Starting phenix.real_space_refine on Sat Aug 8 15:38:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vlw_65170/08_2026/9vlw_65170.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vlw_65170/08_2026/9vlw_65170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vlw_65170/08_2026/9vlw_65170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vlw_65170/08_2026/9vlw_65170.map" model { file = "/net/cci-nas-00/data/ceres_data/9vlw_65170/08_2026/9vlw_65170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vlw_65170/08_2026/9vlw_65170.cif" } resolution = 4.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 13 5.49 5 Mg 2 5.21 5 S 151 5.16 5 C 17665 2.51 5 N 4939 2.21 5 O 5432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28206 Number of models: 1 Model: "" Number of chains: 11 Chain: "2" Number of atoms: 5340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5340 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 29, 'TRANS': 667} Chain breaks: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 3, 'ARG:plan': 8, 'GLU:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 112 Chain: "6" Number of atoms: 5260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5260 Classifications: {'peptide': 666} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 21, 'TRANS': 644} Chain breaks: 3 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 5, 'PHE:plan': 1, 'TYR:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "4" Number of atoms: 4919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 4919 Classifications: {'peptide': 663} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 25, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 462 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PHE:plan': 7, 'ARG:plan': 19, 'GLN:plan1': 5, 'GLU:plan': 10, 'ASP:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 225 Chain: "7" Number of atoms: 4260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4260 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 25, 'TRANS': 538} Chain breaks: 3 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 4, 'PHE:plan': 1, 'ARG:plan': 13, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 121 Chain: "3" Number of atoms: 4043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4043 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 19, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 128 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 3, 'PHE:plan': 1, 'HIS:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 112 Chain: "5" Number of atoms: 4231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4231 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 21, 'TRANS': 538} Chain breaks: 6 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 15, 'GLU:plan': 3, 'HIS:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 119 Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1129 SG CYS 2 329 89.300 78.134 73.284 1.00121.91 S ATOM 1152 SG CYS 2 332 91.129 80.953 75.087 1.00121.71 S ATOM 1303 SG CYS 2 352 87.881 79.795 76.501 1.00118.07 S ATOM 1325 SG CYS 2 355 87.835 81.656 73.267 1.00124.78 S ATOM 6476 SG CYS 6 158 106.956 68.656 81.729 1.00126.95 S ATOM 6498 SG CYS 6 161 110.351 68.123 82.205 1.00126.96 S ATOM 6659 SG CYS 6 180 109.165 71.895 82.241 1.00127.84 S ATOM 6698 SG CYS 6 185 109.433 69.893 79.026 1.00133.97 S ATOM 11630 SG CYS 4 306 110.061 85.895 88.362 1.00102.97 S ATOM 11652 SG CYS 4 309 113.234 87.679 89.356 1.00101.32 S ATOM 11786 SG CYS 4 328 110.999 89.192 86.669 1.00119.16 S ATOM 11801 SG CYS 4 331 112.797 85.894 85.915 1.00135.17 S ATOM 16594 SG CYS 7 184 101.987 106.536 71.479 1.00133.12 S ATOM 16797 SG CYS 7 211 105.070 105.867 69.273 1.00143.28 S Time building chain proxies: 4.70, per 1000 atoms: 0.17 Number of scatterers: 28206 At special positions: 0 Unit cell: (126.14, 144.16, 175.96, 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 4 29.99 S 151 16.00 P 13 15.00 Mg 2 11.99 O 5432 8.00 N 4939 7.00 C 17665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21003 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 332 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 329 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 352 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 355 " pdb=" ZN 4 901 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 331 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 309 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 306 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 328 " pdb=" ZN 6 902 " pdb="ZN ZN 6 902 " - pdb=" SG CYS 6 185 " pdb="ZN ZN 6 902 " - pdb=" SG CYS 6 161 " pdb="ZN ZN 6 902 " - pdb=" SG CYS 6 180 " pdb="ZN ZN 6 902 " - pdb=" SG CYS 6 158 " pdb=" ZN 7 802 " pdb="ZN ZN 7 802 " - pdb=" SG CYS 7 211 " pdb="ZN ZN 7 802 " - pdb=" SG CYS 7 184 " Number of angles added : 18 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7014 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 36 sheets defined 44.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain '2' and resid 191 through 206 Processing helix chain '2' and resid 213 through 225 removed outlier: 4.185A pdb=" N MET 2 222 " --> pdb=" O ARG 2 218 " (cutoff:3.500A) Processing helix chain '2' and resid 234 through 239 removed outlier: 3.649A pdb=" N ALA 2 239 " --> pdb=" O GLU 2 235 " (cutoff:3.500A) Processing helix chain '2' and resid 241 through 247 removed outlier: 3.604A pdb=" N PHE 2 247 " --> pdb=" O VAL 2 243 " (cutoff:3.500A) Processing helix chain '2' and resid 251 through 271 removed outlier: 3.534A pdb=" N ILE 2 258 " --> pdb=" O GLU 2 254 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU 2 261 " --> pdb=" O GLN 2 257 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA 2 263 " --> pdb=" O PHE 2 259 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU 2 264 " --> pdb=" O ASP 2 260 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU 2 265 " --> pdb=" O GLU 2 261 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL 2 266 " --> pdb=" O ALA 2 262 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL 2 267 " --> pdb=" O ALA 2 263 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU 2 268 " --> pdb=" O LEU 2 264 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR 2 271 " --> pdb=" O VAL 2 267 " (cutoff:3.500A) Processing helix chain '2' and resid 272 through 276 removed outlier: 4.159A pdb=" N ARG 2 276 " --> pdb=" O LYS 2 273 " (cutoff:3.500A) Processing helix chain '2' and resid 298 through 302 Processing helix chain '2' and resid 399 through 403 removed outlier: 3.622A pdb=" N VAL 2 403 " --> pdb=" O ALA 2 400 " (cutoff:3.500A) Processing helix chain '2' and resid 446 through 451 removed outlier: 3.786A pdb=" N LYS 2 450 " --> pdb=" O LYS 2 447 " (cutoff:3.500A) Processing helix chain '2' and resid 459 through 470 Processing helix chain '2' and resid 472 through 480 Processing helix chain '2' and resid 488 through 501 Processing helix chain '2' and resid 505 through 512 removed outlier: 3.646A pdb=" N GLY 2 509 " --> pdb=" O ASN 2 506 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS 2 510 " --> pdb=" O PRO 2 507 " (cutoff:3.500A) Processing helix chain '2' and resid 528 through 538 removed outlier: 3.502A pdb=" N PHE 2 532 " --> pdb=" O ALA 2 528 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU 2 533 " --> pdb=" O LYS 2 529 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS 2 538 " --> pdb=" O LYS 2 534 " (cutoff:3.500A) Processing helix chain '2' and resid 574 through 579 Processing helix chain '2' and resid 588 through 592 removed outlier: 3.695A pdb=" N MET 2 592 " --> pdb=" O PHE 2 589 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 606 removed outlier: 3.894A pdb=" N THR 2 598 " --> pdb=" O ASP 2 594 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER 2 599 " --> pdb=" O GLN 2 595 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N HIS 2 601 " --> pdb=" O ARG 2 597 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU 2 602 " --> pdb=" O THR 2 598 " (cutoff:3.500A) Processing helix chain '2' and resid 632 through 636 removed outlier: 4.174A pdb=" N ARG 2 636 " --> pdb=" O ILE 2 633 " (cutoff:3.500A) Processing helix chain '2' and resid 642 through 647 removed outlier: 3.504A pdb=" N VAL 2 647 " --> pdb=" O PHE 2 643 " (cutoff:3.500A) Processing helix chain '2' and resid 650 through 657 removed outlier: 3.526A pdb=" N ARG 2 656 " --> pdb=" O PRO 2 652 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE 2 657 " --> pdb=" O ILE 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 668 through 686 Processing helix chain '2' and resid 719 through 728 removed outlier: 3.895A pdb=" N ILE 2 725 " --> pdb=" O LYS 2 721 " (cutoff:3.500A) Processing helix chain '2' and resid 739 through 758 Processing helix chain '2' and resid 763 through 781 removed outlier: 3.565A pdb=" N ARG 2 772 " --> pdb=" O GLU 2 768 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS 2 781 " --> pdb=" O HIS 2 777 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 803 Processing helix chain '2' and resid 807 through 818 removed outlier: 4.287A pdb=" N SER 2 813 " --> pdb=" O SER 2 809 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE 2 818 " --> pdb=" O MET 2 814 " (cutoff:3.500A) Processing helix chain '2' and resid 818 through 823 Processing helix chain '2' and resid 827 through 851 removed outlier: 3.642A pdb=" N GLN 2 838 " --> pdb=" O PHE 2 834 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU 2 839 " --> pdb=" O ILE 2 835 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN 2 849 " --> pdb=" O THR 2 845 " (cutoff:3.500A) Processing helix chain '2' and resid 862 through 867 removed outlier: 3.924A pdb=" N ASP 2 867 " --> pdb=" O LYS 2 863 " (cutoff:3.500A) Processing helix chain '2' and resid 868 through 870 No H-bonds generated for 'chain '2' and resid 868 through 870' Processing helix chain '2' and resid 876 through 883 removed outlier: 3.556A pdb=" N PHE 2 880 " --> pdb=" O ASN 2 876 " (cutoff:3.500A) Processing helix chain '2' and resid 883 through 889 removed outlier: 4.022A pdb=" N ARG 2 887 " --> pdb=" O SER 2 883 " (cutoff:3.500A) Processing helix chain '6' and resid 21 through 36 removed outlier: 3.652A pdb=" N GLU 6 35 " --> pdb=" O LEU 6 31 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 50 removed outlier: 3.695A pdb=" N GLN 6 48 " --> pdb=" O ILE 6 44 " (cutoff:3.500A) Processing helix chain '6' and resid 51 through 55 Processing helix chain '6' and resid 65 through 70 Processing helix chain '6' and resid 72 through 82 removed outlier: 3.551A pdb=" N GLU 6 81 " --> pdb=" O THR 6 77 " (cutoff:3.500A) Processing helix chain '6' and resid 82 through 100 Proline residue: 6 88 - end of helix removed outlier: 3.867A pdb=" N ARG 6 92 " --> pdb=" O PRO 6 88 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA 6 93 " --> pdb=" O TYR 6 89 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL 6 98 " --> pdb=" O LEU 6 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP 6 100 " --> pdb=" O THR 6 96 " (cutoff:3.500A) Processing helix chain '6' and resid 186 through 189 removed outlier: 4.171A pdb=" N ARG 6 189 " --> pdb=" O ALA 6 186 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 186 through 189' Processing helix chain '6' and resid 211 through 215 Processing helix chain '6' and resid 231 through 233 No H-bonds generated for 'chain '6' and resid 231 through 233' Processing helix chain '6' and resid 321 through 329 removed outlier: 3.687A pdb=" N ILE 6 325 " --> pdb=" O THR 6 321 " (cutoff:3.500A) Processing helix chain '6' and resid 330 through 343 removed outlier: 3.550A pdb=" N LYS 6 336 " --> pdb=" O LYS 6 332 " (cutoff:3.500A) Processing helix chain '6' and resid 345 through 355 removed outlier: 4.108A pdb=" N CYS 6 351 " --> pdb=" O TYR 6 347 " (cutoff:3.500A) Processing helix chain '6' and resid 361 through 374 removed outlier: 3.614A pdb=" N LEU 6 372 " --> pdb=" O VAL 6 368 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE 6 373 " --> pdb=" O LEU 6 369 " (cutoff:3.500A) Processing helix chain '6' and resid 401 through 413 removed outlier: 3.708A pdb=" N LEU 6 406 " --> pdb=" O LYS 6 402 " (cutoff:3.500A) Processing helix chain '6' and resid 461 through 465 removed outlier: 3.905A pdb=" N MET 6 465 " --> pdb=" O PHE 6 462 " (cutoff:3.500A) Processing helix chain '6' and resid 466 through 479 removed outlier: 4.066A pdb=" N VAL 6 471 " --> pdb=" O VAL 6 467 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA 6 472 " --> pdb=" O ARG 6 468 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU 6 475 " --> pdb=" O VAL 6 471 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN 6 479 " --> pdb=" O GLU 6 475 " (cutoff:3.500A) Processing helix chain '6' and resid 515 through 519 Processing helix chain '6' and resid 523 through 529 removed outlier: 3.530A pdb=" N ARG 6 529 " --> pdb=" O PRO 6 525 " (cutoff:3.500A) Processing helix chain '6' and resid 542 through 558 Processing helix chain '6' and resid 571 through 580 Processing helix chain '6' and resid 587 through 604 removed outlier: 3.605A pdb=" N ASP 6 592 " --> pdb=" O LYS 6 588 " (cutoff:3.500A) Processing helix chain '6' and resid 617 through 635 removed outlier: 4.084A pdb=" N LEU 6 621 " --> pdb=" O THR 6 617 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 656 removed outlier: 3.516A pdb=" N VAL 6 645 " --> pdb=" O GLN 6 641 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU 6 647 " --> pdb=" O LYS 6 643 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU 6 652 " --> pdb=" O ALA 6 648 " (cutoff:3.500A) Processing helix chain '6' and resid 721 through 739 removed outlier: 3.723A pdb=" N GLU 6 735 " --> pdb=" O LEU 6 731 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU 6 736 " --> pdb=" O ARG 6 732 " (cutoff:3.500A) Processing helix chain '6' and resid 750 through 757 Processing helix chain '6' and resid 765 through 777 removed outlier: 4.262A pdb=" N ARG 6 771 " --> pdb=" O ILE 6 767 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE 6 773 " --> pdb=" O LYS 6 769 " (cutoff:3.500A) Processing helix chain '4' and resid 161 through 166 Processing helix chain '4' and resid 192 through 204 removed outlier: 4.328A pdb=" N GLY 4 198 " --> pdb=" O MET 4 194 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN 4 201 " --> pdb=" O LEU 4 197 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL 4 202 " --> pdb=" O GLY 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 211 through 219 removed outlier: 3.756A pdb=" N ILE 4 215 " --> pdb=" O ASN 4 211 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE 4 218 " --> pdb=" O HIS 4 214 " (cutoff:3.500A) Processing helix chain '4' and resid 219 through 229 removed outlier: 4.033A pdb=" N TYR 4 223 " --> pdb=" O ASP 4 219 " (cutoff:3.500A) Processing helix chain '4' and resid 229 through 248 Proline residue: 4 235 - end of helix removed outlier: 4.006A pdb=" N PHE 4 246 " --> pdb=" O ASN 4 242 " (cutoff:3.500A) Processing helix chain '4' and resid 275 through 279 removed outlier: 3.848A pdb=" N ILE 4 279 " --> pdb=" O PRO 4 276 " (cutoff:3.500A) Processing helix chain '4' and resid 377 through 379 No H-bonds generated for 'chain '4' and resid 377 through 379' Processing helix chain '4' and resid 445 through 455 removed outlier: 3.784A pdb=" N GLU 4 451 " --> pdb=" O GLU 4 447 " (cutoff:3.500A) Processing helix chain '4' and resid 457 through 467 removed outlier: 4.031A pdb=" N ALA 4 467 " --> pdb=" O ALA 4 463 " (cutoff:3.500A) Processing helix chain '4' and resid 473 through 486 Processing helix chain '4' and resid 516 through 527 removed outlier: 3.640A pdb=" N LEU 4 520 " --> pdb=" O LYS 4 516 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN 4 521 " --> pdb=" O SER 4 517 " (cutoff:3.500A) Processing helix chain '4' and resid 561 through 566 Processing helix chain '4' and resid 580 through 591 Processing helix chain '4' and resid 637 through 643 removed outlier: 3.809A pdb=" N ARG 4 643 " --> pdb=" O THR 4 639 " (cutoff:3.500A) Processing helix chain '4' and resid 655 through 671 Processing helix chain '4' and resid 676 through 698 removed outlier: 3.917A pdb=" N GLU 4 680 " --> pdb=" O GLN 4 676 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA 4 692 " --> pdb=" O LYS 4 688 " (cutoff:3.500A) Processing helix chain '4' and resid 703 through 723 removed outlier: 4.387A pdb=" N GLY 4 721 " --> pdb=" O MET 4 717 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER 4 723 " --> pdb=" O LYS 4 719 " (cutoff:3.500A) Processing helix chain '4' and resid 730 through 748 removed outlier: 3.575A pdb=" N LEU 4 734 " --> pdb=" O TYR 4 730 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU 4 735 " --> pdb=" O PRO 4 731 " (cutoff:3.500A) Processing helix chain '4' and resid 754 through 773 removed outlier: 3.686A pdb=" N VAL 4 758 " --> pdb=" O GLU 4 754 " (cutoff:3.500A) Processing helix chain '4' and resid 783 through 789 Processing helix chain '4' and resid 800 through 805 Processing helix chain '4' and resid 805 through 813 Processing helix chain '4' and resid 819 through 831 Processing helix chain '4' and resid 836 through 847 Processing helix chain '4' and resid 848 through 850 No H-bonds generated for 'chain '4' and resid 848 through 850' Processing helix chain '7' and resid 31 through 42 removed outlier: 3.606A pdb=" N ARG 7 39 " --> pdb=" O ASN 7 35 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 56 removed outlier: 3.781A pdb=" N ALA 7 56 " --> pdb=" O LEU 7 52 " (cutoff:3.500A) Processing helix chain '7' and resid 59 through 69 removed outlier: 3.850A pdb=" N VAL 7 63 " --> pdb=" O ASP 7 59 " (cutoff:3.500A) Processing helix chain '7' and resid 69 through 84 removed outlier: 3.545A pdb=" N TYR 7 73 " --> pdb=" O ASN 7 69 " (cutoff:3.500A) Processing helix chain '7' and resid 128 through 132 Processing helix chain '7' and resid 148 through 153 removed outlier: 4.521A pdb=" N ARG 7 153 " --> pdb=" O ILE 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 213 removed outlier: 3.777A pdb=" N THR 7 213 " --> pdb=" O GLN 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 326 through 330 Processing helix chain '7' and resid 332 through 340 removed outlier: 3.598A pdb=" N ALA 7 338 " --> pdb=" O GLU 7 334 " (cutoff:3.500A) Processing helix chain '7' and resid 347 through 360 removed outlier: 3.744A pdb=" N ALA 7 353 " --> pdb=" O ASP 7 349 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL 7 359 " --> pdb=" O LEU 7 355 " (cutoff:3.500A) Processing helix chain '7' and resid 386 through 398 removed outlier: 3.548A pdb=" N ALA 7 398 " --> pdb=" O ILE 7 394 " (cutoff:3.500A) Processing helix chain '7' and resid 405 through 410 removed outlier: 3.607A pdb=" N SER 7 409 " --> pdb=" O GLY 7 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER 7 410 " --> pdb=" O ARG 7 407 " (cutoff:3.500A) Processing helix chain '7' and resid 454 through 464 removed outlier: 3.508A pdb=" N MET 7 462 " --> pdb=" O ILE 7 458 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU 7 463 " --> pdb=" O HIS 7 459 " (cutoff:3.500A) Processing helix chain '7' and resid 500 through 505 Processing helix chain '7' and resid 508 through 515 removed outlier: 3.512A pdb=" N LEU 7 512 " --> pdb=" O PRO 7 508 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER 7 513 " --> pdb=" O ALA 7 509 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG 7 514 " --> pdb=" O ALA 7 510 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE 7 515 " --> pdb=" O LEU 7 511 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 508 through 515' Processing helix chain '7' and resid 526 through 544 removed outlier: 4.023A pdb=" N HIS 7 543 " --> pdb=" O TYR 7 539 " (cutoff:3.500A) Processing helix chain '7' and resid 555 through 569 Processing helix chain '7' and resid 574 through 576 No H-bonds generated for 'chain '7' and resid 574 through 576' Processing helix chain '7' and resid 577 through 596 Processing helix chain '7' and resid 602 through 620 removed outlier: 3.966A pdb=" N LEU 7 606 " --> pdb=" O SER 7 602 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU 7 607 " --> pdb=" O ALA 7 603 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 7 615 " --> pdb=" O ARG 7 611 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 641 Processing helix chain '3' and resid 19 through 24 removed outlier: 3.539A pdb=" N ASP 3 24 " --> pdb=" O LEU 3 20 " (cutoff:3.500A) Processing helix chain '3' and resid 30 through 42 Processing helix chain '3' and resid 51 through 57 Processing helix chain '3' and resid 58 through 66 removed outlier: 3.697A pdb=" N ARG 3 64 " --> pdb=" O LYS 3 60 " (cutoff:3.500A) Processing helix chain '3' and resid 72 through 88 removed outlier: 3.571A pdb=" N ILE 3 87 " --> pdb=" O PHE 3 83 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 95 removed outlier: 3.604A pdb=" N ALA 3 92 " --> pdb=" O ASP 3 88 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN 3 94 " --> pdb=" O THR 3 90 " (cutoff:3.500A) Processing helix chain '3' and resid 106 through 110 Processing helix chain '3' and resid 117 through 121 Processing helix chain '3' and resid 225 through 229 removed outlier: 4.236A pdb=" N ALA 3 229 " --> pdb=" O VAL 3 226 " (cutoff:3.500A) Processing helix chain '3' and resid 280 through 291 Processing helix chain '3' and resid 295 through 302 Processing helix chain '3' and resid 310 through 323 Processing helix chain '3' and resid 350 through 359 removed outlier: 3.658A pdb=" N LEU 3 354 " --> pdb=" O ALA 3 350 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU 3 355 " --> pdb=" O LYS 3 351 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU 3 359 " --> pdb=" O LEU 3 355 " (cutoff:3.500A) Processing helix chain '3' and resid 360 through 362 No H-bonds generated for 'chain '3' and resid 360 through 362' Processing helix chain '3' and resid 411 through 414 Processing helix chain '3' and resid 415 through 427 removed outlier: 3.601A pdb=" N THR 3 420 " --> pdb=" O ASP 3 416 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA 3 421 " --> pdb=" O MET 3 417 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS 3 423 " --> pdb=" O ARG 3 419 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) Processing helix chain '3' and resid 464 through 469 Processing helix chain '3' and resid 474 through 478 Processing helix chain '3' and resid 490 through 506 removed outlier: 3.570A pdb=" N ARG 3 495 " --> pdb=" O PRO 3 491 " (cutoff:3.500A) Processing helix chain '3' and resid 564 through 577 removed outlier: 3.545A pdb=" N MET 3 568 " --> pdb=" O SER 3 564 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS 3 569 " --> pdb=" O ALA 3 565 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS 3 570 " --> pdb=" O ALA 3 566 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE 3 577 " --> pdb=" O HIS 3 573 " (cutoff:3.500A) Processing helix chain '3' and resid 583 through 599 removed outlier: 4.037A pdb=" N TYR 3 589 " --> pdb=" O GLU 3 585 " (cutoff:3.500A) Processing helix chain '3' and resid 599 through 604 Processing helix chain '3' and resid 614 through 629 removed outlier: 3.938A pdb=" N LEU 3 618 " --> pdb=" O THR 3 614 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU 3 619 " --> pdb=" O ALA 3 615 " (cutoff:3.500A) Processing helix chain '3' and resid 630 through 632 No H-bonds generated for 'chain '3' and resid 630 through 632' Processing helix chain '3' and resid 638 through 654 removed outlier: 3.927A pdb=" N GLU 3 644 " --> pdb=" O GLN 3 640 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA 3 645 " --> pdb=" O ASP 3 641 " (cutoff:3.500A) Processing helix chain '5' and resid 30 through 40 removed outlier: 3.551A pdb=" N PHE 5 35 " --> pdb=" O LEU 5 31 " (cutoff:3.500A) Processing helix chain '5' and resid 53 through 60 removed outlier: 3.593A pdb=" N GLU 5 58 " --> pdb=" O LYS 5 54 " (cutoff:3.500A) Processing helix chain '5' and resid 61 through 66 Processing helix chain '5' and resid 73 through 79 removed outlier: 4.157A pdb=" N LEU 5 77 " --> pdb=" O GLU 5 73 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER 5 79 " --> pdb=" O GLU 5 75 " (cutoff:3.500A) Processing helix chain '5' and resid 81 through 91 removed outlier: 3.619A pdb=" N LEU 5 88 " --> pdb=" O LEU 5 84 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR 5 89 " --> pdb=" O ALA 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 107 removed outlier: 4.336A pdb=" N HIS 5 95 " --> pdb=" O GLN 5 91 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU 5 105 " --> pdb=" O GLU 5 101 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA 5 107 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 316 through 328 removed outlier: 4.163A pdb=" N GLU 5 321 " --> pdb=" O GLN 5 317 " (cutoff:3.500A) Processing helix chain '5' and resid 330 through 339 removed outlier: 4.026A pdb=" N VAL 5 334 " --> pdb=" O ASN 5 330 " (cutoff:3.500A) Processing helix chain '5' and resid 346 through 359 Processing helix chain '5' and resid 383 through 388 removed outlier: 4.332A pdb=" N LYS 5 387 " --> pdb=" O PRO 5 383 " (cutoff:3.500A) Processing helix chain '5' and resid 389 through 398 removed outlier: 3.738A pdb=" N GLU 5 395 " --> pdb=" O LEU 5 391 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS 5 396 " --> pdb=" O LYS 5 392 " (cutoff:3.500A) Processing helix chain '5' and resid 432 through 437 Processing helix chain '5' and resid 446 through 450 removed outlier: 3.809A pdb=" N LYS 5 449 " --> pdb=" O GLU 5 446 " (cutoff:3.500A) Processing helix chain '5' and resid 451 through 456 removed outlier: 3.940A pdb=" N VAL 5 456 " --> pdb=" O GLU 5 452 " (cutoff:3.500A) Processing helix chain '5' and resid 457 through 462 removed outlier: 3.973A pdb=" N MET 5 462 " --> pdb=" O ILE 5 458 " (cutoff:3.500A) Processing helix chain '5' and resid 555 through 570 removed outlier: 3.728A pdb=" N VAL 5 568 " --> pdb=" O ALA 5 564 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS 5 570 " --> pdb=" O CYS 5 566 " (cutoff:3.500A) Processing helix chain '5' and resid 575 through 592 removed outlier: 3.823A pdb=" N ILE 5 588 " --> pdb=" O ASN 5 584 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER 5 591 " --> pdb=" O ILE 5 587 " (cutoff:3.500A) Processing helix chain '5' and resid 594 through 598 Processing helix chain '5' and resid 609 through 627 removed outlier: 3.935A pdb=" N LYS 5 627 " --> pdb=" O LEU 5 623 " (cutoff:3.500A) Processing helix chain '5' and resid 633 through 642 removed outlier: 3.598A pdb=" N GLU 5 639 " --> pdb=" O ALA 5 635 " (cutoff:3.500A) Processing helix chain '5' and resid 647 through 652 Processing helix chain '5' and resid 653 through 658 removed outlier: 3.960A pdb=" N LEU 5 657 " --> pdb=" O LEU 5 653 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER 5 658 " --> pdb=" O SER 5 654 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 653 through 658' Processing helix chain '5' and resid 668 through 683 Processing helix chain '5' and resid 690 through 701 removed outlier: 3.605A pdb=" N GLN 5 701 " --> pdb=" O ASP 5 697 " (cutoff:3.500A) Processing helix chain '5' and resid 704 through 719 Processing sheet with id=AA1, first strand: chain '2' and resid 229 through 233 Processing sheet with id=AA2, first strand: chain '2' and resid 304 through 305 removed outlier: 3.768A pdb=" N GLN 2 304 " --> pdb=" O TYR 2 418 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 314 through 315 removed outlier: 3.840A pdb=" N GLU 2 568 " --> pdb=" O HIS 2 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 339 through 340 removed outlier: 7.114A pdb=" N MET 2 324 " --> pdb=" O THR 2 368 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR 2 368 " --> pdb=" O MET 2 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 334 through 335 removed outlier: 3.612A pdb=" N PHE 2 334 " --> pdb=" O CYS 2 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 421 through 422 removed outlier: 3.862A pdb=" N ASN 2 421 " --> pdb=" O ALA 2 436 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA 2 436 " --> pdb=" O ASN 2 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '2' and resid 520 through 522 removed outlier: 6.588A pdb=" N LEU 2 521 " --> pdb=" O ALA 2 630 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N CYS 2 584 " --> pdb=" O ILE 2 627 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA 2 629 " --> pdb=" O CYS 2 584 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE 2 586 " --> pdb=" O ALA 2 629 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 608 through 613 Processing sheet with id=AA9, first strand: chain '6' and resid 60 through 64 removed outlier: 5.991A pdb=" N LEU 6 61 " --> pdb=" O ALA 6 113 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLN 6 115 " --> pdb=" O LEU 6 61 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL 6 63 " --> pdb=" O GLN 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '6' and resid 134 through 138 removed outlier: 3.636A pdb=" N THR 6 245 " --> pdb=" O CYS 6 302 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N CYS 6 302 " --> pdb=" O THR 6 245 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR 6 247 " --> pdb=" O ALA 6 300 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA 6 300 " --> pdb=" O THR 6 247 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE 6 249 " --> pdb=" O PHE 6 298 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N PHE 6 298 " --> pdb=" O ILE 6 249 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL 6 251 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LEU 6 296 " --> pdb=" O VAL 6 251 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N SER 6 223 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N PHE 6 298 " --> pdb=" O SER 6 223 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU 6 225 " --> pdb=" O PHE 6 298 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA 6 300 " --> pdb=" O GLU 6 225 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE 6 227 " --> pdb=" O ALA 6 300 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N CYS 6 302 " --> pdb=" O ILE 6 227 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ARG 6 229 " --> pdb=" O CYS 6 302 " (cutoff:3.500A) removed outlier: 10.802A pdb=" N ALA 6 304 " --> pdb=" O ARG 6 229 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER 6 153 " --> pdb=" O ARG 6 199 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL 6 201 " --> pdb=" O LEU 6 151 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU 6 151 " --> pdb=" O VAL 6 201 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE 6 203 " --> pdb=" O PRO 6 149 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL 6 152 " --> pdb=" O GLU 6 169 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLU 6 169 " --> pdb=" O VAL 6 152 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY 6 154 " --> pdb=" O ASP 6 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '6' and resid 140 through 144 removed outlier: 6.499A pdb=" N ARG 6 207 " --> pdb=" O VAL 6 142 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR 6 144 " --> pdb=" O LYS 6 205 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LYS 6 205 " --> pdb=" O THR 6 144 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER 6 153 " --> pdb=" O ARG 6 199 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL 6 201 " --> pdb=" O LEU 6 151 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU 6 151 " --> pdb=" O VAL 6 201 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE 6 203 " --> pdb=" O PRO 6 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '6' and resid 417 through 420 removed outlier: 3.760A pdb=" N VAL 6 417 " --> pdb=" O VAL 6 456 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL 6 392 " --> pdb=" O ALA 6 501 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '6' and resid 433 through 435 Processing sheet with id=AB5, first strand: chain '6' and resid 481 through 484 Processing sheet with id=AB6, first strand: chain '6' and resid 585 through 586 removed outlier: 7.471A pdb=" N LYS 6 585 " --> pdb=" O VAL 6 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '4' and resid 207 through 208 removed outlier: 3.688A pdb=" N LEU 4 208 " --> pdb=" O GLN 4 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain '4' and resid 281 through 283 removed outlier: 3.727A pdb=" N GLN 4 281 " --> pdb=" O TYR 4 394 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE 4 393 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL 4 418 " --> pdb=" O ILE 4 393 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG 4 395 " --> pdb=" O ILE 4 416 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE 4 416 " --> pdb=" O ARG 4 395 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL 4 397 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR 4 414 " --> pdb=" O VAL 4 397 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE 4 371 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N HIS 4 375 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N HIS 4 420 " --> pdb=" O HIS 4 375 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU 4 345 " --> pdb=" O GLU 4 301 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU 4 301 " --> pdb=" O LEU 4 345 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 312 through 313 Processing sheet with id=AC1, first strand: chain '4' and resid 531 through 534 removed outlier: 6.405A pdb=" N GLN 4 531 " --> pdb=" O CYS 4 572 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASP 4 574 " --> pdb=" O GLN 4 531 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR 4 533 " --> pdb=" O ASP 4 574 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE 4 506 " --> pdb=" O ALA 4 615 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ALA 4 617 " --> pdb=" O ILE 4 506 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU 4 508 " --> pdb=" O ALA 4 617 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU 4 507 " --> pdb=" O PHE 4 648 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 546 through 550 removed outlier: 3.671A pdb=" N GLN 4 555 " --> pdb=" O ASP 4 550 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '4' and resid 599 through 600 removed outlier: 3.517A pdb=" N LYS 4 600 " --> pdb=" O ILE 4 603 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '4' and resid 701 through 702 removed outlier: 6.585A pdb=" N ARG 4 701 " --> pdb=" O VAL 4 753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain '7' and resid 48 through 50 removed outlier: 6.805A pdb=" N LEU 7 48 " --> pdb=" O TYR 7 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain '7' and resid 192 through 193 removed outlier: 3.845A pdb=" N LYS 7 174 " --> pdb=" O PHE 7 232 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ARG 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '7' and resid 220 through 222 removed outlier: 3.845A pdb=" N LYS 7 174 " --> pdb=" O PHE 7 232 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ARG 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG 7 169 " --> pdb=" O LYS 7 236 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN 7 238 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL 7 167 " --> pdb=" O GLN 7 238 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET 7 306 " --> pdb=" O SER 7 272 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '7' and resid 485 through 487 removed outlier: 6.143A pdb=" N ILE 7 377 " --> pdb=" O ALA 7 486 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET 7 380 " --> pdb=" O TRP 7 519 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '3' and resid 46 through 50 Processing sheet with id=AD1, first strand: chain '3' and resid 234 through 240 removed outlier: 6.870A pdb=" N THR 3 200 " --> pdb=" O THR 3 132 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N CYS 3 134 " --> pdb=" O THR 3 198 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR 3 198 " --> pdb=" O CYS 3 134 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP 3 218 " --> pdb=" O LEU 3 260 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '3' and resid 234 through 240 removed outlier: 3.677A pdb=" N CYS 3 134 " --> pdb=" O LEU 3 393 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '3' and resid 368 through 369 removed outlier: 6.512A pdb=" N THR 3 368 " --> pdb=" O ASP 3 409 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE 3 341 " --> pdb=" O ALA 3 450 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ALA 3 452 " --> pdb=" O ILE 3 341 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU 3 343 " --> pdb=" O ALA 3 452 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU 3 342 " --> pdb=" O PHE 3 483 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N MET 3 485 " --> pdb=" O LEU 3 342 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE 3 344 " --> pdb=" O MET 3 485 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '3' and resid 430 through 432 Processing sheet with id=AD5, first strand: chain '5' and resid 244 through 245 removed outlier: 3.556A pdb=" N VAL 5 263 " --> pdb=" O GLY 5 153 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '5' and resid 363 through 364 Processing sheet with id=AD7, first strand: chain '5' and resid 377 through 380 removed outlier: 4.168A pdb=" N LEU 5 378 " --> pdb=" O MET 5 516 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '5' and resid 401 through 403 removed outlier: 6.401A pdb=" N VAL 5 402 " --> pdb=" O CYS 5 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain '5' and resid 573 through 574 removed outlier: 8.107A pdb=" N ARG 5 573 " --> pdb=" O ALA 5 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 1067 hydrogen bonds defined for protein. 3021 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.60 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9596 1.34 - 1.46: 5320 1.46 - 1.58: 13476 1.58 - 1.70: 20 1.70 - 1.81: 234 Bond restraints: 28646 Sorted by residual: bond pdb=" C4 ADP 3 901 " pdb=" C5 ADP 3 901 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C5 ADP 3 901 " pdb=" C6 ADP 3 901 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" N ASP 7 555 " pdb=" CA ASP 7 555 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.18e-02 7.18e+03 7.67e+00 bond pdb=" N ARG 7 545 " pdb=" CA ARG 7 545 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.21e-02 6.83e+03 7.66e+00 bond pdb=" N SER 7 549 " pdb=" CA SER 7 549 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.16e-02 7.43e+03 7.54e+00 ... (remaining 28641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 38390 2.17 - 4.34: 398 4.34 - 6.51: 52 6.51 - 8.69: 10 8.69 - 10.86: 4 Bond angle restraints: 38854 Sorted by residual: angle pdb=" PB ATP 4 902 " pdb=" O3B ATP 4 902 " pdb=" PG ATP 4 902 " ideal model delta sigma weight residual 139.87 129.01 10.86 1.00e+00 1.00e+00 1.18e+02 angle pdb=" PB ATP 6 901 " pdb=" O3B ATP 6 901 " pdb=" PG ATP 6 901 " ideal model delta sigma weight residual 139.87 131.24 8.63 1.00e+00 1.00e+00 7.44e+01 angle pdb=" PA ATP 6 901 " pdb=" O3A ATP 6 901 " pdb=" PB ATP 6 901 " ideal model delta sigma weight residual 136.83 130.30 6.53 1.00e+00 1.00e+00 4.26e+01 angle pdb=" PA ATP 4 902 " pdb=" O3A ATP 4 902 " pdb=" PB ATP 4 902 " ideal model delta sigma weight residual 136.83 130.80 6.03 1.00e+00 1.00e+00 3.63e+01 angle pdb=" N VAL 7 178 " pdb=" CA VAL 7 178 " pdb=" C VAL 7 178 " ideal model delta sigma weight residual 112.96 107.80 5.16 1.00e+00 1.00e+00 2.66e+01 ... (remaining 38849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.87: 16619 23.87 - 47.75: 787 47.75 - 71.62: 185 71.62 - 95.49: 13 95.49 - 119.37: 2 Dihedral angle restraints: 17606 sinusoidal: 6829 harmonic: 10777 Sorted by residual: dihedral pdb=" O2A ADP 3 901 " pdb=" O3A ADP 3 901 " pdb=" PA ADP 3 901 " pdb=" PB ADP 3 901 " ideal model delta sinusoidal sigma weight residual -60.00 59.37 -119.37 1 2.00e+01 2.50e-03 3.58e+01 dihedral pdb=" O2A ADP 7 801 " pdb=" O3A ADP 7 801 " pdb=" PA ADP 7 801 " pdb=" PB ADP 7 801 " ideal model delta sinusoidal sigma weight residual -60.00 52.38 -112.38 1 2.00e+01 2.50e-03 3.31e+01 dihedral pdb=" CA ARG 2 218 " pdb=" C ARG 2 218 " pdb=" N ILE 2 219 " pdb=" CA ILE 2 219 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 17603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3274 0.039 - 0.079: 911 0.079 - 0.118: 329 0.118 - 0.157: 22 0.157 - 0.196: 4 Chirality restraints: 4540 Sorted by residual: chirality pdb=" CA MET 7 556 " pdb=" N MET 7 556 " pdb=" C MET 7 556 " pdb=" CB MET 7 556 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA GLN 7 550 " pdb=" N GLN 7 550 " pdb=" C GLN 7 550 " pdb=" CB GLN 7 550 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CB THR 7 405 " pdb=" CA THR 7 405 " pdb=" OG1 THR 7 405 " pdb=" CG2 THR 7 405 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.15e-01 ... (remaining 4537 not shown) Planarity restraints: 5050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 6 104 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO 6 105 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO 6 105 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO 6 105 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 2 668 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO 2 669 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO 2 669 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO 2 669 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 7 85 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO 7 86 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO 7 86 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO 7 86 " 0.021 5.00e-02 4.00e+02 ... (remaining 5047 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.07: 19 2.07 - 2.78: 5562 2.78 - 3.49: 40711 3.49 - 4.19: 64606 4.19 - 4.90: 111794 Nonbonded interactions: 222692 Sorted by model distance: nonbonded pdb=" CD2 TYR 4 412 " pdb=" CZ PHE 7 229 " model vdw 1.368 3.640 nonbonded pdb=" CE2 TYR 4 412 " pdb=" CZ PHE 7 229 " model vdw 1.511 3.640 nonbonded pdb=" CE2 TYR 4 412 " pdb=" CE1 PHE 7 229 " model vdw 1.604 3.640 nonbonded pdb=" O SER 4 410 " pdb=" CA LYS 7 176 " model vdw 1.657 3.470 nonbonded pdb=" O TYR 4 412 " pdb=" CG PRO 7 175 " model vdw 1.690 3.440 ... (remaining 222687 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 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: 0.090 Set scattering table: 0.080 Process input model: 24.880 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5563 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 : 0.010 0.845 28662 Z= 0.743 Angle : 0.617 24.545 38872 Z= 0.307 Chirality : 0.041 0.196 4540 Planarity : 0.004 0.057 5050 Dihedral : 14.097 119.367 10592 Min Nonbonded Distance : 1.368 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.14), residues: 3636 helix: -0.59 (0.14), residues: 1392 sheet: -1.54 (0.24), residues: 458 loop : -1.09 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 3 445 TYR 0.011 0.001 TYR 5 731 PHE 0.012 0.001 PHE 5 358 TRP 0.007 0.001 TRP 6 334 HIS 0.007 0.001 HIS 7 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (28646) covalent geometry : angle 0.56658 / 0.30 (38854) hydrogen bonds : bond 0.26359 / 17.79 ( 1056) hydrogen bonds : angle 8.61793 / 6.05 ( 3021) metal coordination : bond 0.31369 / 15.97 ( 14) metal coordination : angle 11.36470 / 7.60 ( 18) Misc. bond : bond 0.82488 / 41.50 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 449 LEU cc_start: 0.8101 (tp) cc_final: 0.7728 (tt) REVERT: 7 636 LEU cc_start: 0.6835 (mp) cc_final: 0.6455 (mt) REVERT: 3 20 LEU cc_start: 0.8377 (mt) cc_final: 0.8114 (mt) REVERT: 5 74 MET cc_start: 0.6210 (ptm) cc_final: 0.5483 (tmm) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1551 time to fit residues: 89.6151 Evaluate side-chains 182 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 206 HIS 2 646 ASN 2 777 HIS 6 115 GLN 6 145 HIS ** 6 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 300 GLN 4 751 ASN 7 196 GLN 3 264 ASN 3 310 HIS 3 353 GLN ** 3 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.053920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.040140 restraints weight = 266349.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.040697 restraints weight = 174011.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.041227 restraints weight = 127478.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.041290 restraints weight = 122328.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.041349 restraints weight = 103388.623| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 28662 Z= 0.222 Angle : 0.686 11.957 38872 Z= 0.349 Chirality : 0.043 0.217 4540 Planarity : 0.005 0.061 5050 Dihedral : 7.296 135.069 4094 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.17 % Allowed : 4.85 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.14), residues: 3636 helix: -0.07 (0.13), residues: 1430 sheet: -1.69 (0.22), residues: 534 loop : -1.04 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 3 478 TYR 0.020 0.002 TYR 7 562 PHE 0.022 0.002 PHE 3 411 TRP 0.012 0.002 TRP 2 569 HIS 0.007 0.001 HIS 5 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (28646) covalent geometry : angle 0.67769 / 0.35 (38854) hydrogen bonds : bond 0.04673 / 3.20 ( 1056) hydrogen bonds : angle 5.89218 / 4.15 ( 3021) metal coordination : bond 0.01035 / 0.50 ( 14) metal coordination : angle 5.08562 / 4.14 ( 18) Misc. bond : bond 0.00249 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 204 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 418 TYR cc_start: 0.8782 (t80) cc_final: 0.8453 (t80) REVERT: 2 674 MET cc_start: 0.8893 (mmp) cc_final: 0.8364 (mmm) REVERT: 2 793 MET cc_start: 0.8266 (mmm) cc_final: 0.8035 (mmm) REVERT: 2 885 LEU cc_start: 0.8258 (mt) cc_final: 0.8053 (pp) REVERT: 6 111 TYR cc_start: 0.8098 (m-80) cc_final: 0.7641 (m-80) REVERT: 6 371 MET cc_start: 0.8796 (ttm) cc_final: 0.8593 (ttt) REVERT: 6 527 MET cc_start: 0.8948 (mtm) cc_final: 0.8595 (mpp) REVERT: 7 49 TYR cc_start: 0.7211 (m-10) cc_final: 0.6969 (m-10) REVERT: 7 447 PHE cc_start: 0.9682 (t80) cc_final: 0.9408 (t80) REVERT: 7 462 MET cc_start: 0.9305 (mmp) cc_final: 0.9054 (mmm) REVERT: 7 559 MET cc_start: 0.9260 (tpp) cc_final: 0.8812 (mmp) REVERT: 7 572 MET cc_start: 0.8918 (tpp) cc_final: 0.8596 (tmm) REVERT: 3 411 PHE cc_start: 0.9677 (t80) cc_final: 0.9379 (t80) REVERT: 3 603 MET cc_start: 0.6591 (ppp) cc_final: 0.6273 (ppp) REVERT: 5 74 MET cc_start: 0.7098 (ptm) cc_final: 0.6396 (tmm) REVERT: 5 127 MET cc_start: 0.5977 (tpt) cc_final: 0.5747 (tpt) REVERT: 5 649 LEU cc_start: 0.9661 (tt) cc_final: 0.9404 (mt) outliers start: 5 outliers final: 0 residues processed: 208 average time/residue: 0.1502 time to fit residues: 52.6707 Evaluate side-chains 150 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 291 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 131 optimal weight: 40.0000 chunk 269 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 187 optimal weight: 8.9990 chunk 311 optimal weight: 7.9990 chunk 325 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 419 HIS 2 442 ASN 2 531 GLN 2 646 ASN 2 889 ASN 6 176 GLN 6 474 HIS ** 6 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 294 GLN 4 300 GLN ** 4 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 695 HIS 7 243 GLN 7 465 GLN ** 3 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 701 GLN 5 706 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.051582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.038380 restraints weight = 279769.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.038523 restraints weight = 192279.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.038937 restraints weight = 144080.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.039003 restraints weight = 145816.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.039126 restraints weight = 124154.350| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28662 Z= 0.222 Angle : 0.671 13.427 38872 Z= 0.341 Chirality : 0.043 0.219 4540 Planarity : 0.004 0.043 5050 Dihedral : 7.389 123.425 4094 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3636 helix: 0.08 (0.14), residues: 1444 sheet: -1.76 (0.21), residues: 531 loop : -1.10 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 6 190 TYR 0.020 0.002 TYR 6 347 PHE 0.024 0.002 PHE 6 65 TRP 0.015 0.001 TRP 2 569 HIS 0.013 0.002 HIS 3 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.22 (28646) covalent geometry : angle 0.66020 / 0.34 (38854) hydrogen bonds : bond 0.04233 / 2.88 ( 1056) hydrogen bonds : angle 5.64966 / 3.99 ( 3021) metal coordination : bond 0.00963 / 0.49 ( 14) metal coordination : angle 5.56598 / 4.62 ( 18) Misc. bond : bond 0.00448 / 0.22 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 229 SER cc_start: 0.8369 (p) cc_final: 0.7978 (p) REVERT: 2 418 TYR cc_start: 0.8849 (t80) cc_final: 0.8575 (t80) REVERT: 2 674 MET cc_start: 0.9098 (mmp) cc_final: 0.8532 (mmm) REVERT: 2 770 MET cc_start: 0.9471 (mmm) cc_final: 0.9239 (mmm) REVERT: 2 798 MET cc_start: 0.8670 (mmp) cc_final: 0.8385 (tpt) REVERT: 2 885 LEU cc_start: 0.8518 (mt) cc_final: 0.8133 (pp) REVERT: 2 889 ASN cc_start: 0.8689 (m110) cc_final: 0.8468 (m-40) REVERT: 6 111 TYR cc_start: 0.8255 (m-80) cc_final: 0.7720 (m-80) REVERT: 6 465 MET cc_start: 0.8141 (tpt) cc_final: 0.7830 (tpp) REVERT: 6 527 MET cc_start: 0.9071 (mtm) cc_final: 0.8826 (mtp) REVERT: 4 299 MET cc_start: 0.8746 (tpt) cc_final: 0.8524 (tpp) REVERT: 4 317 MET cc_start: 0.4828 (tpt) cc_final: 0.4321 (tpt) REVERT: 4 572 CYS cc_start: 0.9340 (m) cc_final: 0.9121 (m) REVERT: 4 591 MET cc_start: 0.9416 (mmm) cc_final: 0.8955 (mmm) REVERT: 4 717 MET cc_start: 0.9643 (mtp) cc_final: 0.9424 (mtp) REVERT: 7 443 CYS cc_start: 0.8555 (m) cc_final: 0.7968 (t) REVERT: 7 447 PHE cc_start: 0.9766 (t80) cc_final: 0.9516 (t80) REVERT: 7 621 MET cc_start: 0.9030 (mmp) cc_final: 0.8786 (mmm) REVERT: 3 603 MET cc_start: 0.6696 (ppp) cc_final: 0.6372 (ppp) REVERT: 5 74 MET cc_start: 0.7770 (ptm) cc_final: 0.7214 (tmm) REVERT: 5 127 MET cc_start: 0.5994 (tpt) cc_final: 0.5771 (tpt) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.1471 time to fit residues: 45.0699 Evaluate side-chains 149 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 204 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 345 optimal weight: 20.0000 chunk 237 optimal weight: 3.9990 chunk 238 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 328 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 196 HIS 2 282 HIS 2 443 HIS 2 646 ASN 4 332 HIS ** 4 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 375 HIS 4 751 ASN 7 459 HIS 3 273 GLN ** 3 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 650 GLN ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 629 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.051207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.038180 restraints weight = 282797.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.038336 restraints weight = 186854.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.038693 restraints weight = 143968.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.038797 restraints weight = 145160.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.038860 restraints weight = 126486.946| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 28662 Z= 0.192 Angle : 0.626 12.669 38872 Z= 0.317 Chirality : 0.042 0.172 4540 Planarity : 0.004 0.075 5050 Dihedral : 7.310 122.342 4094 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.03 % Allowed : 3.22 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.14), residues: 3636 helix: 0.17 (0.14), residues: 1447 sheet: -1.78 (0.21), residues: 508 loop : -1.12 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 5 324 TYR 0.020 0.001 TYR 6 347 PHE 0.019 0.002 PHE 6 65 TRP 0.010 0.002 TRP 7 593 HIS 0.006 0.001 HIS 3 573 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (28646) covalent geometry : angle 0.61613 / 0.32 (38854) hydrogen bonds : bond 0.03730 / 2.56 ( 1056) hydrogen bonds : angle 5.37821 / 3.81 ( 3021) metal coordination : bond 0.00956 / 0.50 ( 14) metal coordination : angle 5.21649 / 4.35 ( 18) Misc. bond : bond 0.00255 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 282 HIS cc_start: 0.9062 (t-90) cc_final: 0.8783 (t-90) REVERT: 2 674 MET cc_start: 0.9144 (mmp) cc_final: 0.8531 (mmm) REVERT: 2 773 MET cc_start: 0.9244 (ptp) cc_final: 0.8790 (ptt) REVERT: 2 798 MET cc_start: 0.8653 (mmp) cc_final: 0.8266 (mmp) REVERT: 2 885 LEU cc_start: 0.8501 (mt) cc_final: 0.8064 (pp) REVERT: 2 889 ASN cc_start: 0.8641 (m110) cc_final: 0.8416 (m-40) REVERT: 6 111 TYR cc_start: 0.8250 (m-80) cc_final: 0.7725 (m-80) REVERT: 6 329 MET cc_start: 0.8765 (ppp) cc_final: 0.8079 (ppp) REVERT: 6 465 MET cc_start: 0.8001 (tpt) cc_final: 0.7611 (tpt) REVERT: 6 477 MET cc_start: 0.9502 (tmm) cc_final: 0.9261 (tmm) REVERT: 6 527 MET cc_start: 0.9147 (mtm) cc_final: 0.8853 (mtp) REVERT: 6 624 MET cc_start: 0.9155 (tpt) cc_final: 0.8892 (tpt) REVERT: 4 299 MET cc_start: 0.8690 (tpt) cc_final: 0.8396 (tpt) REVERT: 4 591 MET cc_start: 0.9379 (mmm) cc_final: 0.8704 (mmm) REVERT: 4 717 MET cc_start: 0.9624 (mtp) cc_final: 0.9409 (mtp) REVERT: 7 443 CYS cc_start: 0.8315 (m) cc_final: 0.7822 (t) REVERT: 7 447 PHE cc_start: 0.9758 (t80) cc_final: 0.9486 (t80) REVERT: 7 559 MET cc_start: 0.9122 (mmp) cc_final: 0.8677 (mmp) REVERT: 3 603 MET cc_start: 0.6955 (ppp) cc_final: 0.6576 (ppp) REVERT: 5 74 MET cc_start: 0.7815 (ptm) cc_final: 0.7281 (tmm) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.1591 time to fit residues: 48.0251 Evaluate side-chains 144 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 65 optimal weight: 7.9990 chunk 21 optimal weight: 0.0980 chunk 59 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 chunk 299 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 250 optimal weight: 0.3980 chunk 329 optimal weight: 9.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 196 HIS 2 646 ASN 2 683 HIS 4 294 GLN 4 341 HIS ** 4 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 389 GLN 3 628 HIS ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 238 HIS ** 5 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 629 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.052622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.039522 restraints weight = 276081.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.039657 restraints weight = 185078.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.040052 restraints weight = 138659.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.040302 restraints weight = 125484.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.040469 restraints weight = 108606.483| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 28662 Z= 0.104 Angle : 0.566 12.756 38872 Z= 0.279 Chirality : 0.042 0.159 4540 Planarity : 0.004 0.075 5050 Dihedral : 7.023 119.701 4094 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3636 helix: 0.46 (0.14), residues: 1440 sheet: -1.57 (0.22), residues: 476 loop : -1.04 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 4 489 TYR 0.022 0.001 TYR 5 87 PHE 0.035 0.001 PHE 5 80 TRP 0.008 0.001 TRP 6 614 HIS 0.005 0.001 HIS 2 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (28646) covalent geometry : angle 0.55683 / 0.28 (38854) hydrogen bonds : bond 0.03330 / 2.28 ( 1056) hydrogen bonds : angle 5.00263 / 3.54 ( 3021) metal coordination : bond 0.00548 / 0.27 ( 14) metal coordination : angle 4.69915 / 3.86 ( 18) Misc. bond : bond 0.00303 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 229 SER cc_start: 0.8406 (p) cc_final: 0.8020 (p) REVERT: 2 282 HIS cc_start: 0.9008 (t-90) cc_final: 0.8766 (t70) REVERT: 2 395 ASP cc_start: 0.8707 (m-30) cc_final: 0.7568 (p0) REVERT: 2 418 TYR cc_start: 0.8854 (t80) cc_final: 0.8363 (t80) REVERT: 2 674 MET cc_start: 0.9093 (mmp) cc_final: 0.8574 (mmm) REVERT: 2 885 LEU cc_start: 0.8491 (mt) cc_final: 0.8034 (pp) REVERT: 2 889 ASN cc_start: 0.8627 (m110) cc_final: 0.8390 (m-40) REVERT: 6 111 TYR cc_start: 0.8002 (m-80) cc_final: 0.7544 (m-80) REVERT: 6 329 MET cc_start: 0.8815 (ppp) cc_final: 0.8277 (ppp) REVERT: 6 393 CYS cc_start: 0.8795 (t) cc_final: 0.8505 (t) REVERT: 6 465 MET cc_start: 0.8154 (tpt) cc_final: 0.7699 (tpp) REVERT: 6 477 MET cc_start: 0.9445 (tmm) cc_final: 0.9149 (tmm) REVERT: 6 527 MET cc_start: 0.9184 (mtm) cc_final: 0.8899 (mtp) REVERT: 6 624 MET cc_start: 0.9161 (tpt) cc_final: 0.8872 (tpt) REVERT: 4 317 MET cc_start: 0.4694 (tpt) cc_final: 0.4318 (tpt) REVERT: 4 508 LEU cc_start: 0.9675 (mm) cc_final: 0.9440 (tp) REVERT: 4 576 PHE cc_start: 0.9301 (t80) cc_final: 0.8821 (t80) REVERT: 4 591 MET cc_start: 0.9359 (mmm) cc_final: 0.8514 (mmm) REVERT: 7 306 MET cc_start: 0.8976 (ppp) cc_final: 0.8758 (ppp) REVERT: 7 443 CYS cc_start: 0.8036 (m) cc_final: 0.7833 (m) REVERT: 7 447 PHE cc_start: 0.9683 (t80) cc_final: 0.9479 (t80) REVERT: 7 507 LEU cc_start: 0.8936 (mt) cc_final: 0.8588 (mt) REVERT: 7 559 MET cc_start: 0.9011 (mmp) cc_final: 0.8651 (mmp) REVERT: 7 621 MET cc_start: 0.8977 (mmp) cc_final: 0.8775 (mmm) REVERT: 3 603 MET cc_start: 0.6969 (ppp) cc_final: 0.6687 (ppp) REVERT: 5 74 MET cc_start: 0.7761 (ptm) cc_final: 0.7241 (tmm) REVERT: 5 649 LEU cc_start: 0.9698 (tt) cc_final: 0.9436 (mt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1440 time to fit residues: 45.0510 Evaluate side-chains 154 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 282 optimal weight: 7.9990 chunk 309 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 351 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 343 GLN ** 2 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 646 ASN 2 889 ASN 6 768 ASN 4 294 GLN ** 4 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 415 HIS 7 233 GLN 7 374 ASN 7 389 GLN 7 535 GLN ** 3 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 706 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.050572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.037293 restraints weight = 277916.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.037555 restraints weight = 196142.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.038021 restraints weight = 142309.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.038094 restraints weight = 126967.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.038222 restraints weight = 117596.736| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28662 Z= 0.204 Angle : 0.645 13.207 38872 Z= 0.326 Chirality : 0.042 0.175 4540 Planarity : 0.004 0.061 5050 Dihedral : 7.310 120.550 4094 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3636 helix: 0.39 (0.14), residues: 1451 sheet: -1.80 (0.21), residues: 502 loop : -1.12 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 5 323 TYR 0.023 0.002 TYR 6 347 PHE 0.054 0.002 PHE 7 515 TRP 0.011 0.002 TRP 2 569 HIS 0.006 0.001 HIS 2 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (28646) covalent geometry : angle 0.63530 / 0.33 (38854) hydrogen bonds : bond 0.03576 / 2.42 ( 1056) hydrogen bonds : angle 5.16656 / 3.65 ( 3021) metal coordination : bond 0.01010 / 0.52 ( 14) metal coordination : angle 5.31288 / 4.44 ( 18) Misc. bond : bond 0.00282 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 418 TYR cc_start: 0.8948 (t80) cc_final: 0.8488 (t80) REVERT: 2 674 MET cc_start: 0.9192 (mmp) cc_final: 0.8617 (mmm) REVERT: 2 770 MET cc_start: 0.9571 (mmp) cc_final: 0.9343 (mmt) REVERT: 2 885 LEU cc_start: 0.8521 (mt) cc_final: 0.8148 (pp) REVERT: 6 111 TYR cc_start: 0.8258 (m-80) cc_final: 0.7721 (m-80) REVERT: 6 329 MET cc_start: 0.8918 (ppp) cc_final: 0.8652 (ppp) REVERT: 6 465 MET cc_start: 0.8240 (tpt) cc_final: 0.7829 (tpt) REVERT: 6 477 MET cc_start: 0.9560 (tmm) cc_final: 0.9291 (tmm) REVERT: 6 757 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8089 (tp30) REVERT: 4 572 CYS cc_start: 0.9343 (m) cc_final: 0.9140 (m) REVERT: 4 591 MET cc_start: 0.9334 (mmm) cc_final: 0.8660 (tmm) REVERT: 4 717 MET cc_start: 0.9650 (mtp) cc_final: 0.9404 (mtp) REVERT: 7 177 MET cc_start: 0.8743 (pmm) cc_final: 0.8452 (pmm) REVERT: 7 443 CYS cc_start: 0.8458 (m) cc_final: 0.8200 (m) REVERT: 7 450 MET cc_start: 0.8374 (ppp) cc_final: 0.8149 (ppp) REVERT: 7 559 MET cc_start: 0.9114 (mmp) cc_final: 0.8779 (mmp) REVERT: 3 414 MET cc_start: 0.8913 (ppp) cc_final: 0.8453 (ppp) REVERT: 3 603 MET cc_start: 0.7088 (ppp) cc_final: 0.6701 (ppp) REVERT: 5 74 MET cc_start: 0.7937 (ptm) cc_final: 0.7438 (tmm) REVERT: 5 379 MET cc_start: 0.8609 (pmm) cc_final: 0.8313 (ppp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1370 time to fit residues: 40.1403 Evaluate side-chains 143 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 234 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 55 optimal weight: 0.0070 chunk 297 optimal weight: 7.9990 chunk 60 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 29 optimal weight: 0.0670 chunk 334 optimal weight: 9.9990 chunk 293 optimal weight: 3.9990 overall best weight: 0.4340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 646 ASN 2 889 ASN 4 294 GLN 7 374 ASN 7 389 GLN 7 465 GLN ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 426 ASN ** 5 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 701 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.051958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.038843 restraints weight = 272840.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.039000 restraints weight = 186331.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.039409 restraints weight = 139900.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.039535 restraints weight = 140152.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.039597 restraints weight = 120414.003| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 28662 Z= 0.103 Angle : 0.576 13.556 38872 Z= 0.283 Chirality : 0.042 0.245 4540 Planarity : 0.003 0.054 5050 Dihedral : 7.024 117.465 4094 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3636 helix: 0.62 (0.14), residues: 1447 sheet: -1.51 (0.22), residues: 489 loop : -1.05 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG 3 478 TYR 0.022 0.001 TYR 6 347 PHE 0.027 0.001 PHE 7 515 TRP 0.006 0.001 TRP 7 593 HIS 0.006 0.001 HIS 3 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (28646) covalent geometry : angle 0.56689 / 0.28 (38854) hydrogen bonds : bond 0.03146 / 2.16 ( 1056) hydrogen bonds : angle 4.83342 / 3.42 ( 3021) metal coordination : bond 0.00592 / 0.29 ( 14) metal coordination : angle 4.84837 / 3.93 ( 18) Misc. bond : bond 0.00303 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 229 SER cc_start: 0.8250 (p) cc_final: 0.7781 (p) REVERT: 2 282 HIS cc_start: 0.9289 (t-90) cc_final: 0.8994 (t70) REVERT: 2 418 TYR cc_start: 0.8843 (t80) cc_final: 0.8292 (t80) REVERT: 2 594 ASP cc_start: 0.9078 (t0) cc_final: 0.8795 (m-30) REVERT: 2 674 MET cc_start: 0.9082 (mmp) cc_final: 0.8541 (mmm) REVERT: 2 773 MET cc_start: 0.9308 (ptm) cc_final: 0.8817 (ptm) REVERT: 2 885 LEU cc_start: 0.8563 (mt) cc_final: 0.8052 (pp) REVERT: 2 889 ASN cc_start: 0.8657 (m110) cc_final: 0.8430 (m-40) REVERT: 6 111 TYR cc_start: 0.7981 (m-80) cc_final: 0.7515 (m-80) REVERT: 6 371 MET cc_start: 0.8625 (tpp) cc_final: 0.8035 (tpp) REVERT: 6 393 CYS cc_start: 0.8814 (t) cc_final: 0.8487 (t) REVERT: 6 465 MET cc_start: 0.8290 (tpt) cc_final: 0.7785 (tpp) REVERT: 6 477 MET cc_start: 0.9546 (tmm) cc_final: 0.9273 (tmm) REVERT: 6 527 MET cc_start: 0.9130 (mtp) cc_final: 0.8781 (mtp) REVERT: 4 317 MET cc_start: 0.3936 (tpt) cc_final: 0.3273 (tpt) REVERT: 4 572 CYS cc_start: 0.9326 (m) cc_final: 0.9107 (m) REVERT: 4 576 PHE cc_start: 0.9397 (t80) cc_final: 0.8910 (t80) REVERT: 4 591 MET cc_start: 0.9400 (mmm) cc_final: 0.8627 (tmm) REVERT: 7 177 MET cc_start: 0.8740 (pmm) cc_final: 0.8487 (pmm) REVERT: 7 559 MET cc_start: 0.9033 (mmp) cc_final: 0.8723 (mmp) REVERT: 7 621 MET cc_start: 0.9082 (mmp) cc_final: 0.8862 (mmm) REVERT: 3 414 MET cc_start: 0.8935 (ppp) cc_final: 0.8410 (ppp) REVERT: 3 603 MET cc_start: 0.7041 (ppp) cc_final: 0.6700 (ppp) REVERT: 5 74 MET cc_start: 0.7840 (ptm) cc_final: 0.7382 (tmm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1556 time to fit residues: 48.7609 Evaluate side-chains 148 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 109 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 315 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 335 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 226 ASN ** 2 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 646 ASN 2 683 HIS 2 889 ASN 2 893 HIS 6 38 GLN 4 294 GLN ** 4 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 483 GLN 4 588 HIS ** 3 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 300 GLN ** 5 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.049756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.036817 restraints weight = 285077.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.036992 restraints weight = 172378.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.037203 restraints weight = 147211.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.037311 restraints weight = 147847.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.037363 restraints weight = 128292.977| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28662 Z= 0.226 Angle : 0.671 12.432 38872 Z= 0.341 Chirality : 0.043 0.194 4540 Planarity : 0.004 0.049 5050 Dihedral : 7.361 120.002 4094 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.03 % Allowed : 1.26 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 3636 helix: 0.39 (0.14), residues: 1470 sheet: -1.76 (0.21), residues: 517 loop : -1.17 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 7 481 TYR 0.030 0.002 TYR 6 347 PHE 0.019 0.002 PHE 5 80 TRP 0.015 0.003 TRP 6 334 HIS 0.008 0.001 HIS 2 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.23 (28646) covalent geometry : angle 0.66160 / 0.34 (38854) hydrogen bonds : bond 0.03602 / 2.43 ( 1056) hydrogen bonds : angle 5.16664 / 3.66 ( 3021) metal coordination : bond 0.01055 / 0.55 ( 14) metal coordination : angle 5.34274 / 4.43 ( 18) Misc. bond : bond 0.00263 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 418 TYR cc_start: 0.8970 (t80) cc_final: 0.8444 (t80) REVERT: 2 674 MET cc_start: 0.9124 (mmp) cc_final: 0.8667 (mmm) REVERT: 2 784 ASP cc_start: 0.9045 (p0) cc_final: 0.8768 (t0) REVERT: 2 885 LEU cc_start: 0.8622 (mt) cc_final: 0.8232 (pp) REVERT: 6 111 TYR cc_start: 0.8320 (m-80) cc_final: 0.7787 (m-80) REVERT: 6 329 MET cc_start: 0.8962 (ppp) cc_final: 0.8625 (ppp) REVERT: 6 465 MET cc_start: 0.8313 (tpt) cc_final: 0.7865 (tpt) REVERT: 6 527 MET cc_start: 0.9205 (mtp) cc_final: 0.8869 (mtp) REVERT: 6 757 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8124 (tp30) REVERT: 4 576 PHE cc_start: 0.9491 (t80) cc_final: 0.9050 (t80) REVERT: 4 591 MET cc_start: 0.9290 (mmm) cc_final: 0.8675 (tmm) REVERT: 4 717 MET cc_start: 0.9672 (mtp) cc_final: 0.9434 (mtp) REVERT: 7 443 CYS cc_start: 0.8207 (m) cc_final: 0.7943 (m) REVERT: 7 559 MET cc_start: 0.9127 (mmp) cc_final: 0.8800 (mmp) REVERT: 7 621 MET cc_start: 0.9124 (mmp) cc_final: 0.8868 (mmm) REVERT: 3 319 CYS cc_start: 0.9206 (t) cc_final: 0.8981 (p) REVERT: 3 414 MET cc_start: 0.9085 (ppp) cc_final: 0.8577 (ppp) REVERT: 5 74 MET cc_start: 0.7932 (ptm) cc_final: 0.7438 (tmm) REVERT: 5 300 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.5488 (mp10) REVERT: 5 479 ASN cc_start: 0.8476 (m-40) cc_final: 0.8239 (m-40) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.1654 time to fit residues: 49.2740 Evaluate side-chains 139 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 98 optimal weight: 0.3980 chunk 168 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 344 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 317 optimal weight: 7.9990 chunk 356 optimal weight: 0.2980 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 646 ASN 6 480 GLN ** 4 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 629 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.050727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.037352 restraints weight = 275454.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.037846 restraints weight = 189412.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.038289 restraints weight = 136127.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.038419 restraints weight = 124450.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.038519 restraints weight = 109636.656| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28662 Z= 0.118 Angle : 0.597 13.806 38872 Z= 0.297 Chirality : 0.042 0.190 4540 Planarity : 0.003 0.048 5050 Dihedral : 7.112 116.571 4094 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3636 helix: 0.53 (0.14), residues: 1458 sheet: -1.70 (0.21), residues: 480 loop : -1.10 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG 2 656 TYR 0.028 0.001 TYR 6 347 PHE 0.032 0.002 PHE 3 411 TRP 0.008 0.001 TRP 7 519 HIS 0.004 0.001 HIS 7 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (28646) covalent geometry : angle 0.58717 / 0.30 (38854) hydrogen bonds : bond 0.03172 / 2.17 ( 1056) hydrogen bonds : angle 4.94867 / 3.50 ( 3021) metal coordination : bond 0.00725 / 0.36 ( 14) metal coordination : angle 5.13780 / 4.17 ( 18) Misc. bond : bond 0.00277 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 395 ASP cc_start: 0.8835 (m-30) cc_final: 0.7587 (p0) REVERT: 2 418 TYR cc_start: 0.8920 (t80) cc_final: 0.8434 (t80) REVERT: 2 594 ASP cc_start: 0.9029 (t0) cc_final: 0.8721 (m-30) REVERT: 2 674 MET cc_start: 0.9110 (mmp) cc_final: 0.8627 (mmm) REVERT: 2 784 ASP cc_start: 0.8981 (p0) cc_final: 0.8638 (m-30) REVERT: 2 885 LEU cc_start: 0.8644 (mt) cc_final: 0.8265 (pp) REVERT: 6 111 TYR cc_start: 0.8174 (m-80) cc_final: 0.7712 (m-80) REVERT: 6 329 MET cc_start: 0.8827 (ppp) cc_final: 0.8272 (ppp) REVERT: 6 371 MET cc_start: 0.8497 (tpp) cc_final: 0.7951 (tpp) REVERT: 6 393 CYS cc_start: 0.8729 (t) cc_final: 0.8450 (t) REVERT: 6 465 MET cc_start: 0.8231 (tpt) cc_final: 0.7845 (tpp) REVERT: 6 527 MET cc_start: 0.9266 (mtp) cc_final: 0.8843 (mtp) REVERT: 6 757 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8097 (tp30) REVERT: 4 576 PHE cc_start: 0.9330 (t80) cc_final: 0.8899 (t80) REVERT: 4 591 MET cc_start: 0.9284 (mmm) cc_final: 0.8621 (tmm) REVERT: 4 717 MET cc_start: 0.9624 (mtp) cc_final: 0.9397 (mtp) REVERT: 7 177 MET cc_start: 0.8705 (pmm) cc_final: 0.8142 (pmm) REVERT: 7 443 CYS cc_start: 0.7798 (m) cc_final: 0.7538 (m) REVERT: 7 559 MET cc_start: 0.9081 (mmp) cc_final: 0.8745 (mmp) REVERT: 7 621 MET cc_start: 0.9097 (mmp) cc_final: 0.8849 (mmm) REVERT: 3 204 MET cc_start: 0.7686 (mpp) cc_final: 0.7386 (mmt) REVERT: 3 414 MET cc_start: 0.9104 (ppp) cc_final: 0.8521 (ppp) REVERT: 3 603 MET cc_start: 0.6904 (ppp) cc_final: 0.6380 (ppp) REVERT: 5 74 MET cc_start: 0.7927 (ptm) cc_final: 0.7446 (tmm) REVERT: 5 479 ASN cc_start: 0.8424 (m-40) cc_final: 0.8198 (m-40) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1549 time to fit residues: 45.8701 Evaluate side-chains 143 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 202 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 201 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 252 optimal weight: 0.0570 chunk 345 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 chunk 28 optimal weight: 0.0670 chunk 102 optimal weight: 0.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 646 ASN ** 4 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 629 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.051084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.037728 restraints weight = 276764.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.038186 restraints weight = 185294.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.038849 restraints weight = 135508.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.038873 restraints weight = 114924.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.038933 restraints weight = 104507.326| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 28662 Z= 0.107 Angle : 0.591 13.660 38872 Z= 0.292 Chirality : 0.042 0.187 4540 Planarity : 0.003 0.048 5050 Dihedral : 6.985 115.633 4094 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3636 helix: 0.65 (0.14), residues: 1448 sheet: -1.68 (0.21), residues: 478 loop : -1.01 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 478 TYR 0.026 0.001 TYR 6 347 PHE 0.017 0.001 PHE 5 80 TRP 0.007 0.001 TRP 7 519 HIS 0.004 0.001 HIS 4 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (28646) covalent geometry : angle 0.58190 / 0.29 (38854) hydrogen bonds : bond 0.03074 / 2.11 ( 1056) hydrogen bonds : angle 4.86683 / 3.44 ( 3021) metal coordination : bond 0.00616 / 0.30 ( 14) metal coordination : angle 4.95100 / 4.02 ( 18) Misc. bond : bond 0.00282 / 0.13 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 395 ASP cc_start: 0.8795 (m-30) cc_final: 0.7588 (p0) REVERT: 2 418 TYR cc_start: 0.8902 (t80) cc_final: 0.8343 (t80) REVERT: 2 594 ASP cc_start: 0.8982 (t0) cc_final: 0.8695 (m-30) REVERT: 2 674 MET cc_start: 0.9060 (mmp) cc_final: 0.8615 (mmm) REVERT: 2 784 ASP cc_start: 0.8967 (p0) cc_final: 0.8645 (m-30) REVERT: 2 885 LEU cc_start: 0.8677 (mt) cc_final: 0.8278 (pp) REVERT: 6 111 TYR cc_start: 0.8061 (m-80) cc_final: 0.7613 (m-80) REVERT: 6 329 MET cc_start: 0.8790 (ppp) cc_final: 0.8221 (ppp) REVERT: 6 371 MET cc_start: 0.8531 (tpp) cc_final: 0.7934 (tpp) REVERT: 6 393 CYS cc_start: 0.8724 (t) cc_final: 0.8381 (t) REVERT: 6 465 MET cc_start: 0.8213 (tpt) cc_final: 0.7885 (tpp) REVERT: 6 527 MET cc_start: 0.9283 (mtp) cc_final: 0.8887 (mtp) REVERT: 6 757 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8058 (tp30) REVERT: 4 576 PHE cc_start: 0.9385 (t80) cc_final: 0.8880 (t80) REVERT: 7 177 MET cc_start: 0.8670 (pmm) cc_final: 0.8090 (pmm) REVERT: 7 443 CYS cc_start: 0.7769 (m) cc_final: 0.7514 (m) REVERT: 7 450 MET cc_start: 0.8469 (ppp) cc_final: 0.7854 (ppp) REVERT: 7 559 MET cc_start: 0.9042 (mmp) cc_final: 0.8724 (mmp) REVERT: 7 621 MET cc_start: 0.9078 (mmp) cc_final: 0.8855 (mmm) REVERT: 3 414 MET cc_start: 0.9148 (ppp) cc_final: 0.8478 (ppp) REVERT: 3 485 MET cc_start: 0.2533 (mtp) cc_final: 0.1391 (pmm) REVERT: 3 603 MET cc_start: 0.6860 (ppp) cc_final: 0.6353 (ppp) REVERT: 5 74 MET cc_start: 0.7912 (ptm) cc_final: 0.7417 (tmm) REVERT: 5 479 ASN cc_start: 0.8396 (m-40) cc_final: 0.8173 (m-40) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1609 time to fit residues: 47.0533 Evaluate side-chains 146 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 325 optimal weight: 20.0000 chunk 266 optimal weight: 0.2980 chunk 105 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 195 optimal weight: 20.0000 chunk 209 optimal weight: 0.4980 chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 199 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 646 ASN 4 242 ASN ** 4 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 629 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.050761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.037778 restraints weight = 279943.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.037872 restraints weight = 177952.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.037990 restraints weight = 148065.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.038269 restraints weight = 134737.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.038360 restraints weight = 120020.946| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 28662 Z= 0.116 Angle : 0.584 13.446 38872 Z= 0.289 Chirality : 0.042 0.175 4540 Planarity : 0.003 0.045 5050 Dihedral : 6.923 115.997 4094 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3636 helix: 0.70 (0.14), residues: 1450 sheet: -1.60 (0.22), residues: 469 loop : -1.00 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 3 478 TYR 0.027 0.001 TYR 6 347 PHE 0.034 0.001 PHE 3 411 TRP 0.009 0.001 TRP 2 569 HIS 0.004 0.001 HIS 5 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (28646) covalent geometry : angle 0.57382 / 0.29 (38854) hydrogen bonds : bond 0.03000 / 2.05 ( 1056) hydrogen bonds : angle 4.82888 / 3.41 ( 3021) metal coordination : bond 0.00660 / 0.33 ( 14) metal coordination : angle 4.95189 / 4.01 ( 18) Misc. bond : bond 0.00271 / 0.13 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4094.90 seconds wall clock time: 72 minutes 0.25 seconds (4320.25 seconds total)