Starting phenix.real_space_refine on Fri Jun 5 11:00:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rsh_54219/06_2026/9rsh_54219.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rsh_54219/06_2026/9rsh_54219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rsh_54219/06_2026/9rsh_54219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rsh_54219/06_2026/9rsh_54219.map" model { file = "/net/cci-nas-00/data/ceres_data/9rsh_54219/06_2026/9rsh_54219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rsh_54219/06_2026/9rsh_54219.cif" } resolution = 3.0 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= 0.025 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 108 5.16 5 C 12784 2.51 5 N 3268 2.21 5 O 3444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19608 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4901 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 24, 'TRANS': 578} Chain breaks: 8 Chain: "B" Number of atoms: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4901 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 24, 'TRANS': 578} Chain breaks: 8 Chain: "C" Number of atoms: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4901 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 24, 'TRANS': 578} Chain breaks: 8 Chain: "D" Number of atoms: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4901 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 24, 'TRANS': 578} Chain breaks: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 881 SG CYS A 176 106.106 59.212 50.489 1.00161.10 S ATOM 895 SG CYS A 178 108.944 60.524 48.174 1.00165.88 S ATOM 917 SG CYS A 181 105.188 61.552 47.628 1.00167.02 S ATOM 5782 SG CYS B 176 64.237 106.033 50.078 1.00171.89 S ATOM 5818 SG CYS B 181 61.551 104.333 48.192 1.00164.88 S ATOM 10683 SG CYS C 176 58.899 17.487 50.271 1.00151.37 S ATOM 10697 SG CYS C 178 61.271 15.345 48.361 1.00151.65 S ATOM 10719 SG CYS C 181 61.696 19.135 48.165 1.00151.07 S ATOM 15584 SG CYS D 176 17.815 64.328 50.087 1.00166.95 S ATOM 15620 SG CYS D 181 18.366 62.107 48.791 1.00167.22 S Time building chain proxies: 5.02, per 1000 atoms: 0.26 Number of scatterers: 19608 At special positions: 0 Unit cell: (124.122, 124.122, 124.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 108 16.00 O 3444 8.00 N 3268 7.00 C 12784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 845.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 176 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 181 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 178 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 801 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 176 " pdb=" ZN C 801 " pdb="ZN ZN C 801 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 176 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 181 " pdb=" ZN D 801 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 176 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 801 " - pdb=" ND1 HIS D 172 " Number of angles added : 6 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4656 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 4 sheets defined 78.5% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 34 through 42 removed outlier: 3.563A pdb=" N ASN A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 81 removed outlier: 3.560A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.826A pdb=" N LEU A 101 " --> pdb=" O GLY A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.806A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.609A pdb=" N GLN A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.572A pdb=" N ASP A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.623A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.517A pdb=" N GLN A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.568A pdb=" N ILE A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.682A pdb=" N LEU A 358 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 401 through 422 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 434 through 460 removed outlier: 3.541A pdb=" N MET A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.682A pdb=" N GLU A 468 " --> pdb=" O PRO A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 491 Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.924A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 3.543A pdb=" N GLN A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.709A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.693A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 614 Processing helix chain 'A' and resid 614 through 632 removed outlier: 3.530A pdb=" N ASN A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 649 Processing helix chain 'A' and resid 658 through 663 removed outlier: 4.272A pdb=" N ILE A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 732 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'B' and resid 73 through 81 removed outlier: 3.955A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 107 removed outlier: 3.505A pdb=" N LEU B 101 " --> pdb=" O GLY B 97 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.571A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 163 removed outlier: 3.605A pdb=" N GLN B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 removed outlier: 3.540A pdb=" N ASP B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.621A pdb=" N TYR B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 321 through 325 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.769A pdb=" N LEU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 359 removed outlier: 3.637A pdb=" N LEU B 358 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 384 Processing helix chain 'B' and resid 401 through 422 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 434 through 460 Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.705A pdb=" N GLU B 468 " --> pdb=" O PRO B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 491 Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.880A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 3.539A pdb=" N GLN B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 520 " --> pdb=" O ASP B 516 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 549 through 553 removed outlier: 3.513A pdb=" N CYS B 553 " --> pdb=" O PRO B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 580 removed outlier: 3.677A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.639A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 614 Processing helix chain 'B' and resid 614 through 649 removed outlier: 3.792A pdb=" N ASN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASP B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE B 637 " --> pdb=" O ASP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 663 removed outlier: 4.120A pdb=" N ILE B 663 " --> pdb=" O PRO B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 732 removed outlier: 3.578A pdb=" N HIS B 712 " --> pdb=" O ILE B 708 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 730 " --> pdb=" O ALA B 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.516A pdb=" N ASN C 38 " --> pdb=" O LYS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 removed outlier: 4.265A pdb=" N ILE C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 removed outlier: 3.564A pdb=" N LEU C 101 " --> pdb=" O GLY C 97 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 116 removed outlier: 4.041A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 removed outlier: 3.566A pdb=" N GLN C 163 " --> pdb=" O LYS C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.508A pdb=" N GLN C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 326 through 340 removed outlier: 3.536A pdb=" N ILE C 337 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 355 through 359 removed outlier: 3.718A pdb=" N LEU C 358 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 359 " --> pdb=" O LEU C 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 359' Processing helix chain 'C' and resid 362 through 384 Processing helix chain 'C' and resid 401 through 422 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 434 through 460 removed outlier: 3.551A pdb=" N MET C 438 " --> pdb=" O TRP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 removed outlier: 3.754A pdb=" N GLU C 468 " --> pdb=" O PRO C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 491 Processing helix chain 'C' and resid 492 through 500 removed outlier: 4.018A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 540 removed outlier: 4.074A pdb=" N LEU C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 520 " --> pdb=" O ASP C 516 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.510A pdb=" N CYS C 553 " --> pdb=" O PRO C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.612A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 614 Processing helix chain 'C' and resid 615 through 634 removed outlier: 4.337A pdb=" N ASP C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N HIS C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 649 Processing helix chain 'C' and resid 658 through 663 removed outlier: 4.204A pdb=" N ILE C 663 " --> pdb=" O PRO C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 732 Processing helix chain 'D' and resid 34 through 42 Processing helix chain 'D' and resid 72 through 81 removed outlier: 4.445A pdb=" N ILE D 76 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D 77 " --> pdb=" O ALA D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 107 removed outlier: 3.629A pdb=" N LEU D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 116 removed outlier: 3.729A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.578A pdb=" N GLN D 163 " --> pdb=" O LYS D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 213 removed outlier: 3.525A pdb=" N SER D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 234 removed outlier: 3.591A pdb=" N LYS D 232 " --> pdb=" O LYS D 228 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.717A pdb=" N TYR D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 340 through 351 Processing helix chain 'D' and resid 355 through 359 removed outlier: 3.720A pdb=" N LEU D 358 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 359 " --> pdb=" O LEU D 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 355 through 359' Processing helix chain 'D' and resid 362 through 384 Processing helix chain 'D' and resid 401 through 422 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 434 through 460 removed outlier: 3.552A pdb=" N MET D 438 " --> pdb=" O TRP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 removed outlier: 3.692A pdb=" N GLU D 468 " --> pdb=" O PRO D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 491 removed outlier: 3.573A pdb=" N ILE D 487 " --> pdb=" O ALA D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 500 removed outlier: 3.798A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 3.933A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 549 through 553 Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.644A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 614 Processing helix chain 'D' and resid 615 through 632 Processing helix chain 'D' and resid 634 through 649 Processing helix chain 'D' and resid 703 through 732 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 19 Processing sheet with id=AA4, first strand: chain 'C' and resid 167 through 168 1252 hydrogen bonds defined for protein. 3600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.37 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6157 1.34 - 1.46: 4712 1.46 - 1.58: 9003 1.58 - 1.70: 0 1.70 - 1.82: 176 Bond restraints: 20048 Sorted by residual: bond pdb=" N ASN D 551 " pdb=" CA ASN D 551 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.93e+00 bond pdb=" N GLU C 32 " pdb=" CA GLU C 32 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.84e+00 bond pdb=" N ARG C 24 " pdb=" CA ARG C 24 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.52e+00 bond pdb=" CB GLU B 240 " pdb=" CG GLU B 240 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" CB ASN B 625 " pdb=" CG ASN B 625 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.31e+00 ... (remaining 20043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 26915 2.61 - 5.23: 189 5.23 - 7.84: 41 7.84 - 10.45: 4 10.45 - 13.07: 3 Bond angle restraints: 27152 Sorted by residual: angle pdb=" C VAL C 23 " pdb=" N ARG C 24 " pdb=" CA ARG C 24 " ideal model delta sigma weight residual 121.54 132.01 -10.47 1.91e+00 2.74e-01 3.00e+01 angle pdb=" CA LEU C 29 " pdb=" CB LEU C 29 " pdb=" CG LEU C 29 " ideal model delta sigma weight residual 116.30 129.37 -13.07 3.50e+00 8.16e-02 1.39e+01 angle pdb=" CB MET A 619 " pdb=" CG MET A 619 " pdb=" SD MET A 619 " ideal model delta sigma weight residual 112.70 123.64 -10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" C GLU C 32 " pdb=" CA GLU C 32 " pdb=" CB GLU C 32 " ideal model delta sigma weight residual 110.42 117.63 -7.21 1.99e+00 2.53e-01 1.31e+01 angle pdb=" C VAL B 23 " pdb=" N ARG B 24 " pdb=" CA ARG B 24 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 ... (remaining 27147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10035 17.98 - 35.96: 1411 35.96 - 53.95: 452 53.95 - 71.93: 83 71.93 - 89.91: 27 Dihedral angle restraints: 12008 sinusoidal: 4892 harmonic: 7116 Sorted by residual: dihedral pdb=" CA LEU C 89 " pdb=" C LEU C 89 " pdb=" N LEU C 90 " pdb=" CA LEU C 90 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA MET B 513 " pdb=" C MET B 513 " pdb=" N LEU B 514 " pdb=" CA LEU B 514 " ideal model delta harmonic sigma weight residual 180.00 162.52 17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA LEU D 89 " pdb=" C LEU D 89 " pdb=" N LEU D 90 " pdb=" CA LEU D 90 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 12005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1991 0.031 - 0.061: 771 0.061 - 0.091: 238 0.091 - 0.122: 76 0.122 - 0.152: 16 Chirality restraints: 3092 Sorted by residual: chirality pdb=" CA PHE B 341 " pdb=" N PHE B 341 " pdb=" C PHE B 341 " pdb=" CB PHE B 341 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA PHE C 341 " pdb=" N PHE C 341 " pdb=" C PHE C 341 " pdb=" CB PHE C 341 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA PHE D 341 " pdb=" N PHE D 341 " pdb=" C PHE D 341 " pdb=" CB PHE D 341 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 3089 not shown) Planarity restraints: 3372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 36 " -0.014 2.00e-02 2.50e+03 1.83e-02 5.85e+00 pdb=" CG PHE D 36 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE D 36 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE D 36 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE D 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 36 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 36 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 397 " -0.038 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO C 398 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 398 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 398 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 397 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO B 398 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 398 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 398 " -0.031 5.00e-02 4.00e+02 ... (remaining 3369 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 122 2.69 - 3.24: 19530 3.24 - 3.79: 30887 3.79 - 4.35: 41031 4.35 - 4.90: 67071 Nonbonded interactions: 158641 Sorted by model distance: nonbonded pdb=" CD2 HIS D 172 " pdb="ZN ZN D 801 " model vdw 2.135 1.960 nonbonded pdb=" CB HIS D 172 " pdb="ZN ZN D 801 " model vdw 2.447 2.104 nonbonded pdb=" N GLU C 300 " pdb=" OE1 GLU C 300 " model vdw 2.495 3.120 nonbonded pdb=" N GLU A 236 " pdb=" OE1 GLU A 236 " model vdw 2.508 3.120 nonbonded pdb=" O ASN D 731 " pdb=" OD1 ASN D 731 " model vdw 2.568 3.040 ... (remaining 158636 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.970 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: 0.060 Set scattering table: 0.060 Process input model: 21.430 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.002 0.046 20066 Z= 0.109 Angle : 0.571 13.066 27166 Z= 0.282 Chirality : 0.038 0.152 3092 Planarity : 0.005 0.067 3372 Dihedral : 18.716 89.910 7340 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.82 % Allowed : 32.36 % Favored : 65.83 % 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: 0.53 (0.16), residues: 2340 helix: 0.67 (0.12), residues: 1640 sheet: None (None), residues: 0 loop : -0.16 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 263 TYR 0.020 0.001 TYR D 586 PHE 0.042 0.001 PHE D 36 TRP 0.016 0.001 TRP B 410 HIS 0.010 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (20048) covalent geometry : angle 0.56964 / 0.28 (27152) SS BOND : bond 0.00072 / 0.04 ( 4) SS BOND : angle 0.90142 / 0.45 ( 8) hydrogen bonds : bond 0.22868 / 15.40 ( 1252) hydrogen bonds : angle 6.46801 / 4.69 ( 3600) metal coordination : bond 0.00706 / 0.79 ( 14) metal coordination : angle 2.66561 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 456 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.7901 (ptt-90) cc_final: 0.7195 (ttm-80) REVERT: A 180 GLU cc_start: 0.7254 (pp20) cc_final: 0.7009 (pp20) REVERT: A 240 GLU cc_start: 0.7908 (mp0) cc_final: 0.7635 (mp0) REVERT: A 343 MET cc_start: 0.6797 (tpp) cc_final: 0.6386 (tpp) REVERT: A 386 GLN cc_start: 0.6986 (mp10) cc_final: 0.6755 (mp10) REVERT: A 404 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7088 (tm-30) REVERT: A 529 LEU cc_start: 0.8760 (mt) cc_final: 0.8507 (tt) REVERT: A 708 ILE cc_start: 0.7802 (mt) cc_final: 0.7580 (mt) REVERT: A 728 MET cc_start: 0.7479 (mmm) cc_final: 0.6765 (ppp) REVERT: B 229 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7225 (mt-10) REVERT: B 232 LYS cc_start: 0.8301 (mtmt) cc_final: 0.7928 (ptpp) REVERT: B 335 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6875 (mtt) REVERT: B 362 LYS cc_start: 0.6986 (mmtt) cc_final: 0.6698 (mttt) REVERT: B 406 MET cc_start: 0.7476 (mtm) cc_final: 0.6675 (mmm) REVERT: B 422 MET cc_start: 0.6199 (ttp) cc_final: 0.5677 (mmt) REVERT: B 439 ASP cc_start: 0.7520 (m-30) cc_final: 0.7193 (m-30) REVERT: B 443 ASN cc_start: 0.8119 (m-40) cc_final: 0.7684 (m110) REVERT: B 455 MET cc_start: 0.7360 (ttm) cc_final: 0.6977 (ttt) REVERT: B 468 GLU cc_start: 0.8350 (pm20) cc_final: 0.7997 (pm20) REVERT: B 518 LEU cc_start: 0.8515 (mp) cc_final: 0.8064 (tt) REVERT: B 519 LYS cc_start: 0.8243 (mttp) cc_final: 0.7835 (mtmm) REVERT: B 521 LEU cc_start: 0.8480 (tt) cc_final: 0.8188 (tt) REVERT: B 591 LYS cc_start: 0.8767 (tmtt) cc_final: 0.8547 (tmtp) REVERT: B 638 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7782 (mp0) REVERT: B 657 LEU cc_start: 0.7417 (mt) cc_final: 0.7145 (mt) REVERT: C 34 LYS cc_start: 0.6088 (ptmm) cc_final: 0.5664 (pmtt) REVERT: C 84 GLU cc_start: 0.4953 (OUTLIER) cc_final: 0.4619 (mm-30) REVERT: C 113 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6856 (mm-30) REVERT: C 156 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7557 (mm-30) REVERT: C 170 ARG cc_start: 0.7291 (ptt-90) cc_final: 0.6397 (ttm-80) REVERT: C 191 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7654 (ttm-80) REVERT: C 246 GLN cc_start: 0.8062 (mm110) cc_final: 0.7557 (mp10) REVERT: C 380 MET cc_start: 0.8479 (mmt) cc_final: 0.8198 (mmm) REVERT: C 404 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7225 (mt-10) REVERT: C 422 MET cc_start: 0.6091 (ttt) cc_final: 0.5578 (tpt) REVERT: C 454 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8516 (mp) REVERT: C 458 VAL cc_start: 0.8098 (t) cc_final: 0.7839 (m) REVERT: C 460 TYR cc_start: 0.6702 (m-80) cc_final: 0.6307 (m-80) REVERT: C 467 GLU cc_start: 0.8154 (pm20) cc_final: 0.7877 (pm20) REVERT: C 471 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7647 (tmm) REVERT: C 490 SER cc_start: 0.9329 (t) cc_final: 0.8984 (m) REVERT: C 513 MET cc_start: 0.6396 (ptp) cc_final: 0.6178 (pp-130) REVERT: C 567 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8375 (p) REVERT: C 619 MET cc_start: 0.7437 (tpp) cc_final: 0.6507 (tmm) REVERT: C 628 TYR cc_start: 0.7810 (t80) cc_final: 0.7144 (t80) REVERT: C 652 ASP cc_start: 0.7583 (m-30) cc_final: 0.6871 (p0) REVERT: C 708 ILE cc_start: 0.7614 (mm) cc_final: 0.7321 (tp) REVERT: C 711 GLN cc_start: 0.8166 (tp40) cc_final: 0.7862 (tm-30) REVERT: C 715 GLU cc_start: 0.8533 (tp30) cc_final: 0.8289 (tp30) REVERT: D 166 VAL cc_start: 0.8563 (t) cc_final: 0.8290 (m) REVERT: D 229 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7463 (mm-30) REVERT: D 238 LYS cc_start: 0.8266 (ttpp) cc_final: 0.7883 (ttmm) REVERT: D 243 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7289 (mt-10) REVERT: D 250 LEU cc_start: 0.7942 (tm) cc_final: 0.7345 (mm) REVERT: D 317 ASP cc_start: 0.8273 (t0) cc_final: 0.7865 (t0) REVERT: D 406 MET cc_start: 0.8355 (mtm) cc_final: 0.7827 (mtm) REVERT: D 439 ASP cc_start: 0.7227 (m-30) cc_final: 0.6918 (m-30) REVERT: D 467 GLU cc_start: 0.8487 (pt0) cc_final: 0.8190 (pt0) REVERT: D 490 SER cc_start: 0.9209 (t) cc_final: 0.8970 (m) REVERT: D 521 LEU cc_start: 0.8486 (tt) cc_final: 0.8170 (mm) REVERT: D 567 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8187 (p) REVERT: D 570 GLU cc_start: 0.8707 (tp30) cc_final: 0.8298 (mt-10) REVERT: D 619 MET cc_start: 0.7087 (tpp) cc_final: 0.6631 (ttp) REVERT: D 715 GLU cc_start: 0.8117 (tp30) cc_final: 0.7865 (tp30) REVERT: D 718 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8130 (ttp80) outliers start: 39 outliers final: 20 residues processed: 477 average time/residue: 0.5937 time to fit residues: 321.1877 Evaluate side-chains 452 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 426 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 638 GLU Chi-restraints excluded: chain D residue 656 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.4980 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN B 396 GLN C 38 ASN C 173 GLN C 618 ASN ** D 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 ASN D 625 ASN D 709 GLN D 711 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.157716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118041 restraints weight = 21007.168| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.12 r_work: 0.3113 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20066 Z= 0.151 Angle : 0.566 8.333 27166 Z= 0.286 Chirality : 0.040 0.195 3092 Planarity : 0.005 0.059 3372 Dihedral : 6.089 85.766 2631 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.73 % Allowed : 27.09 % Favored : 67.18 % 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: 1.59 (0.17), residues: 2340 helix: 1.55 (0.12), residues: 1692 sheet: None (None), residues: 0 loop : -0.15 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 222 TYR 0.013 0.001 TYR A 200 PHE 0.018 0.001 PHE D 341 TRP 0.012 0.001 TRP B 410 HIS 0.008 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (20048) covalent geometry : angle 0.56466 / 0.29 (27152) SS BOND : bond 0.00186 / 0.09 ( 4) SS BOND : angle 0.78814 / 0.45 ( 8) hydrogen bonds : bond 0.05185 / 3.52 ( 1252) hydrogen bonds : angle 4.04392 / 2.96 ( 3600) metal coordination : bond 0.00696 / 0.69 ( 14) metal coordination : angle 2.85375 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 447 time to evaluate : 0.599 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: A 180 GLU cc_start: 0.6848 (pp20) cc_final: 0.6502 (pm20) REVERT: A 186 GLU cc_start: 0.7615 (pp20) cc_final: 0.7393 (pp20) REVERT: A 211 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8082 (tt) REVERT: A 343 MET cc_start: 0.6691 (tpp) cc_final: 0.6213 (tpp) REVERT: A 359 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7235 (t80) REVERT: A 529 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8198 (tt) REVERT: A 537 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8244 (mm-40) REVERT: A 653 GLU cc_start: 0.7840 (tp30) cc_final: 0.7419 (tp30) REVERT: A 708 ILE cc_start: 0.7542 (mt) cc_final: 0.7318 (mt) REVERT: A 728 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6775 (ppp) REVERT: B 24 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.4981 (ptp90) REVERT: B 229 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7171 (mt-10) REVERT: B 250 LEU cc_start: 0.7428 (mt) cc_final: 0.7188 (mt) REVERT: B 362 LYS cc_start: 0.6806 (mmtt) cc_final: 0.6555 (mttt) REVERT: B 368 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7824 (mt) REVERT: B 406 MET cc_start: 0.7497 (mtm) cc_final: 0.6596 (mmm) REVERT: B 422 MET cc_start: 0.6071 (ttp) cc_final: 0.5512 (mmt) REVERT: B 442 MET cc_start: 0.8335 (ttt) cc_final: 0.8015 (ptp) REVERT: B 443 ASN cc_start: 0.8160 (m-40) cc_final: 0.7688 (m110) REVERT: B 455 MET cc_start: 0.7197 (ttm) cc_final: 0.6820 (ttt) REVERT: B 468 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8145 (pm20) REVERT: B 518 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7899 (tt) REVERT: B 519 LYS cc_start: 0.8072 (mttp) cc_final: 0.7710 (mptp) REVERT: B 521 LEU cc_start: 0.8139 (tt) cc_final: 0.7920 (tt) REVERT: B 591 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8505 (tmtp) REVERT: B 595 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7594 (mt-10) REVERT: B 657 LEU cc_start: 0.7581 (mt) cc_final: 0.7267 (mt) REVERT: C 17 ARG cc_start: 0.6087 (OUTLIER) cc_final: 0.5382 (tpm170) REVERT: C 138 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: C 156 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7519 (mm-30) REVERT: C 159 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8475 (ttpp) REVERT: C 191 ARG cc_start: 0.7667 (ttp80) cc_final: 0.7443 (ttm-80) REVERT: C 229 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: C 317 ASP cc_start: 0.8525 (t0) cc_final: 0.8314 (t0) REVERT: C 380 MET cc_start: 0.8161 (mmt) cc_final: 0.7889 (mmm) REVERT: C 404 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7315 (mt-10) REVERT: C 422 MET cc_start: 0.6103 (ttt) cc_final: 0.5541 (tpt) REVERT: C 464 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6399 (tmt90) REVERT: C 467 GLU cc_start: 0.8120 (pm20) cc_final: 0.7849 (pm20) REVERT: C 468 GLU cc_start: 0.8853 (pt0) cc_final: 0.8636 (pt0) REVERT: C 471 MET cc_start: 0.8032 (tpp) cc_final: 0.7697 (tmm) REVERT: C 490 SER cc_start: 0.9023 (t) cc_final: 0.8554 (m) REVERT: C 619 MET cc_start: 0.7343 (tpp) cc_final: 0.6567 (tmm) REVERT: C 627 SER cc_start: 0.6898 (m) cc_final: 0.6638 (t) REVERT: C 640 LYS cc_start: 0.8182 (mttt) cc_final: 0.7950 (mttp) REVERT: C 652 ASP cc_start: 0.7601 (m-30) cc_final: 0.6874 (p0) REVERT: C 711 GLN cc_start: 0.7899 (tp40) cc_final: 0.7567 (mt0) REVERT: D 108 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8028 (m) REVERT: D 228 LYS cc_start: 0.8440 (tppp) cc_final: 0.8220 (tttp) REVERT: D 229 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7530 (mm-30) REVERT: D 243 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7425 (mt-10) REVERT: D 250 LEU cc_start: 0.8040 (tm) cc_final: 0.7444 (mm) REVERT: D 309 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7760 (tp40) REVERT: D 317 ASP cc_start: 0.8328 (t0) cc_final: 0.7893 (t0) REVERT: D 406 MET cc_start: 0.8434 (mtm) cc_final: 0.8045 (mtm) REVERT: D 467 GLU cc_start: 0.8576 (pt0) cc_final: 0.8306 (pt0) REVERT: D 471 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.6997 (tpp) REVERT: D 490 SER cc_start: 0.9195 (t) cc_final: 0.8918 (m) REVERT: D 552 ASN cc_start: 0.7997 (m-40) cc_final: 0.7316 (t0) REVERT: D 567 THR cc_start: 0.8513 (m) cc_final: 0.8208 (p) REVERT: D 619 MET cc_start: 0.7248 (tpp) cc_final: 0.6849 (ttp) REVERT: D 652 ASP cc_start: 0.7945 (m-30) cc_final: 0.7658 (m-30) REVERT: D 718 ARG cc_start: 0.8483 (ttm110) cc_final: 0.7970 (ttp80) outliers start: 123 outliers final: 39 residues processed: 533 average time/residue: 0.5781 time to fit residues: 348.5093 Evaluate side-chains 455 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 400 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 729 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 144 optimal weight: 0.2980 chunk 139 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 551 ASN B 92 HIS B 173 GLN B 396 GLN B 486 ASN B 533 ASN C 173 GLN C 177 ASN C 246 GLN C 306 ASN D 163 GLN D 711 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.158175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118647 restraints weight = 21077.870| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.11 r_work: 0.3108 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20066 Z= 0.157 Angle : 0.557 8.943 27166 Z= 0.277 Chirality : 0.039 0.189 3092 Planarity : 0.005 0.059 3372 Dihedral : 5.469 85.780 2603 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.59 % Allowed : 27.70 % Favored : 66.71 % 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: 1.85 (0.17), residues: 2340 helix: 1.79 (0.12), residues: 1696 sheet: None (None), residues: 0 loop : -0.21 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 730 TYR 0.014 0.001 TYR A 200 PHE 0.019 0.001 PHE C 341 TRP 0.015 0.001 TRP C 315 HIS 0.005 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (20048) covalent geometry : angle 0.55552 / 0.28 (27152) SS BOND : bond 0.00197 / 0.10 ( 4) SS BOND : angle 0.68421 / 0.34 ( 8) hydrogen bonds : bond 0.04582 / 3.11 ( 1252) hydrogen bonds : angle 3.80536 / 2.78 ( 3600) metal coordination : bond 0.00665 / 0.62 ( 14) metal coordination : angle 2.82126 / 1.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 419 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8140 (tt) REVERT: A 343 MET cc_start: 0.6705 (tpp) cc_final: 0.6212 (tpp) REVERT: A 382 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7670 (mt) REVERT: A 392 ASP cc_start: 0.5544 (p0) cc_final: 0.5130 (p0) REVERT: A 537 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8219 (mm-40) REVERT: A 653 GLU cc_start: 0.7824 (tp30) cc_final: 0.7613 (tp30) REVERT: A 728 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6790 (ppp) REVERT: B 24 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.4997 (ptp90) REVERT: B 229 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7118 (mt-10) REVERT: B 250 LEU cc_start: 0.7402 (mt) cc_final: 0.7188 (mp) REVERT: B 362 LYS cc_start: 0.6901 (mmtt) cc_final: 0.6620 (mttt) REVERT: B 406 MET cc_start: 0.7554 (mtm) cc_final: 0.6628 (mmm) REVERT: B 422 MET cc_start: 0.6128 (ttp) cc_final: 0.5541 (mmt) REVERT: B 443 ASN cc_start: 0.8212 (m-40) cc_final: 0.7809 (m110) REVERT: B 455 MET cc_start: 0.7243 (ttm) cc_final: 0.6872 (ttt) REVERT: B 468 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: B 518 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7876 (tt) REVERT: B 519 LYS cc_start: 0.8069 (mttp) cc_final: 0.7679 (mptp) REVERT: B 529 LEU cc_start: 0.8862 (tp) cc_final: 0.8648 (tm) REVERT: B 591 LYS cc_start: 0.8811 (tmtt) cc_final: 0.8566 (tmtp) REVERT: B 595 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7612 (mt-10) REVERT: B 598 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8533 (mt-10) REVERT: B 657 LEU cc_start: 0.7719 (mt) cc_final: 0.7371 (mt) REVERT: C 159 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8507 (ttpp) REVERT: C 166 VAL cc_start: 0.8992 (p) cc_final: 0.8608 (m) REVERT: C 175 ARG cc_start: 0.7127 (ptp90) cc_final: 0.6859 (ptp90) REVERT: C 317 ASP cc_start: 0.8622 (t0) cc_final: 0.8421 (t0) REVERT: C 380 MET cc_start: 0.8171 (mmt) cc_final: 0.7839 (mmm) REVERT: C 404 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7641 (mt-10) REVERT: C 422 MET cc_start: 0.5857 (ttt) cc_final: 0.5454 (tpt) REVERT: C 464 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6430 (tmt90) REVERT: C 467 GLU cc_start: 0.8133 (pm20) cc_final: 0.7868 (pm20) REVERT: C 471 MET cc_start: 0.8131 (tpp) cc_final: 0.7767 (tmm) REVERT: C 490 SER cc_start: 0.9050 (t) cc_final: 0.8563 (m) REVERT: C 619 MET cc_start: 0.7467 (tpp) cc_final: 0.6870 (tmm) REVERT: C 640 LYS cc_start: 0.8205 (mttt) cc_final: 0.7946 (mttp) REVERT: C 711 GLN cc_start: 0.7860 (tp40) cc_final: 0.7615 (mt0) REVERT: D 108 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8152 (m) REVERT: D 174 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7272 (tp) REVERT: D 229 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7598 (mm-30) REVERT: D 243 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7436 (tp30) REVERT: D 250 LEU cc_start: 0.8081 (tm) cc_final: 0.7782 (tp) REVERT: D 309 GLN cc_start: 0.8139 (mt0) cc_final: 0.7758 (tp40) REVERT: D 317 ASP cc_start: 0.8393 (t0) cc_final: 0.7984 (t0) REVERT: D 467 GLU cc_start: 0.8580 (pt0) cc_final: 0.8311 (pt0) REVERT: D 471 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7079 (tpp) REVERT: D 490 SER cc_start: 0.9231 (t) cc_final: 0.8933 (m) REVERT: D 552 ASN cc_start: 0.7994 (m-40) cc_final: 0.7363 (t0) REVERT: D 567 THR cc_start: 0.8524 (m) cc_final: 0.8249 (p) REVERT: D 619 MET cc_start: 0.7394 (tpp) cc_final: 0.7027 (ttp) REVERT: D 715 GLU cc_start: 0.7921 (tp30) cc_final: 0.7650 (mm-30) REVERT: D 718 ARG cc_start: 0.8517 (ttm110) cc_final: 0.8015 (ttp80) outliers start: 120 outliers final: 52 residues processed: 491 average time/residue: 0.5558 time to fit residues: 310.1200 Evaluate side-chains 467 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 404 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 GLN Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 656 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 152 optimal weight: 0.6980 chunk 73 optimal weight: 0.1980 chunk 108 optimal weight: 0.9990 chunk 237 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 71 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN B 92 HIS B 396 GLN B 486 ASN B 533 ASN C 82 ASN C 173 GLN C 537 GLN C 626 ASN D 163 GLN D 711 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.159086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.119753 restraints weight = 21003.576| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.10 r_work: 0.3137 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20066 Z= 0.126 Angle : 0.536 9.487 27166 Z= 0.264 Chirality : 0.038 0.185 3092 Planarity : 0.005 0.060 3372 Dihedral : 5.087 86.022 2598 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.54 % Allowed : 28.26 % Favored : 66.20 % 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: 2.07 (0.17), residues: 2340 helix: 1.98 (0.12), residues: 1696 sheet: None (None), residues: 0 loop : -0.21 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 222 TYR 0.015 0.001 TYR D 348 PHE 0.019 0.001 PHE C 341 TRP 0.014 0.001 TRP C 315 HIS 0.004 0.000 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (20048) covalent geometry : angle 0.53444 / 0.26 (27152) SS BOND : bond 0.00151 / 0.08 ( 4) SS BOND : angle 0.57860 / 0.31 ( 8) hydrogen bonds : bond 0.04064 / 2.76 ( 1252) hydrogen bonds : angle 3.68555 / 2.69 ( 3600) metal coordination : bond 0.00490 / 0.43 ( 14) metal coordination : angle 2.33772 / 1.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 408 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8106 (tt) REVERT: A 343 MET cc_start: 0.6653 (tpp) cc_final: 0.6174 (tpp) REVERT: A 359 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7241 (t80) REVERT: A 382 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7653 (mt) REVERT: A 392 ASP cc_start: 0.5547 (p0) cc_final: 0.5120 (p0) REVERT: A 510 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7931 (mp) REVERT: A 537 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8186 (mm-40) REVERT: A 653 GLU cc_start: 0.7819 (tp30) cc_final: 0.7612 (tp30) REVERT: A 728 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.6720 (ppp) REVERT: B 24 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.4948 (ptp90) REVERT: B 229 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7082 (mt-10) REVERT: B 362 LYS cc_start: 0.6936 (mmtt) cc_final: 0.6660 (mttt) REVERT: B 386 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6262 (mp10) REVERT: B 396 GLN cc_start: 0.7387 (mt0) cc_final: 0.6792 (mt0) REVERT: B 406 MET cc_start: 0.7481 (mtm) cc_final: 0.6569 (mmm) REVERT: B 422 MET cc_start: 0.5934 (ttp) cc_final: 0.5413 (mmt) REVERT: B 455 MET cc_start: 0.7229 (ttm) cc_final: 0.6852 (ttt) REVERT: B 468 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: B 518 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7757 (tt) REVERT: B 519 LYS cc_start: 0.7997 (mttp) cc_final: 0.7665 (mptp) REVERT: B 529 LEU cc_start: 0.8848 (tp) cc_final: 0.8570 (tm) REVERT: B 536 ASN cc_start: 0.9070 (t0) cc_final: 0.8757 (t160) REVERT: B 591 LYS cc_start: 0.8835 (tmtt) cc_final: 0.8611 (tmtt) REVERT: B 595 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7524 (mt-10) REVERT: B 598 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8423 (mt-10) REVERT: B 619 MET cc_start: 0.7392 (tpp) cc_final: 0.7062 (tpp) REVERT: B 657 LEU cc_start: 0.7772 (mt) cc_final: 0.7449 (mt) REVERT: C 166 VAL cc_start: 0.8988 (p) cc_final: 0.8638 (m) REVERT: C 317 ASP cc_start: 0.8580 (t0) cc_final: 0.8342 (t0) REVERT: C 380 MET cc_start: 0.8165 (mmt) cc_final: 0.7875 (mmm) REVERT: C 404 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7647 (mt-10) REVERT: C 422 MET cc_start: 0.5761 (ttt) cc_final: 0.5330 (tpt) REVERT: C 464 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6322 (tmt90) REVERT: C 467 GLU cc_start: 0.8139 (pm20) cc_final: 0.7878 (pm20) REVERT: C 471 MET cc_start: 0.8172 (tpp) cc_final: 0.7800 (tmm) REVERT: C 490 SER cc_start: 0.9050 (t) cc_final: 0.8545 (m) REVERT: C 613 LEU cc_start: 0.7827 (mt) cc_final: 0.7483 (mt) REVERT: C 619 MET cc_start: 0.7440 (tpp) cc_final: 0.6817 (tmm) REVERT: C 640 LYS cc_start: 0.8192 (mttt) cc_final: 0.7938 (mttp) REVERT: D 108 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8186 (m) REVERT: D 174 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7253 (tp) REVERT: D 228 LYS cc_start: 0.8349 (tppp) cc_final: 0.8137 (tttp) REVERT: D 229 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7582 (mm-30) REVERT: D 243 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7114 (mm-30) REVERT: D 250 LEU cc_start: 0.8104 (tm) cc_final: 0.7755 (tp) REVERT: D 309 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7617 (tp40) REVERT: D 317 ASP cc_start: 0.8406 (t0) cc_final: 0.7979 (t0) REVERT: D 406 MET cc_start: 0.8420 (mtm) cc_final: 0.7847 (mtm) REVERT: D 467 GLU cc_start: 0.8556 (pt0) cc_final: 0.8347 (pt0) REVERT: D 471 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7099 (tpp) REVERT: D 490 SER cc_start: 0.9248 (t) cc_final: 0.8922 (m) REVERT: D 529 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8133 (mm) REVERT: D 552 ASN cc_start: 0.7959 (m-40) cc_final: 0.7398 (t0) REVERT: D 567 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8256 (p) REVERT: D 619 MET cc_start: 0.7445 (tpp) cc_final: 0.7185 (ttp) REVERT: D 652 ASP cc_start: 0.7937 (m-30) cc_final: 0.7655 (m-30) REVERT: D 715 GLU cc_start: 0.7881 (tp30) cc_final: 0.7600 (mm-30) REVERT: D 718 ARG cc_start: 0.8460 (ttm110) cc_final: 0.8008 (ttp80) outliers start: 119 outliers final: 50 residues processed: 481 average time/residue: 0.5605 time to fit residues: 306.6071 Evaluate side-chains 451 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 385 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 GLN Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 729 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 196 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 161 optimal weight: 0.0770 chunk 98 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN A 537 GLN A 551 ASN B 92 HIS B 443 ASN B 533 ASN C 173 GLN C 537 GLN D 163 GLN D 711 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.157894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.118753 restraints weight = 21052.857| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.08 r_work: 0.3018 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20066 Z= 0.143 Angle : 0.549 10.705 27166 Z= 0.269 Chirality : 0.039 0.192 3092 Planarity : 0.005 0.060 3372 Dihedral : 4.908 86.125 2595 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 6.24 % Allowed : 27.79 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.17), residues: 2340 helix: 2.04 (0.12), residues: 1696 sheet: None (None), residues: 0 loop : -0.23 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 222 TYR 0.020 0.001 TYR D 348 PHE 0.018 0.001 PHE C 341 TRP 0.016 0.001 TRP C 315 HIS 0.004 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (20048) covalent geometry : angle 0.54754 / 0.27 (27152) SS BOND : bond 0.00234 / 0.12 ( 4) SS BOND : angle 0.70043 / 0.34 ( 8) hydrogen bonds : bond 0.04036 / 2.73 ( 1252) hydrogen bonds : angle 3.61878 / 2.64 ( 3600) metal coordination : bond 0.00545 / 0.45 ( 14) metal coordination : angle 2.46331 / 1.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 390 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7082 (pp20) REVERT: A 343 MET cc_start: 0.6535 (tpp) cc_final: 0.6070 (tpp) REVERT: A 359 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7150 (t80) REVERT: A 382 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7560 (mt) REVERT: A 392 ASP cc_start: 0.5651 (p0) cc_final: 0.5182 (p0) REVERT: A 404 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6702 (tm-30) REVERT: A 510 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7882 (mp) REVERT: A 529 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8207 (tm) REVERT: A 537 GLN cc_start: 0.8557 (mm110) cc_final: 0.8005 (mm-40) REVERT: A 549 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7686 (mm-30) REVERT: A 728 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.6655 (ppp) REVERT: B 24 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.4896 (ptp90) REVERT: B 33 GLU cc_start: 0.5401 (OUTLIER) cc_final: 0.4284 (pp20) REVERT: B 88 LEU cc_start: 0.5532 (OUTLIER) cc_final: 0.5303 (tt) REVERT: B 92 HIS cc_start: 0.5592 (OUTLIER) cc_final: 0.5387 (t-170) REVERT: B 229 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7050 (mt-10) REVERT: B 362 LYS cc_start: 0.6909 (mmtt) cc_final: 0.6601 (mttt) REVERT: B 386 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6153 (mp10) REVERT: B 406 MET cc_start: 0.7405 (mtm) cc_final: 0.6531 (mmm) REVERT: B 422 MET cc_start: 0.5988 (ttp) cc_final: 0.5457 (mmt) REVERT: B 455 MET cc_start: 0.7134 (ttm) cc_final: 0.6756 (ttt) REVERT: B 468 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: B 518 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7729 (tt) REVERT: B 519 LYS cc_start: 0.7966 (mttp) cc_final: 0.7609 (mptp) REVERT: B 529 LEU cc_start: 0.8776 (tp) cc_final: 0.8555 (tm) REVERT: B 536 ASN cc_start: 0.9038 (t0) cc_final: 0.8734 (t160) REVERT: B 591 LYS cc_start: 0.8891 (tmtt) cc_final: 0.8661 (tmtt) REVERT: B 595 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7444 (mt-10) REVERT: B 598 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8380 (mt-10) REVERT: B 657 LEU cc_start: 0.7788 (mt) cc_final: 0.7506 (mt) REVERT: C 166 VAL cc_start: 0.8937 (p) cc_final: 0.8597 (m) REVERT: C 178 CYS cc_start: 0.4485 (OUTLIER) cc_final: 0.4102 (p) REVERT: C 317 ASP cc_start: 0.8598 (t0) cc_final: 0.8349 (t0) REVERT: C 380 MET cc_start: 0.8118 (mmt) cc_final: 0.7845 (mmm) REVERT: C 386 GLN cc_start: 0.6380 (OUTLIER) cc_final: 0.5495 (mp10) REVERT: C 404 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7646 (mt-10) REVERT: C 422 MET cc_start: 0.5772 (ttt) cc_final: 0.5231 (tpt) REVERT: C 464 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6212 (tmt90) REVERT: C 467 GLU cc_start: 0.8176 (pm20) cc_final: 0.7908 (pm20) REVERT: C 471 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7803 (tmm) REVERT: C 490 SER cc_start: 0.9010 (t) cc_final: 0.8506 (m) REVERT: C 619 MET cc_start: 0.7478 (tpp) cc_final: 0.6873 (tmm) REVERT: C 640 LYS cc_start: 0.8049 (mttt) cc_final: 0.7802 (mttp) REVERT: D 108 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8137 (m) REVERT: D 170 ARG cc_start: 0.7193 (ptt-90) cc_final: 0.6636 (ttm-80) REVERT: D 174 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7283 (tp) REVERT: D 229 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7554 (mm-30) REVERT: D 243 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7052 (mm-30) REVERT: D 250 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7676 (tp) REVERT: D 317 ASP cc_start: 0.8411 (t0) cc_final: 0.7953 (t0) REVERT: D 406 MET cc_start: 0.8394 (mtm) cc_final: 0.7820 (mtm) REVERT: D 471 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7131 (tpp) REVERT: D 490 SER cc_start: 0.9182 (t) cc_final: 0.8721 (m) REVERT: D 529 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8040 (mm) REVERT: D 541 TYR cc_start: 0.8449 (m-80) cc_final: 0.8243 (m-80) REVERT: D 547 ILE cc_start: 0.8776 (mp) cc_final: 0.8545 (pt) REVERT: D 552 ASN cc_start: 0.7914 (m-40) cc_final: 0.7335 (t0) REVERT: D 567 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8171 (p) REVERT: D 718 ARG cc_start: 0.8378 (ttm110) cc_final: 0.8049 (ttp80) outliers start: 134 outliers final: 59 residues processed: 474 average time/residue: 0.5747 time to fit residues: 309.5645 Evaluate side-chains 459 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 376 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 GLN Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 729 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN B 92 HIS B 396 GLN B 533 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 537 GLN C 562 ASN D 163 GLN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 GLN D 711 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.156173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117817 restraints weight = 21571.421| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.03 r_work: 0.3064 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20066 Z= 0.164 Angle : 0.566 9.884 27166 Z= 0.277 Chirality : 0.040 0.213 3092 Planarity : 0.005 0.060 3372 Dihedral : 4.791 86.081 2592 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.59 % Allowed : 28.54 % Favored : 65.88 % 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: 2.13 (0.17), residues: 2340 helix: 2.05 (0.12), residues: 1696 sheet: None (None), residues: 0 loop : -0.27 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 730 TYR 0.023 0.001 TYR D 348 PHE 0.023 0.001 PHE A 341 TRP 0.017 0.001 TRP C 315 HIS 0.010 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (20048) covalent geometry : angle 0.56424 / 0.28 (27152) SS BOND : bond 0.00280 / 0.14 ( 4) SS BOND : angle 0.80783 / 0.39 ( 8) hydrogen bonds : bond 0.04099 / 2.78 ( 1252) hydrogen bonds : angle 3.62404 / 2.65 ( 3600) metal coordination : bond 0.00601 / 0.45 ( 14) metal coordination : angle 2.69587 / 1.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 387 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 MET cc_start: 0.6801 (tpp) cc_final: 0.6349 (tpp) REVERT: A 359 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7458 (t80) REVERT: A 382 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7957 (mt) REVERT: A 392 ASP cc_start: 0.5747 (p0) cc_final: 0.5324 (p0) REVERT: A 404 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: A 510 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8204 (mp) REVERT: A 537 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8166 (mm-40) REVERT: A 549 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7909 (mm-30) REVERT: A 728 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.6916 (ppp) REVERT: B 24 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.5036 (ptp90) REVERT: B 33 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.4267 (pp20) REVERT: B 229 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7331 (mt-10) REVERT: B 362 LYS cc_start: 0.7381 (mmtt) cc_final: 0.7090 (mttt) REVERT: B 386 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6532 (mp10) REVERT: B 396 GLN cc_start: 0.7456 (mt0) cc_final: 0.6920 (mt0) REVERT: B 404 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: B 406 MET cc_start: 0.7582 (mtm) cc_final: 0.6715 (mmm) REVERT: B 422 MET cc_start: 0.5954 (ttp) cc_final: 0.5524 (mmt) REVERT: B 455 MET cc_start: 0.7368 (ttm) cc_final: 0.6968 (ttt) REVERT: B 518 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8033 (tt) REVERT: B 519 LYS cc_start: 0.8200 (mttp) cc_final: 0.7838 (mptp) REVERT: B 529 LEU cc_start: 0.9019 (tp) cc_final: 0.8800 (tm) REVERT: B 536 ASN cc_start: 0.9162 (t0) cc_final: 0.8818 (t160) REVERT: B 591 LYS cc_start: 0.8863 (tmtt) cc_final: 0.8645 (tmtt) REVERT: B 595 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7626 (mt-10) REVERT: B 598 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8554 (mt-10) REVERT: B 657 LEU cc_start: 0.8065 (mt) cc_final: 0.7771 (mt) REVERT: C 166 VAL cc_start: 0.9087 (p) cc_final: 0.8810 (m) REVERT: C 178 CYS cc_start: 0.4975 (OUTLIER) cc_final: 0.4522 (p) REVERT: C 232 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7910 (mtmt) REVERT: C 317 ASP cc_start: 0.8679 (t0) cc_final: 0.8473 (t0) REVERT: C 380 MET cc_start: 0.8349 (mmt) cc_final: 0.8109 (mmm) REVERT: C 386 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.5963 (mp10) REVERT: C 422 MET cc_start: 0.5424 (ttt) cc_final: 0.5058 (tpt) REVERT: C 464 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6638 (tmt90) REVERT: C 467 GLU cc_start: 0.8235 (pm20) cc_final: 0.8032 (pm20) REVERT: C 471 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8008 (tmm) REVERT: C 490 SER cc_start: 0.9198 (t) cc_final: 0.8734 (m) REVERT: C 513 MET cc_start: 0.7344 (ptp) cc_final: 0.6901 (pp-130) REVERT: C 518 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8406 (tp) REVERT: C 619 MET cc_start: 0.7755 (tpp) cc_final: 0.7248 (tmm) REVERT: C 640 LYS cc_start: 0.8556 (mttt) cc_final: 0.8296 (mttp) REVERT: D 108 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8348 (m) REVERT: D 170 ARG cc_start: 0.7453 (ptt-90) cc_final: 0.6811 (ttp80) REVERT: D 174 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7476 (tp) REVERT: D 229 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7870 (mm-30) REVERT: D 232 LYS cc_start: 0.8326 (mtpp) cc_final: 0.8041 (mtmm) REVERT: D 243 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7353 (mm-30) REVERT: D 250 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8129 (tp) REVERT: D 317 ASP cc_start: 0.8553 (t0) cc_final: 0.8160 (t0) REVERT: D 406 MET cc_start: 0.8546 (mtm) cc_final: 0.8006 (mtm) REVERT: D 471 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7323 (tpp) REVERT: D 510 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7816 (mp) REVERT: D 547 ILE cc_start: 0.8937 (mp) cc_final: 0.8729 (pt) REVERT: D 552 ASN cc_start: 0.8151 (m-40) cc_final: 0.7497 (t0) REVERT: D 715 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7816 (pt0) REVERT: D 718 ARG cc_start: 0.8552 (ttm110) cc_final: 0.8270 (ttp80) outliers start: 120 outliers final: 63 residues processed: 463 average time/residue: 0.5810 time to fit residues: 305.2605 Evaluate side-chains 458 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 374 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 GLN Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 715 GLU Chi-restraints excluded: chain D residue 729 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 24 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 10 optimal weight: 0.0040 chunk 93 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 185 optimal weight: 0.6980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN B 533 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 GLN D 163 GLN D 507 GLN D 711 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.156548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.117886 restraints weight = 21191.846| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.06 r_work: 0.3097 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20066 Z= 0.155 Angle : 0.569 9.853 27166 Z= 0.277 Chirality : 0.040 0.218 3092 Planarity : 0.005 0.061 3372 Dihedral : 4.802 86.087 2592 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.87 % Allowed : 28.21 % Favored : 65.92 % 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: 2.19 (0.17), residues: 2340 helix: 2.11 (0.12), residues: 1692 sheet: None (None), residues: 0 loop : -0.29 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 730 TYR 0.025 0.001 TYR D 348 PHE 0.020 0.001 PHE A 341 TRP 0.018 0.001 TRP C 315 HIS 0.004 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (20048) covalent geometry : angle 0.56722 / 0.28 (27152) SS BOND : bond 0.00258 / 0.13 ( 4) SS BOND : angle 0.76626 / 0.36 ( 8) hydrogen bonds : bond 0.04022 / 2.73 ( 1252) hydrogen bonds : angle 3.62100 / 2.65 ( 3600) metal coordination : bond 0.00571 / 0.43 ( 14) metal coordination : angle 2.67664 / 1.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 388 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 MET cc_start: 0.6609 (tpp) cc_final: 0.6146 (tpp) REVERT: A 359 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7211 (t80) REVERT: A 382 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7627 (mt) REVERT: A 392 ASP cc_start: 0.5640 (p0) cc_final: 0.5193 (p0) REVERT: A 404 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6778 (tm-30) REVERT: A 450 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7427 (mp) REVERT: A 510 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7952 (mp) REVERT: A 537 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8078 (mm-40) REVERT: A 549 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 728 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6690 (ppp) REVERT: B 24 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.4902 (ptp90) REVERT: B 33 GLU cc_start: 0.5537 (OUTLIER) cc_final: 0.4412 (pp20) REVERT: B 229 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7112 (mt-10) REVERT: B 343 MET cc_start: 0.7576 (ptm) cc_final: 0.7175 (ptm) REVERT: B 362 LYS cc_start: 0.7165 (mmtt) cc_final: 0.6851 (mttt) REVERT: B 386 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6249 (mp10) REVERT: B 396 GLN cc_start: 0.7361 (mt0) cc_final: 0.6842 (mt0) REVERT: B 406 MET cc_start: 0.7355 (mtm) cc_final: 0.6491 (mmm) REVERT: B 422 MET cc_start: 0.5883 (ttp) cc_final: 0.5433 (mmt) REVERT: B 455 MET cc_start: 0.7102 (ttm) cc_final: 0.6715 (ttt) REVERT: B 457 TYR cc_start: 0.8214 (t80) cc_final: 0.7987 (t80) REVERT: B 518 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7808 (tt) REVERT: B 519 LYS cc_start: 0.7937 (mttp) cc_final: 0.7546 (ttpp) REVERT: B 529 LEU cc_start: 0.8827 (tp) cc_final: 0.8615 (tm) REVERT: B 536 ASN cc_start: 0.9070 (t0) cc_final: 0.8746 (t160) REVERT: B 591 LYS cc_start: 0.8903 (tmtt) cc_final: 0.8676 (tmtt) REVERT: B 595 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7357 (mt-10) REVERT: B 598 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8372 (mt-10) REVERT: B 657 LEU cc_start: 0.7977 (mt) cc_final: 0.7682 (mt) REVERT: C 87 GLU cc_start: 0.4719 (OUTLIER) cc_final: 0.3266 (pm20) REVERT: C 166 VAL cc_start: 0.8951 (p) cc_final: 0.8631 (m) REVERT: C 178 CYS cc_start: 0.4640 (OUTLIER) cc_final: 0.4242 (p) REVERT: C 317 ASP cc_start: 0.8622 (t0) cc_final: 0.8366 (t0) REVERT: C 380 MET cc_start: 0.8156 (mmt) cc_final: 0.7900 (mmm) REVERT: C 386 GLN cc_start: 0.6513 (OUTLIER) cc_final: 0.5612 (mp10) REVERT: C 422 MET cc_start: 0.5129 (ttt) cc_final: 0.4809 (tpt) REVERT: C 464 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6241 (tmt90) REVERT: C 467 GLU cc_start: 0.8247 (pm20) cc_final: 0.7995 (pm20) REVERT: C 471 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7841 (tmm) REVERT: C 490 SER cc_start: 0.9068 (t) cc_final: 0.8562 (m) REVERT: C 513 MET cc_start: 0.7303 (ptp) cc_final: 0.6751 (pp-130) REVERT: C 518 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8226 (tp) REVERT: C 619 MET cc_start: 0.7592 (tpp) cc_final: 0.7034 (tmm) REVERT: C 640 LYS cc_start: 0.8162 (mttt) cc_final: 0.7914 (mttp) REVERT: D 87 GLU cc_start: 0.5968 (OUTLIER) cc_final: 0.4806 (pm20) REVERT: D 108 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8238 (m) REVERT: D 170 ARG cc_start: 0.7266 (ptt-90) cc_final: 0.6603 (ttp80) REVERT: D 174 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7429 (tp) REVERT: D 229 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7655 (mm-30) REVERT: D 232 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7833 (mtmm) REVERT: D 243 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7096 (mm-30) REVERT: D 250 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7824 (tp) REVERT: D 317 ASP cc_start: 0.8480 (t0) cc_final: 0.8038 (t0) REVERT: D 406 MET cc_start: 0.8436 (mtm) cc_final: 0.7829 (mtm) REVERT: D 471 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7195 (tpp) REVERT: D 510 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7619 (mp) REVERT: D 529 LEU cc_start: 0.8611 (tm) cc_final: 0.8058 (mm) REVERT: D 547 ILE cc_start: 0.8812 (mp) cc_final: 0.8587 (pt) REVERT: D 552 ASN cc_start: 0.8029 (m-40) cc_final: 0.7370 (t0) REVERT: D 715 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: D 718 ARG cc_start: 0.8315 (ttm110) cc_final: 0.8028 (ttp80) outliers start: 126 outliers final: 65 residues processed: 471 average time/residue: 0.5781 time to fit residues: 309.7872 Evaluate side-chains 468 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 380 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 GLN Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 638 GLU Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 715 GLU Chi-restraints excluded: chain D residue 729 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 155 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 185 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 239 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 237 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 ASN B 533 ASN B 709 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 537 GLN D 163 GLN D 306 ASN D 711 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.156000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117353 restraints weight = 21006.200| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.05 r_work: 0.3012 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20066 Z= 0.165 Angle : 0.585 10.027 27166 Z= 0.285 Chirality : 0.040 0.222 3092 Planarity : 0.005 0.062 3372 Dihedral : 4.839 86.159 2592 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.26 % Allowed : 29.33 % Favored : 65.41 % 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: 2.18 (0.17), residues: 2340 helix: 2.11 (0.12), residues: 1692 sheet: None (None), residues: 0 loop : -0.32 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 730 TYR 0.027 0.001 TYR D 348 PHE 0.023 0.001 PHE B 237 TRP 0.019 0.001 TRP C 315 HIS 0.005 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (20048) covalent geometry : angle 0.58298 / 0.28 (27152) SS BOND : bond 0.00272 / 0.14 ( 4) SS BOND : angle 0.84220 / 0.39 ( 8) hydrogen bonds : bond 0.04072 / 2.76 ( 1252) hydrogen bonds : angle 3.60860 / 2.64 ( 3600) metal coordination : bond 0.00685 / 0.54 ( 14) metal coordination : angle 2.88363 / 1.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 386 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 MET cc_start: 0.6462 (tpp) cc_final: 0.6009 (tpp) REVERT: A 359 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.7038 (t80) REVERT: A 382 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7504 (mt) REVERT: A 392 ASP cc_start: 0.5653 (p0) cc_final: 0.5231 (p0) REVERT: A 404 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6641 (tm-30) REVERT: A 450 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7324 (mp) REVERT: A 510 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7844 (mp) REVERT: A 537 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8001 (mm-40) REVERT: A 549 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7675 (mm-30) REVERT: A 728 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6590 (ppp) REVERT: B 24 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.4812 (ptp90) REVERT: B 33 GLU cc_start: 0.5473 (OUTLIER) cc_final: 0.4380 (pp20) REVERT: B 137 SER cc_start: 0.7902 (t) cc_final: 0.7685 (p) REVERT: B 229 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7011 (mt-10) REVERT: B 362 LYS cc_start: 0.7013 (mmtt) cc_final: 0.6694 (mttt) REVERT: B 386 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6083 (mp10) REVERT: B 396 GLN cc_start: 0.7340 (mt0) cc_final: 0.6823 (mt0) REVERT: B 406 MET cc_start: 0.7236 (mtm) cc_final: 0.6403 (mmm) REVERT: B 422 MET cc_start: 0.5864 (ttp) cc_final: 0.5331 (mmt) REVERT: B 455 MET cc_start: 0.6980 (ttm) cc_final: 0.6597 (ttt) REVERT: B 457 TYR cc_start: 0.8143 (t80) cc_final: 0.7915 (t80) REVERT: B 518 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7638 (tt) REVERT: B 519 LYS cc_start: 0.7867 (mttp) cc_final: 0.7495 (ttpp) REVERT: B 529 LEU cc_start: 0.8710 (tp) cc_final: 0.8480 (tm) REVERT: B 591 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8655 (tmtt) REVERT: B 595 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7243 (mt-10) REVERT: B 598 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8300 (mt-10) REVERT: B 657 LEU cc_start: 0.7968 (mt) cc_final: 0.7700 (mt) REVERT: C 87 GLU cc_start: 0.4748 (OUTLIER) cc_final: 0.4220 (pm20) REVERT: C 166 VAL cc_start: 0.8840 (p) cc_final: 0.8507 (m) REVERT: C 232 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7717 (mtmt) REVERT: C 317 ASP cc_start: 0.8631 (t0) cc_final: 0.8382 (t0) REVERT: C 380 MET cc_start: 0.8037 (mmt) cc_final: 0.7778 (mmm) REVERT: C 386 GLN cc_start: 0.6327 (OUTLIER) cc_final: 0.5411 (mp10) REVERT: C 422 MET cc_start: 0.5218 (ttt) cc_final: 0.4828 (tpt) REVERT: C 464 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.4984 (tmt90) REVERT: C 467 GLU cc_start: 0.8221 (pm20) cc_final: 0.7948 (pm20) REVERT: C 471 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7758 (tmm) REVERT: C 490 SER cc_start: 0.8924 (t) cc_final: 0.8404 (m) REVERT: C 512 ARG cc_start: 0.7522 (tpp80) cc_final: 0.7052 (mmm-85) REVERT: C 513 MET cc_start: 0.7120 (ptp) cc_final: 0.6616 (pp-130) REVERT: C 518 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8105 (tp) REVERT: C 619 MET cc_start: 0.7480 (tpp) cc_final: 0.6912 (tmm) REVERT: C 640 LYS cc_start: 0.7929 (mttt) cc_final: 0.7692 (mttp) REVERT: D 87 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5220 (pm20) REVERT: D 108 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8144 (m) REVERT: D 170 ARG cc_start: 0.7219 (ptt-90) cc_final: 0.6511 (ttp80) REVERT: D 174 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7391 (tp) REVERT: D 229 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7500 (mm-30) REVERT: D 232 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7704 (mtmm) REVERT: D 243 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6990 (mm-30) REVERT: D 250 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7651 (tp) REVERT: D 309 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7601 (tp40) REVERT: D 317 ASP cc_start: 0.8445 (t0) cc_final: 0.8023 (t0) REVERT: D 406 MET cc_start: 0.8374 (mtm) cc_final: 0.7761 (mtm) REVERT: D 471 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7175 (tpp) REVERT: D 529 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7932 (mm) REVERT: D 547 ILE cc_start: 0.8736 (mp) cc_final: 0.8508 (pt) REVERT: D 552 ASN cc_start: 0.7978 (m-40) cc_final: 0.7347 (t0) REVERT: D 718 ARG cc_start: 0.8202 (ttm110) cc_final: 0.7919 (ttp80) outliers start: 113 outliers final: 63 residues processed: 460 average time/residue: 0.5988 time to fit residues: 311.7816 Evaluate side-chains 470 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 384 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 GLN Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 638 GLU Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 729 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 69 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 170 optimal weight: 0.3980 chunk 192 optimal weight: 2.9990 chunk 180 optimal weight: 0.0270 chunk 63 optimal weight: 0.5980 chunk 121 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 219 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN A 552 ASN B 533 ASN C 173 GLN C 246 GLN C 306 ASN D 163 GLN D 507 GLN D 711 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.157458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.119086 restraints weight = 20904.126| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.04 r_work: 0.3127 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20066 Z= 0.126 Angle : 0.567 9.928 27166 Z= 0.276 Chirality : 0.039 0.240 3092 Planarity : 0.005 0.067 3372 Dihedral : 4.790 86.141 2592 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.19 % Allowed : 30.49 % Favored : 65.32 % 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: 2.27 (0.17), residues: 2340 helix: 2.18 (0.12), residues: 1692 sheet: None (None), residues: 0 loop : -0.30 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 730 TYR 0.028 0.001 TYR D 348 PHE 0.020 0.001 PHE B 237 TRP 0.020 0.001 TRP C 315 HIS 0.005 0.000 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (20048) covalent geometry : angle 0.56595 / 0.28 (27152) SS BOND : bond 0.00208 / 0.10 ( 4) SS BOND : angle 0.67376 / 0.34 ( 8) hydrogen bonds : bond 0.03783 / 2.56 ( 1252) hydrogen bonds : angle 3.59120 / 2.63 ( 3600) metal coordination : bond 0.00494 / 0.42 ( 14) metal coordination : angle 2.35152 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 392 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 MET cc_start: 0.6685 (tpp) cc_final: 0.6207 (tpp) REVERT: A 359 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7264 (t80) REVERT: A 382 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7601 (mt) REVERT: A 392 ASP cc_start: 0.5685 (p0) cc_final: 0.5280 (p0) REVERT: A 404 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6779 (tm-30) REVERT: A 450 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7460 (mp) REVERT: A 510 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7970 (mp) REVERT: A 537 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8022 (mm-40) REVERT: A 549 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7621 (mm-30) REVERT: A 728 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.6677 (ppp) REVERT: B 24 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.4918 (ptp90) REVERT: B 33 GLU cc_start: 0.5504 (OUTLIER) cc_final: 0.5230 (pm20) REVERT: B 137 SER cc_start: 0.7920 (t) cc_final: 0.7696 (p) REVERT: B 229 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7096 (mt-10) REVERT: B 362 LYS cc_start: 0.7234 (mmtt) cc_final: 0.6903 (mttt) REVERT: B 386 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6230 (mp10) REVERT: B 396 GLN cc_start: 0.7402 (mt0) cc_final: 0.6882 (mt0) REVERT: B 406 MET cc_start: 0.7342 (mtm) cc_final: 0.6508 (mmm) REVERT: B 422 MET cc_start: 0.5896 (ttp) cc_final: 0.5428 (mmt) REVERT: B 455 MET cc_start: 0.7093 (ttm) cc_final: 0.6703 (ttt) REVERT: B 457 TYR cc_start: 0.8175 (t80) cc_final: 0.7961 (t80) REVERT: B 519 LYS cc_start: 0.7960 (mttp) cc_final: 0.7550 (ttpp) REVERT: B 536 ASN cc_start: 0.9056 (t0) cc_final: 0.8723 (t160) REVERT: B 591 LYS cc_start: 0.8889 (tmtt) cc_final: 0.8684 (tmtt) REVERT: B 595 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7317 (mt-10) REVERT: B 598 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8339 (mt-10) REVERT: B 657 LEU cc_start: 0.8040 (mt) cc_final: 0.7759 (mt) REVERT: C 87 GLU cc_start: 0.4655 (OUTLIER) cc_final: 0.2881 (pt0) REVERT: C 166 VAL cc_start: 0.8980 (p) cc_final: 0.8669 (m) REVERT: C 178 CYS cc_start: 0.4650 (OUTLIER) cc_final: 0.4240 (p) REVERT: C 380 MET cc_start: 0.8155 (mmt) cc_final: 0.7896 (mmm) REVERT: C 386 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.5644 (mp10) REVERT: C 422 MET cc_start: 0.5133 (ttt) cc_final: 0.4803 (tpt) REVERT: C 464 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.5039 (tmt90) REVERT: C 467 GLU cc_start: 0.8220 (pm20) cc_final: 0.7969 (pm20) REVERT: C 471 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7877 (tmm) REVERT: C 490 SER cc_start: 0.9044 (t) cc_final: 0.8517 (m) REVERT: C 512 ARG cc_start: 0.7540 (tpp80) cc_final: 0.7090 (mmm-85) REVERT: C 513 MET cc_start: 0.7106 (ptp) cc_final: 0.6810 (pp-130) REVERT: C 518 LEU cc_start: 0.8534 (tp) cc_final: 0.8258 (tp) REVERT: C 536 ASN cc_start: 0.9207 (t0) cc_final: 0.8923 (t0) REVERT: C 619 MET cc_start: 0.7562 (tpp) cc_final: 0.7034 (tmm) REVERT: C 640 LYS cc_start: 0.8170 (mttt) cc_final: 0.7928 (mttp) REVERT: D 108 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8261 (m) REVERT: D 170 ARG cc_start: 0.7315 (ptt-90) cc_final: 0.6618 (ttp80) REVERT: D 229 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7640 (mm-30) REVERT: D 232 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7835 (mtmm) REVERT: D 243 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7110 (mm-30) REVERT: D 250 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7810 (tp) REVERT: D 309 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7738 (tp40) REVERT: D 317 ASP cc_start: 0.8476 (t0) cc_final: 0.8074 (t0) REVERT: D 406 MET cc_start: 0.8454 (mtm) cc_final: 0.7849 (mtm) REVERT: D 421 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7562 (tm-30) REVERT: D 454 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7900 (mp) REVERT: D 510 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7736 (mp) REVERT: D 529 LEU cc_start: 0.8642 (tm) cc_final: 0.8075 (mm) REVERT: D 547 ILE cc_start: 0.8804 (mp) cc_final: 0.8585 (pt) REVERT: D 552 ASN cc_start: 0.8062 (m-40) cc_final: 0.7423 (t0) REVERT: D 623 MET cc_start: 0.6648 (ptt) cc_final: 0.6226 (ptt) REVERT: D 718 ARG cc_start: 0.8332 (ttm110) cc_final: 0.8047 (ttp80) outliers start: 90 outliers final: 52 residues processed: 449 average time/residue: 0.5685 time to fit residues: 290.2490 Evaluate side-chains 453 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 382 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 GLN Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 729 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 64 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.0270 chunk 58 optimal weight: 0.5980 chunk 97 optimal weight: 0.0870 chunk 152 optimal weight: 0.6980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN C 537 GLN D 163 GLN D 711 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.159304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120652 restraints weight = 21170.158| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.08 r_work: 0.3044 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20066 Z= 0.120 Angle : 0.569 10.101 27166 Z= 0.276 Chirality : 0.039 0.232 3092 Planarity : 0.005 0.069 3372 Dihedral : 4.753 86.088 2592 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.68 % Allowed : 31.10 % Favored : 65.22 % 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: 2.34 (0.17), residues: 2340 helix: 2.24 (0.12), residues: 1692 sheet: None (None), residues: 0 loop : -0.29 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 730 TYR 0.028 0.001 TYR D 348 PHE 0.020 0.001 PHE A 341 TRP 0.021 0.001 TRP C 315 HIS 0.004 0.000 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (20048) covalent geometry : angle 0.56798 / 0.28 (27152) SS BOND : bond 0.00199 / 0.10 ( 4) SS BOND : angle 0.64134 / 0.34 ( 8) hydrogen bonds : bond 0.03687 / 2.49 ( 1252) hydrogen bonds : angle 3.58002 / 2.62 ( 3600) metal coordination : bond 0.00428 / 0.37 ( 14) metal coordination : angle 2.14688 / 1.12 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 391 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 MET cc_start: 0.6489 (tpp) cc_final: 0.6024 (tpp) REVERT: A 359 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7106 (t80) REVERT: A 382 LEU cc_start: 0.7721 (mp) cc_final: 0.7480 (mt) REVERT: A 392 ASP cc_start: 0.5776 (p0) cc_final: 0.5355 (p0) REVERT: A 404 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: A 450 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7302 (mp) REVERT: A 510 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7688 (mp) REVERT: A 537 GLN cc_start: 0.8520 (mm-40) cc_final: 0.7490 (tm-30) REVERT: A 549 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 728 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.6592 (ppp) REVERT: B 24 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.4773 (ptp90) REVERT: B 229 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7066 (mt-10) REVERT: B 362 LYS cc_start: 0.7021 (mmtt) cc_final: 0.6690 (mttt) REVERT: B 386 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6047 (mp10) REVERT: B 396 GLN cc_start: 0.7380 (mt0) cc_final: 0.6846 (mt0) REVERT: B 406 MET cc_start: 0.7262 (mtm) cc_final: 0.6421 (mmm) REVERT: B 422 MET cc_start: 0.5911 (ttp) cc_final: 0.5422 (mmt) REVERT: B 455 MET cc_start: 0.6984 (ttm) cc_final: 0.6607 (ttt) REVERT: B 457 TYR cc_start: 0.8120 (t80) cc_final: 0.7916 (t80) REVERT: B 519 LYS cc_start: 0.7829 (mttp) cc_final: 0.7443 (ttpp) REVERT: B 591 LYS cc_start: 0.8873 (tmtt) cc_final: 0.8658 (tmtt) REVERT: B 595 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7175 (mt-10) REVERT: B 598 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8263 (mt-10) REVERT: B 657 LEU cc_start: 0.7928 (mt) cc_final: 0.7674 (mt) REVERT: C 84 GLU cc_start: 0.4961 (OUTLIER) cc_final: 0.4290 (mm-30) REVERT: C 87 GLU cc_start: 0.4701 (OUTLIER) cc_final: 0.2993 (pt0) REVERT: C 166 VAL cc_start: 0.8863 (p) cc_final: 0.8536 (m) REVERT: C 178 CYS cc_start: 0.4380 (OUTLIER) cc_final: 0.3997 (p) REVERT: C 380 MET cc_start: 0.8051 (mmt) cc_final: 0.7791 (mmm) REVERT: C 386 GLN cc_start: 0.6517 (OUTLIER) cc_final: 0.5611 (mp10) REVERT: C 422 MET cc_start: 0.5311 (ttt) cc_final: 0.4871 (tpt) REVERT: C 464 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.5019 (tmt90) REVERT: C 467 GLU cc_start: 0.8217 (pm20) cc_final: 0.7949 (pm20) REVERT: C 471 MET cc_start: 0.8105 (tpp) cc_final: 0.7734 (tmm) REVERT: C 490 SER cc_start: 0.8959 (t) cc_final: 0.8409 (m) REVERT: C 512 ARG cc_start: 0.7513 (tpp80) cc_final: 0.7056 (mmm-85) REVERT: C 513 MET cc_start: 0.7045 (ptp) cc_final: 0.6693 (pp-130) REVERT: C 518 LEU cc_start: 0.8359 (tp) cc_final: 0.8105 (tp) REVERT: C 619 MET cc_start: 0.7417 (tpp) cc_final: 0.6894 (tmm) REVERT: C 640 LYS cc_start: 0.7979 (mttt) cc_final: 0.7749 (mttp) REVERT: D 36 PHE cc_start: 0.4680 (p90) cc_final: 0.3616 (p90) REVERT: D 108 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8198 (m) REVERT: D 170 ARG cc_start: 0.7203 (ptt-90) cc_final: 0.6512 (ttp80) REVERT: D 229 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7537 (mm-30) REVERT: D 232 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7668 (mttm) REVERT: D 243 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7018 (mm-30) REVERT: D 250 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7638 (tp) REVERT: D 317 ASP cc_start: 0.8424 (t0) cc_final: 0.7997 (t0) REVERT: D 406 MET cc_start: 0.8388 (mtm) cc_final: 0.7758 (mtm) REVERT: D 421 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7492 (tm-30) REVERT: D 454 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7648 (mp) REVERT: D 510 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7699 (mp) REVERT: D 529 LEU cc_start: 0.8533 (tm) cc_final: 0.7934 (mm) REVERT: D 547 ILE cc_start: 0.8741 (mp) cc_final: 0.8536 (pt) REVERT: D 552 ASN cc_start: 0.7979 (m-40) cc_final: 0.7370 (t0) REVERT: D 623 MET cc_start: 0.6460 (ptt) cc_final: 0.6055 (ptt) REVERT: D 718 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7946 (ttp80) outliers start: 79 outliers final: 53 residues processed: 445 average time/residue: 0.5558 time to fit residues: 281.3251 Evaluate side-chains 449 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 380 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 GLN Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 729 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 209 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 158 optimal weight: 0.5980 chunk 167 optimal weight: 0.0970 chunk 228 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 214 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN A 552 ASN B 533 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 537 GLN D 163 GLN D 177 ASN D 507 GLN D 711 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.156893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.118440 restraints weight = 21203.473| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.06 r_work: 0.3152 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20066 Z= 0.142 Angle : 0.578 9.905 27166 Z= 0.281 Chirality : 0.039 0.228 3092 Planarity : 0.005 0.068 3372 Dihedral : 4.674 86.143 2589 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.10 % Allowed : 30.87 % Favored : 65.04 % 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: 2.28 (0.17), residues: 2340 helix: 2.20 (0.12), residues: 1692 sheet: None (None), residues: 0 loop : -0.32 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 730 TYR 0.028 0.001 TYR D 348 PHE 0.022 0.001 PHE B 237 TRP 0.021 0.001 TRP C 315 HIS 0.005 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (20048) covalent geometry : angle 0.57646 / 0.28 (27152) SS BOND : bond 0.00158 / 0.08 ( 4) SS BOND : angle 0.71083 / 0.36 ( 8) hydrogen bonds : bond 0.03845 / 2.60 ( 1252) hydrogen bonds : angle 3.57951 / 2.62 ( 3600) metal coordination : bond 0.00538 / 0.44 ( 14) metal coordination : angle 2.50439 / 1.33 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8133.40 seconds wall clock time: 139 minutes 18.51 seconds (8358.51 seconds total)