle 17.47661 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9899.63 seconds wall clock time: 168 minutes 34.66 seconds (10114.66 seconds total)