Starting phenix.real_space_refine on Fri Jun 5 08:24:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rsg_54218/06_2026/9rsg_54218.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rsg_54218/06_2026/9rsg_54218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rsg_54218/06_2026/9rsg_54218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rsg_54218/06_2026/9rsg_54218.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rsg_54218/06_2026/9rsg_54218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rsg_54218/06_2026/9rsg_54218.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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 112 5.16 5 C 12326 2.51 5 N 3121 2.21 5 O 3293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 18856 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4783 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 23, 'TRANS': 563} Chain breaks: 5 Chain: "B" Number of atoms: 4715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4715 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 23, 'TRANS': 555} Chain breaks: 5 Chain: "C" Number of atoms: 4696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4696 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 22, 'TRANS': 553} Chain breaks: 5 Chain: "D" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4658 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 22, 'TRANS': 548} Chain breaks: 5 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 730 SG CYS A 176 86.942 103.602 52.086 1.00138.98 S ATOM 744 SG CYS A 178 88.028 106.868 51.135 1.00144.26 S ATOM 766 SG CYS A 181 85.437 105.383 48.952 1.00136.28 S ATOM 5506 SG CYS B 176 109.624 46.183 52.110 1.00142.11 S ATOM 5520 SG CYS B 178 112.364 46.669 49.489 1.00139.19 S ATOM 5542 SG CYS B 181 110.049 49.461 50.144 1.00139.50 S ATOM 10221 SG CYS C 176 29.776 82.948 52.283 1.00119.42 S ATOM 10235 SG CYS C 178 26.953 82.160 49.991 1.00139.32 S ATOM 10257 SG CYS C 181 30.162 80.104 49.761 1.00128.53 S ATOM 14910 SG CYS D 178 53.014 23.081 51.020 1.00153.31 S ATOM 14932 SG CYS D 181 54.490 24.510 49.284 1.00150.42 S Time building chain proxies: 4.55, per 1000 atoms: 0.24 Number of scatterers: 18856 At special positions: 0 Unit cell: (134.808, 130.698, 126.588, 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 112 16.00 O 3293 8.00 N 3121 7.00 C 12326 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: 1.58 Conformation dependent library (CDL) restraints added in 760.5 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 178 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 176 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 181 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 178 " 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 176 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 181 " pdb=" ZN D 801 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 801 " - pdb=" ND1 HIS D 172 " Number of angles added : 9 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4468 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.550A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 92 removed outlier: 4.058A pdb=" N LEU A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.767A pdb=" N TYR A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.546A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 179 through 188 removed outlier: 3.556A pdb=" N SER A 184 " --> pdb=" O GLU A 180 " (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 removed outlier: 3.508A pdb=" N ALA A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 257 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 327 through 340 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 362 through 383 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: 3.726A pdb=" N MET A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.577A pdb=" N TRP A 469 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 500 removed outlier: 4.263A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 540 removed outlier: 3.885A pdb=" N LEU A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.771A 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 578 Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.563A 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 615 through 632 Processing helix chain 'A' and resid 634 through 649 Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 703 through 731 Processing helix chain 'B' and resid 72 through 79 removed outlier: 3.528A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 removed outlier: 3.683A pdb=" N LEU B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.706A pdb=" N TYR B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 118 removed outlier: 3.845A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.685A pdb=" N LYS B 164 " --> pdb=" O LEU B 160 " (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 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 315 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 355 through 359 removed outlier: 3.879A pdb=" N LEU B 358 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 383 Processing helix chain 'B' and resid 401 through 422 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 434 through 459 removed outlier: 3.533A pdb=" N MET B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.793A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 540 removed outlier: 4.227A pdb=" N LEU B 506 " --> pdb=" O HIS B 502 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 520 " --> pdb=" O ASP B 516 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 553 removed outlier: 3.765A pdb=" N CYS B 553 " --> pdb=" O PRO B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.533A 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 615 through 631 removed outlier: 4.302A pdb=" N ILE B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 652 removed outlier: 3.777A pdb=" N TYR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP B 652 " --> pdb=" O MET B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 731 Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 91 removed outlier: 3.896A pdb=" N LEU C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 89 " --> pdb=" O ILE C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 106 Processing helix chain 'C' and resid 109 through 118 removed outlier: 3.636A pdb=" N GLU C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 removed outlier: 3.599A 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 removed outlier: 3.669A pdb=" N LYS C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 258 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 removed outlier: 3.831A pdb=" N LEU C 311 " --> pdb=" O CYS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.650A pdb=" N ILE C 360 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 385 removed outlier: 4.044A pdb=" N SER C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 420 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 434 through 460 removed outlier: 3.638A pdb=" N MET C 438 " --> pdb=" O TRP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 491 removed outlier: 3.649A pdb=" N ALA C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 499 removed outlier: 3.872A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 540 removed outlier: 4.017A pdb=" N LEU C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE C 520 " --> pdb=" O ASP C 516 " (cutoff:3.500A) removed outlier: 3.651A 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 Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.636A 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 632 Processing helix chain 'C' and resid 634 through 649 Processing helix chain 'C' and resid 658 through 662 Processing helix chain 'C' and resid 705 through 731 removed outlier: 4.271A pdb=" N GLN C 709 " --> pdb=" O ASP C 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 removed outlier: 3.800A pdb=" N ILE D 76 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 77 " --> pdb=" O ALA D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.864A pdb=" N MET D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 109 through 117 removed outlier: 3.688A pdb=" N GLU D 113 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 152 Processing helix chain 'D' and resid 154 through 164 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 Processing helix chain 'D' and resid 215 through 234 removed outlier: 3.646A pdb=" N LYS D 232 " --> pdb=" O LYS D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.722A pdb=" N GLU D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.698A 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 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 removed outlier: 3.553A pdb=" N THR D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 350 Proline residue: D 342 - end of helix Processing helix chain 'D' and resid 362 through 385 removed outlier: 3.966A pdb=" N SER D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 422 removed outlier: 3.605A pdb=" N MET D 406 " --> pdb=" O VAL D 402 " (cutoff:3.500A) Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 434 through 460 removed outlier: 3.518A pdb=" N MET D 438 " --> pdb=" O TRP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 removed outlier: 3.559A pdb=" N GLU D 468 " --> pdb=" O PRO D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.673A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 499 " --> pdb=" O LEU D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 513 removed outlier: 4.141A pdb=" N LEU D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 540 removed outlier: 3.550A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 3.683A 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 removed outlier: 3.586A pdb=" N CYS D 553 " --> pdb=" O PRO D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 585 through 589 Processing helix chain 'D' and resid 594 through 623 removed outlier: 3.974A pdb=" N VAL D 614 " --> pdb=" O VAL D 610 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 615 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU D 617 " --> pdb=" O LEU D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 634 removed outlier: 3.778A pdb=" N ASP D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N HIS D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 649 Processing helix chain 'D' and resid 707 through 731 removed outlier: 3.695A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D 716 " --> pdb=" O HIS D 712 " (cutoff:3.500A) 1200 hydrogen bonds defined for protein. 3480 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: 3.10 Time building geometry restraints manager: 2.02 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: 5844 1.34 - 1.46: 3293 1.46 - 1.58: 9988 1.58 - 1.70: 0 1.70 - 1.82: 184 Bond restraints: 19309 Sorted by residual: bond pdb=" CB GLU D 81 " pdb=" CG GLU D 81 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.41e+00 bond pdb=" CB ASP A 317 " pdb=" CG ASP A 317 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.19e+00 bond pdb=" CB CYS A 178 " pdb=" SG CYS A 178 " ideal model delta sigma weight residual 1.808 1.775 0.033 3.30e-02 9.18e+02 1.02e+00 bond pdb=" N TRP B 322 " pdb=" CA TRP B 322 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 9.26e-01 bond pdb=" CB ASP B 633 " pdb=" CG ASP B 633 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.68e-01 ... (remaining 19304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 26021 2.82 - 5.64: 132 5.64 - 8.46: 25 8.46 - 11.28: 1 11.28 - 14.10: 2 Bond angle restraints: 26181 Sorted by residual: angle pdb=" CB GLU D 81 " pdb=" CG GLU D 81 " pdb=" CD GLU D 81 " ideal model delta sigma weight residual 112.60 119.42 -6.82 1.70e+00 3.46e-01 1.61e+01 angle pdb=" CA GLU D 81 " pdb=" CB GLU D 81 " pdb=" CG GLU D 81 " ideal model delta sigma weight residual 114.10 121.60 -7.50 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA LEU A 160 " pdb=" CB LEU A 160 " pdb=" CG LEU A 160 " ideal model delta sigma weight residual 116.30 129.10 -12.80 3.50e+00 8.16e-02 1.34e+01 angle pdb=" C LYS D 330 " pdb=" N LEU D 331 " pdb=" CA LEU D 331 " ideal model delta sigma weight residual 121.54 127.93 -6.39 1.91e+00 2.74e-01 1.12e+01 angle pdb=" CA GLN A 173 " pdb=" CB GLN A 173 " pdb=" CG GLN A 173 " ideal model delta sigma weight residual 114.10 120.69 -6.59 2.00e+00 2.50e-01 1.09e+01 ... (remaining 26176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 9739 18.00 - 35.99: 1291 35.99 - 53.99: 401 53.99 - 71.99: 56 71.99 - 89.99: 25 Dihedral angle restraints: 11512 sinusoidal: 4664 harmonic: 6848 Sorted by residual: dihedral pdb=" CA VAL B 182 " pdb=" C VAL B 182 " pdb=" N SER B 183 " pdb=" CA SER B 183 " ideal model delta harmonic sigma weight residual -180.00 -142.36 -37.64 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA CYS A 178 " pdb=" C CYS A 178 " pdb=" N VAL A 179 " pdb=" CA VAL A 179 " ideal model delta harmonic sigma weight residual 180.00 -149.96 -30.04 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA MET D 513 " pdb=" C MET D 513 " pdb=" N LEU D 514 " pdb=" CA LEU D 514 " ideal model delta harmonic sigma weight residual 180.00 157.06 22.94 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 11509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2515 0.052 - 0.104: 420 0.104 - 0.156: 36 0.156 - 0.208: 1 0.208 - 0.260: 1 Chirality restraints: 2973 Sorted by residual: chirality pdb=" CB VAL A 96 " pdb=" CA VAL A 96 " pdb=" CG1 VAL A 96 " pdb=" CG2 VAL A 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ASP B 633 " pdb=" N ASP B 633 " pdb=" C ASP B 633 " pdb=" CB ASP B 633 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CG LEU B 115 " pdb=" CB LEU B 115 " pdb=" CD1 LEU B 115 " pdb=" CD2 LEU B 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 2970 not shown) Planarity restraints: 3239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 397 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO C 398 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 398 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 398 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 397 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO A 398 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 398 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 398 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 464 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 465 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 465 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 465 " -0.027 5.00e-02 4.00e+02 ... (remaining 3236 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 9596 3.00 - 3.48: 19865 3.48 - 3.95: 30540 3.95 - 4.43: 36304 4.43 - 4.90: 56296 Nonbonded interactions: 152601 Sorted by model distance: nonbonded pdb=" O CYS A 178 " pdb=" N GLU A 180 " model vdw 2.529 3.120 nonbonded pdb=" O CYS D 176 " pdb=" OD1 ASN D 177 " model vdw 2.533 3.040 nonbonded pdb=" N GLN C 173 " pdb=" OE1 GLN C 173 " model vdw 2.577 3.120 nonbonded pdb=" N GLU D 81 " pdb=" OE1 GLU D 81 " model vdw 2.580 3.120 nonbonded pdb=" OD1 ASN A 562 " pdb=" N ASN A 563 " model vdw 2.603 3.120 ... (remaining 152596 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 71 through 117 or resid 136 through 272 or resid 287 throu \ gh 385 or resid 396 or resid 398 through 663 or resid 706 through 801)) selection = (chain 'B' and (resid 71 through 117 or resid 136 through 272 or resid 287 throu \ gh 385 or resid 396 or resid 398 through 663 or resid 706 through 801)) selection = (chain 'C' and (resid 71 through 117 or resid 136 through 385 or resid 396 or re \ sid 398 through 663 or resid 706 through 801)) selection = (chain 'D' and (resid 71 through 272 or resid 287 through 386 or resid 398 throu \ gh 801)) } 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: 5.920 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.190 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 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 : 0.003 0.039 19328 Z= 0.134 Angle : 0.538 14.103 26198 Z= 0.267 Chirality : 0.037 0.260 2973 Planarity : 0.004 0.054 3239 Dihedral : 18.006 89.986 7032 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.87 % Favored : 97.00 % Rotamer: Outliers : 1.40 % Allowed : 27.04 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.33 (0.17), residues: 2265 helix: 0.40 (0.12), residues: 1649 sheet: None (None), residues: 0 loop : 0.10 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 545 TYR 0.009 0.001 TYR B 316 PHE 0.025 0.001 PHE A 339 TRP 0.018 0.001 TRP B 315 HIS 0.003 0.000 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (19309) covalent geometry : angle 0.53033 / 0.27 (26181) SS BOND : bond 0.00179 / 0.09 ( 4) SS BOND : angle 0.40346 / 0.26 ( 8) hydrogen bonds : bond 0.23606 / 15.92 ( 1200) hydrogen bonds : angle 6.65520 / 4.78 ( 3480) metal coordination : bond 0.01351 / 0.86 ( 15) metal coordination : angle 4.77665 / 2.68 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 420 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6505 (ptm-80) REVERT: A 98 ASP cc_start: 0.8566 (p0) cc_final: 0.8292 (p0) REVERT: A 170 ARG cc_start: 0.8243 (mtp180) cc_final: 0.6911 (mtm-85) REVERT: A 227 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8187 (mp) REVERT: A 243 GLU cc_start: 0.8004 (tt0) cc_final: 0.7648 (tt0) REVERT: A 319 PHE cc_start: 0.7783 (m-80) cc_final: 0.7544 (m-80) REVERT: B 71 ARG cc_start: 0.7362 (mtm110) cc_final: 0.6192 (mtm-85) REVERT: B 109 VAL cc_start: 0.8903 (p) cc_final: 0.8572 (t) REVERT: B 240 GLU cc_start: 0.7840 (mp0) cc_final: 0.7575 (mp0) REVERT: B 406 MET cc_start: 0.7008 (ptp) cc_final: 0.6021 (mmp) REVERT: B 422 MET cc_start: 0.4445 (OUTLIER) cc_final: 0.3209 (tpp) REVERT: B 516 ASP cc_start: 0.8593 (t70) cc_final: 0.8201 (t70) REVERT: B 722 LYS cc_start: 0.8947 (ttpt) cc_final: 0.8680 (ttpp) REVERT: C 81 GLU cc_start: 0.8037 (pm20) cc_final: 0.7220 (pm20) REVERT: C 522 PHE cc_start: 0.7818 (m-80) cc_final: 0.7409 (t80) REVERT: C 653 GLU cc_start: 0.7047 (mp0) cc_final: 0.6735 (mp0) REVERT: C 711 GLN cc_start: 0.8347 (tp40) cc_final: 0.7983 (tm-30) REVERT: D 102 TYR cc_start: 0.8237 (m-80) cc_final: 0.7840 (m-80) REVERT: D 267 ILE cc_start: 0.8816 (mm) cc_final: 0.8481 (mt) REVERT: D 361 LYS cc_start: 0.7539 (mttp) cc_final: 0.7128 (mtmt) REVERT: D 422 MET cc_start: 0.7355 (mtm) cc_final: 0.7104 (mmt) REVERT: D 471 MET cc_start: 0.8625 (ttp) cc_final: 0.8378 (ttp) REVERT: D 516 ASP cc_start: 0.8186 (m-30) cc_final: 0.7976 (m-30) REVERT: D 522 PHE cc_start: 0.8509 (m-80) cc_final: 0.8086 (m-80) REVERT: D 623 MET cc_start: 0.6137 (mpp) cc_final: 0.5269 (mtt) outliers start: 29 outliers final: 20 residues processed: 437 average time/residue: 0.1499 time to fit residues: 97.9266 Evaluate side-chains 432 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 409 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 618 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.2980 chunk 200 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN B 625 ASN B 626 ASN C 594 HIS D 443 ASN D 629 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.133419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.097582 restraints weight = 20480.471| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.96 r_work: 0.2809 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19328 Z= 0.146 Angle : 0.541 14.504 26198 Z= 0.276 Chirality : 0.038 0.192 2973 Planarity : 0.004 0.054 3239 Dihedral : 5.461 56.597 2532 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.22 % Favored : 96.64 % Rotamer: Outliers : 3.24 % Allowed : 24.82 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.75 (0.18), residues: 2265 helix: 1.58 (0.12), residues: 1679 sheet: None (None), residues: 0 loop : 0.07 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 545 TYR 0.012 0.001 TYR B 200 PHE 0.015 0.001 PHE C 341 TRP 0.018 0.001 TRP B 315 HIS 0.003 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (19309) covalent geometry : angle 0.53526 / 0.28 (26181) SS BOND : bond 0.00163 / 0.08 ( 4) SS BOND : angle 0.43760 / 0.28 ( 8) hydrogen bonds : bond 0.05338 / 3.64 ( 1200) hydrogen bonds : angle 4.12079 / 2.93 ( 3480) metal coordination : bond 0.01298 / 0.75 ( 15) metal coordination : angle 4.33335 / 2.49 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 412 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8366 (m90) cc_final: 0.8129 (m90) REVERT: A 98 ASP cc_start: 0.8498 (p0) cc_final: 0.8230 (p0) REVERT: A 170 ARG cc_start: 0.8347 (mtp180) cc_final: 0.7088 (mtm-85) REVERT: A 319 PHE cc_start: 0.7756 (m-80) cc_final: 0.7495 (m-80) REVERT: A 513 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7889 (mmt) REVERT: B 71 ARG cc_start: 0.7224 (mtm110) cc_final: 0.6190 (mtm-85) REVERT: B 108 VAL cc_start: 0.8726 (p) cc_final: 0.8297 (m) REVERT: B 189 SER cc_start: 0.8803 (t) cc_final: 0.8508 (p) REVERT: B 234 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7327 (mm-30) REVERT: B 240 GLU cc_start: 0.7880 (mp0) cc_final: 0.7561 (mp0) REVERT: B 304 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: B 406 MET cc_start: 0.6813 (ptp) cc_final: 0.6055 (mmp) REVERT: B 516 ASP cc_start: 0.8624 (t70) cc_final: 0.8369 (t70) REVERT: B 545 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7421 (mtm-85) REVERT: B 623 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7548 (ptt) REVERT: B 722 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8700 (ttpp) REVERT: C 81 GLU cc_start: 0.8079 (pm20) cc_final: 0.7214 (pm20) REVERT: C 102 TYR cc_start: 0.8357 (m-80) cc_final: 0.8000 (m-80) REVERT: C 559 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8115 (mt-10) REVERT: C 653 GLU cc_start: 0.7091 (mp0) cc_final: 0.6785 (mp0) REVERT: C 662 ASN cc_start: 0.8145 (t0) cc_final: 0.7699 (t0) REVERT: C 722 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8839 (mtpp) REVERT: D 102 TYR cc_start: 0.8311 (m-80) cc_final: 0.7854 (m-80) REVERT: D 228 LYS cc_start: 0.8598 (tppt) cc_final: 0.8019 (tppt) REVERT: D 335 MET cc_start: 0.6700 (mmm) cc_final: 0.6214 (mmm) REVERT: D 361 LYS cc_start: 0.7594 (mttp) cc_final: 0.7144 (mtmt) REVERT: D 468 GLU cc_start: 0.8125 (mp0) cc_final: 0.7808 (mp0) REVERT: D 471 MET cc_start: 0.8585 (ttp) cc_final: 0.8373 (ttp) REVERT: D 623 MET cc_start: 0.6110 (mpp) cc_final: 0.5070 (mpt) outliers start: 67 outliers final: 36 residues processed: 449 average time/residue: 0.1516 time to fit residues: 102.5800 Evaluate side-chains 443 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 403 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 517 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 618 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 203 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN B 309 GLN B 552 ASN D 443 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.132867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.098082 restraints weight = 20802.449| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.80 r_work: 0.2798 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19328 Z= 0.155 Angle : 0.537 14.615 26198 Z= 0.271 Chirality : 0.039 0.199 2973 Planarity : 0.004 0.054 3239 Dihedral : 4.636 57.729 2498 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer: Outliers : 4.54 % Allowed : 23.85 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.12 (0.18), residues: 2265 helix: 1.91 (0.12), residues: 1683 sheet: None (None), residues: 0 loop : 0.02 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 545 TYR 0.017 0.001 TYR C 348 PHE 0.018 0.001 PHE C 341 TRP 0.021 0.001 TRP B 315 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (19309) covalent geometry : angle 0.53109 / 0.27 (26181) SS BOND : bond 0.00142 / 0.07 ( 4) SS BOND : angle 0.35995 / 0.24 ( 8) hydrogen bonds : bond 0.04757 / 3.25 ( 1200) hydrogen bonds : angle 3.81623 / 2.70 ( 3480) metal coordination : bond 0.01365 / 0.82 ( 15) metal coordination : angle 4.22130 / 2.47 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 412 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8287 (m90) cc_final: 0.8040 (m90) REVERT: A 98 ASP cc_start: 0.8514 (p0) cc_final: 0.8285 (p0) REVERT: A 170 ARG cc_start: 0.8416 (mtp180) cc_final: 0.7111 (mtm-85) REVERT: A 173 GLN cc_start: 0.7082 (tp-100) cc_final: 0.6336 (pt0) REVERT: A 319 PHE cc_start: 0.7686 (m-80) cc_final: 0.7383 (m-80) REVERT: A 324 ARG cc_start: 0.1121 (OUTLIER) cc_final: 0.0744 (mmt90) REVERT: A 361 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7994 (mttt) REVERT: A 380 MET cc_start: 0.8565 (mtp) cc_final: 0.8337 (mtt) REVERT: B 71 ARG cc_start: 0.7210 (mtm110) cc_final: 0.6140 (mtm-85) REVERT: B 82 ASN cc_start: 0.8127 (m-40) cc_final: 0.7877 (m-40) REVERT: B 108 VAL cc_start: 0.8711 (p) cc_final: 0.8316 (m) REVERT: B 176 CYS cc_start: 0.6578 (t) cc_final: 0.6317 (t) REVERT: B 189 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8458 (p) REVERT: B 234 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7293 (mm-30) REVERT: B 240 GLU cc_start: 0.7777 (mp0) cc_final: 0.7351 (mp0) REVERT: B 304 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: B 406 MET cc_start: 0.6649 (ptp) cc_final: 0.6009 (mmp) REVERT: B 516 ASP cc_start: 0.8577 (t70) cc_final: 0.8352 (t70) REVERT: B 545 ARG cc_start: 0.7982 (mtm-85) cc_final: 0.7562 (mtm-85) REVERT: B 722 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8558 (ttpp) REVERT: C 81 GLU cc_start: 0.8068 (pm20) cc_final: 0.7290 (pm20) REVERT: C 102 TYR cc_start: 0.8401 (m-80) cc_final: 0.8055 (m-80) REVERT: C 170 ARG cc_start: 0.8222 (ttp-110) cc_final: 0.6280 (ptp90) REVERT: C 222 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8205 (ttp80) REVERT: C 559 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8111 (mt-10) REVERT: C 638 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: C 653 GLU cc_start: 0.7041 (mp0) cc_final: 0.6727 (mp0) REVERT: C 662 ASN cc_start: 0.8125 (t0) cc_final: 0.7772 (t0) REVERT: C 722 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8790 (mtpp) REVERT: D 102 TYR cc_start: 0.8227 (m-80) cc_final: 0.7796 (m-80) REVERT: D 228 LYS cc_start: 0.8437 (tppt) cc_final: 0.7345 (ttpp) REVERT: D 335 MET cc_start: 0.6668 (mmm) cc_final: 0.6197 (mmm) REVERT: D 361 LYS cc_start: 0.7549 (mttp) cc_final: 0.7101 (mtmt) REVERT: D 468 GLU cc_start: 0.8088 (mp0) cc_final: 0.7726 (mp0) REVERT: D 471 MET cc_start: 0.8575 (ttp) cc_final: 0.8271 (ttp) REVERT: D 545 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7736 (mtm-85) REVERT: D 623 MET cc_start: 0.5996 (mpp) cc_final: 0.4976 (mpt) REVERT: D 730 ARG cc_start: 0.7715 (ttt90) cc_final: 0.7301 (ttt180) outliers start: 94 outliers final: 51 residues processed: 465 average time/residue: 0.1489 time to fit residues: 103.6271 Evaluate side-chains 450 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 392 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 562 ASN Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 182 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 GLN B 552 ASN C 625 ASN D 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.132649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.097103 restraints weight = 20860.303| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.92 r_work: 0.2766 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19328 Z= 0.174 Angle : 0.545 14.822 26198 Z= 0.275 Chirality : 0.039 0.205 2973 Planarity : 0.004 0.054 3239 Dihedral : 4.532 53.056 2495 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.31 % Favored : 96.56 % Rotamer: Outliers : 4.68 % Allowed : 23.76 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.22 (0.18), residues: 2265 helix: 1.98 (0.12), residues: 1687 sheet: None (None), residues: 0 loop : 0.04 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 730 TYR 0.019 0.001 TYR C 348 PHE 0.017 0.001 PHE C 341 TRP 0.021 0.001 TRP B 315 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (19309) covalent geometry : angle 0.53965 / 0.27 (26181) SS BOND : bond 0.00150 / 0.07 ( 4) SS BOND : angle 0.39124 / 0.26 ( 8) hydrogen bonds : bond 0.04591 / 3.14 ( 1200) hydrogen bonds : angle 3.73611 / 2.65 ( 3480) metal coordination : bond 0.01368 / 0.85 ( 15) metal coordination : angle 4.18079 / 2.47 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 404 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8309 (m90) cc_final: 0.8025 (m90) REVERT: A 98 ASP cc_start: 0.8544 (p0) cc_final: 0.8282 (p0) REVERT: A 170 ARG cc_start: 0.8461 (mtp180) cc_final: 0.7213 (mtm-85) REVERT: A 343 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7735 (ttm) REVERT: A 361 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8012 (mttt) REVERT: A 380 MET cc_start: 0.8596 (mtp) cc_final: 0.8368 (mtt) REVERT: B 71 ARG cc_start: 0.7273 (mtm110) cc_final: 0.6210 (mtm-85) REVERT: B 108 VAL cc_start: 0.8705 (p) cc_final: 0.8360 (m) REVERT: B 189 SER cc_start: 0.8782 (OUTLIER) cc_final: 0.8499 (p) REVERT: B 234 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7328 (mm-30) REVERT: B 240 GLU cc_start: 0.7834 (mp0) cc_final: 0.7435 (mp0) REVERT: B 304 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: B 406 MET cc_start: 0.6742 (ptp) cc_final: 0.6124 (mmp) REVERT: B 516 ASP cc_start: 0.8701 (t70) cc_final: 0.8496 (t70) REVERT: B 545 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7572 (mtm-85) REVERT: C 81 GLU cc_start: 0.8167 (pm20) cc_final: 0.7415 (pm20) REVERT: C 170 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.6348 (ptp90) REVERT: C 222 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8247 (ttp80) REVERT: C 620 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8343 (tp) REVERT: C 638 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: C 653 GLU cc_start: 0.7090 (mp0) cc_final: 0.6763 (mp0) REVERT: C 662 ASN cc_start: 0.8222 (t0) cc_final: 0.7871 (t0) REVERT: C 722 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8801 (mtpp) REVERT: D 102 TYR cc_start: 0.8293 (m-80) cc_final: 0.7823 (m-80) REVERT: D 228 LYS cc_start: 0.8452 (tppt) cc_final: 0.7370 (ttpp) REVERT: D 335 MET cc_start: 0.6690 (mmm) cc_final: 0.6226 (mmm) REVERT: D 350 ILE cc_start: 0.6565 (OUTLIER) cc_final: 0.6045 (tt) REVERT: D 361 LYS cc_start: 0.7587 (mttp) cc_final: 0.7169 (mtmt) REVERT: D 468 GLU cc_start: 0.8087 (mp0) cc_final: 0.7762 (mp0) REVERT: D 471 MET cc_start: 0.8612 (ttp) cc_final: 0.8298 (ttp) REVERT: D 623 MET cc_start: 0.6044 (mpp) cc_final: 0.5018 (mpt) outliers start: 97 outliers final: 63 residues processed: 460 average time/residue: 0.1496 time to fit residues: 102.9678 Evaluate side-chains 469 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 397 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 562 ASN Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 625 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 184 optimal weight: 0.9990 chunk 178 optimal weight: 0.0980 chunk 175 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 552 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.133542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.098174 restraints weight = 20716.755| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.91 r_work: 0.2784 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19328 Z= 0.143 Angle : 0.534 14.707 26198 Z= 0.266 Chirality : 0.038 0.215 2973 Planarity : 0.004 0.054 3239 Dihedral : 4.460 51.694 2495 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 4.64 % Allowed : 23.71 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.37 (0.18), residues: 2265 helix: 2.13 (0.12), residues: 1681 sheet: None (None), residues: 0 loop : -0.03 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 545 TYR 0.019 0.001 TYR C 348 PHE 0.017 0.001 PHE C 341 TRP 0.020 0.001 TRP B 315 HIS 0.004 0.000 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (19309) covalent geometry : angle 0.52879 / 0.27 (26181) SS BOND : bond 0.00162 / 0.08 ( 4) SS BOND : angle 0.34105 / 0.22 ( 8) hydrogen bonds : bond 0.04291 / 2.93 ( 1200) hydrogen bonds : angle 3.66689 / 2.60 ( 3480) metal coordination : bond 0.01248 / 0.83 ( 15) metal coordination : angle 4.06621 / 2.40 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 410 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8296 (m90) cc_final: 0.7994 (m90) REVERT: A 98 ASP cc_start: 0.8519 (p0) cc_final: 0.8253 (p0) REVERT: A 170 ARG cc_start: 0.8466 (mtp180) cc_final: 0.7217 (mtm-85) REVERT: A 380 MET cc_start: 0.8573 (mtp) cc_final: 0.8347 (mtt) REVERT: B 71 ARG cc_start: 0.7261 (mtm110) cc_final: 0.6185 (mtm-85) REVERT: B 108 VAL cc_start: 0.8738 (p) cc_final: 0.8403 (m) REVERT: B 189 SER cc_start: 0.8729 (t) cc_final: 0.8443 (p) REVERT: B 234 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 240 GLU cc_start: 0.7837 (mp0) cc_final: 0.7449 (mp0) REVERT: B 304 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: B 406 MET cc_start: 0.6621 (ptp) cc_final: 0.6080 (mmp) REVERT: B 516 ASP cc_start: 0.8704 (t70) cc_final: 0.8376 (t70) REVERT: B 521 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8061 (tp) REVERT: B 545 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7471 (mtm-85) REVERT: B 551 ASN cc_start: 0.8395 (t0) cc_final: 0.8094 (t0) REVERT: C 98 ASP cc_start: 0.7993 (t0) cc_final: 0.7684 (t0) REVERT: C 102 TYR cc_start: 0.8423 (m-80) cc_final: 0.8063 (m-80) REVERT: C 170 ARG cc_start: 0.8222 (ttp-110) cc_final: 0.6319 (ptp90) REVERT: C 222 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8246 (ttp80) REVERT: C 620 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8318 (tp) REVERT: C 636 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7916 (t0) REVERT: C 638 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8199 (mt-10) REVERT: C 653 GLU cc_start: 0.7043 (mp0) cc_final: 0.6733 (mp0) REVERT: C 662 ASN cc_start: 0.8217 (t0) cc_final: 0.7763 (t0) REVERT: C 722 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8823 (mtpp) REVERT: D 228 LYS cc_start: 0.8431 (tppt) cc_final: 0.7310 (ttpp) REVERT: D 242 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7857 (mm-30) REVERT: D 267 ILE cc_start: 0.8827 (mm) cc_final: 0.8535 (mt) REVERT: D 335 MET cc_start: 0.6658 (mmm) cc_final: 0.6193 (mmm) REVERT: D 350 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.5997 (tt) REVERT: D 361 LYS cc_start: 0.7568 (mttp) cc_final: 0.7117 (mtmt) REVERT: D 468 GLU cc_start: 0.8086 (mp0) cc_final: 0.7831 (mp0) REVERT: D 471 MET cc_start: 0.8594 (ttp) cc_final: 0.8314 (ttp) REVERT: D 545 ARG cc_start: 0.8028 (mtm-85) cc_final: 0.7807 (mtm-85) outliers start: 96 outliers final: 63 residues processed: 471 average time/residue: 0.1494 time to fit residues: 106.0070 Evaluate side-chains 465 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 394 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 562 ASN Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 132 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 178 optimal weight: 0.0040 chunk 220 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 204 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.133731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.098831 restraints weight = 20139.718| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.82 r_work: 0.2818 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19328 Z= 0.128 Angle : 0.518 14.261 26198 Z= 0.258 Chirality : 0.038 0.227 2973 Planarity : 0.004 0.054 3239 Dihedral : 4.381 51.033 2495 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 4.83 % Allowed : 23.61 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.52 (0.18), residues: 2265 helix: 2.27 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : -0.06 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 730 TYR 0.020 0.001 TYR C 348 PHE 0.018 0.001 PHE A 341 TRP 0.018 0.001 TRP A 315 HIS 0.004 0.000 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (19309) covalent geometry : angle 0.51318 / 0.26 (26181) SS BOND : bond 0.00149 / 0.07 ( 4) SS BOND : angle 0.26677 / 0.18 ( 8) hydrogen bonds : bond 0.04054 / 2.77 ( 1200) hydrogen bonds : angle 3.60621 / 2.56 ( 3480) metal coordination : bond 0.01092 / 0.71 ( 15) metal coordination : angle 3.97440 / 2.31 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 402 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 87 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8003 (tp30) REVERT: A 92 HIS cc_start: 0.8223 (m90) cc_final: 0.7912 (m90) REVERT: A 98 ASP cc_start: 0.8520 (p0) cc_final: 0.8218 (p0) REVERT: A 170 ARG cc_start: 0.8397 (mtp180) cc_final: 0.7139 (mtm-85) REVERT: A 324 ARG cc_start: 0.1373 (OUTLIER) cc_final: 0.1028 (mtt-85) REVERT: A 343 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7752 (ttm) REVERT: A 380 MET cc_start: 0.8553 (mtp) cc_final: 0.8332 (mtt) REVERT: B 71 ARG cc_start: 0.7233 (mtm110) cc_final: 0.6162 (mtm-85) REVERT: B 108 VAL cc_start: 0.8691 (p) cc_final: 0.8388 (m) REVERT: B 176 CYS cc_start: 0.6446 (t) cc_final: 0.6203 (t) REVERT: B 189 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8321 (p) REVERT: B 234 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7140 (mm-30) REVERT: B 240 GLU cc_start: 0.7762 (mp0) cc_final: 0.7350 (mp0) REVERT: B 304 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: B 406 MET cc_start: 0.6472 (ptp) cc_final: 0.5994 (mmp) REVERT: B 521 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7982 (tp) REVERT: B 545 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7414 (mtm-85) REVERT: B 551 ASN cc_start: 0.8413 (t0) cc_final: 0.8064 (t0) REVERT: B 722 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8498 (ttpp) REVERT: C 79 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6818 (mm-30) REVERT: C 81 GLU cc_start: 0.8093 (pm20) cc_final: 0.7399 (pm20) REVERT: C 98 ASP cc_start: 0.7914 (t0) cc_final: 0.7465 (t0) REVERT: C 102 TYR cc_start: 0.8253 (m-80) cc_final: 0.7837 (m-80) REVERT: C 222 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8181 (ttp80) REVERT: C 638 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: C 653 GLU cc_start: 0.7016 (mp0) cc_final: 0.6719 (mp0) REVERT: C 662 ASN cc_start: 0.8134 (t0) cc_final: 0.7668 (t0) REVERT: C 722 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8718 (mtpp) REVERT: D 228 LYS cc_start: 0.8255 (tppt) cc_final: 0.7180 (ttpp) REVERT: D 242 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7749 (mm-30) REVERT: D 267 ILE cc_start: 0.8755 (mm) cc_final: 0.8466 (mt) REVERT: D 335 MET cc_start: 0.6578 (mmm) cc_final: 0.6192 (mmm) REVERT: D 350 ILE cc_start: 0.6428 (OUTLIER) cc_final: 0.5942 (tt) REVERT: D 361 LYS cc_start: 0.7463 (mttp) cc_final: 0.6968 (mtmt) REVERT: D 468 GLU cc_start: 0.8080 (mp0) cc_final: 0.7703 (mp0) REVERT: D 471 MET cc_start: 0.8563 (ttp) cc_final: 0.8254 (ttp) outliers start: 100 outliers final: 67 residues processed: 461 average time/residue: 0.1483 time to fit residues: 103.6575 Evaluate side-chains 464 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 387 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 562 ASN Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 98 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 0.0060 chunk 163 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 210 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 GLN D 443 ASN D 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.133540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.097738 restraints weight = 20280.858| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.95 r_work: 0.2784 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19328 Z= 0.136 Angle : 0.527 14.257 26198 Z= 0.262 Chirality : 0.038 0.233 2973 Planarity : 0.004 0.054 3239 Dihedral : 4.360 50.100 2495 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 4.73 % Allowed : 23.76 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.53 (0.18), residues: 2265 helix: 2.28 (0.12), residues: 1677 sheet: None (None), residues: 0 loop : -0.07 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 545 TYR 0.021 0.001 TYR C 348 PHE 0.019 0.001 PHE A 341 TRP 0.019 0.001 TRP B 315 HIS 0.003 0.000 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (19309) covalent geometry : angle 0.52187 / 0.26 (26181) SS BOND : bond 0.00147 / 0.07 ( 4) SS BOND : angle 0.32128 / 0.22 ( 8) hydrogen bonds : bond 0.04083 / 2.79 ( 1200) hydrogen bonds : angle 3.59371 / 2.55 ( 3480) metal coordination : bond 0.01123 / 0.71 ( 15) metal coordination : angle 3.82665 / 2.23 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 396 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 87 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8020 (tp30) REVERT: A 92 HIS cc_start: 0.8280 (m90) cc_final: 0.7988 (m90) REVERT: A 98 ASP cc_start: 0.8502 (p0) cc_final: 0.8221 (p0) REVERT: A 170 ARG cc_start: 0.8414 (mtp180) cc_final: 0.7225 (mtm-85) REVERT: A 242 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7529 (mm-30) REVERT: A 343 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7824 (ttm) REVERT: A 380 MET cc_start: 0.8612 (mtp) cc_final: 0.8402 (mtt) REVERT: B 71 ARG cc_start: 0.7298 (mtm110) cc_final: 0.6241 (mtm-85) REVERT: B 108 VAL cc_start: 0.8699 (p) cc_final: 0.8413 (m) REVERT: B 189 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8446 (p) REVERT: B 240 GLU cc_start: 0.7835 (mp0) cc_final: 0.7465 (mp0) REVERT: B 304 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: B 406 MET cc_start: 0.6575 (ptp) cc_final: 0.6077 (mmp) REVERT: B 521 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8090 (tp) REVERT: B 545 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7447 (mtm-85) REVERT: B 551 ASN cc_start: 0.8449 (t0) cc_final: 0.8103 (t0) REVERT: B 722 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8627 (ttpp) REVERT: C 79 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6923 (mm-30) REVERT: C 81 GLU cc_start: 0.8155 (pm20) cc_final: 0.7443 (pm20) REVERT: C 98 ASP cc_start: 0.7964 (t0) cc_final: 0.7651 (t0) REVERT: C 102 TYR cc_start: 0.8364 (m-80) cc_final: 0.7995 (m-80) REVERT: C 222 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8276 (ttp80) REVERT: C 396 GLN cc_start: 0.8113 (mt0) cc_final: 0.7856 (mt0) REVERT: C 638 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: C 653 GLU cc_start: 0.7024 (mp0) cc_final: 0.6735 (mp0) REVERT: C 662 ASN cc_start: 0.8199 (t0) cc_final: 0.7747 (t0) REVERT: C 722 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8799 (mtpp) REVERT: D 228 LYS cc_start: 0.8351 (tppt) cc_final: 0.7306 (ttpp) REVERT: D 242 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7887 (mm-30) REVERT: D 267 ILE cc_start: 0.8835 (mm) cc_final: 0.8544 (mt) REVERT: D 335 MET cc_start: 0.6648 (mmm) cc_final: 0.6274 (mmm) REVERT: D 350 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.6081 (tt) REVERT: D 361 LYS cc_start: 0.7537 (mttp) cc_final: 0.7062 (mtmm) REVERT: D 468 GLU cc_start: 0.8104 (mp0) cc_final: 0.7745 (mp0) REVERT: D 471 MET cc_start: 0.8597 (ttp) cc_final: 0.8298 (ttp) outliers start: 98 outliers final: 71 residues processed: 459 average time/residue: 0.1501 time to fit residues: 104.4586 Evaluate side-chains 466 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 385 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 640 LYS Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 562 ASN Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 59 optimal weight: 0.0980 chunk 161 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 218 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 GLN D 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.133764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.098001 restraints weight = 20312.637| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.95 r_work: 0.2815 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19328 Z= 0.129 Angle : 0.526 14.207 26198 Z= 0.260 Chirality : 0.038 0.252 2973 Planarity : 0.004 0.053 3239 Dihedral : 4.341 49.934 2495 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 4.25 % Allowed : 23.95 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.60 (0.18), residues: 2265 helix: 2.34 (0.12), residues: 1675 sheet: None (None), residues: 0 loop : -0.07 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 545 TYR 0.021 0.001 TYR C 348 PHE 0.025 0.001 PHE A 319 TRP 0.017 0.001 TRP B 315 HIS 0.003 0.000 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (19309) covalent geometry : angle 0.52118 / 0.26 (26181) SS BOND : bond 0.00146 / 0.07 ( 4) SS BOND : angle 0.30306 / 0.20 ( 8) hydrogen bonds : bond 0.03989 / 2.73 ( 1200) hydrogen bonds : angle 3.57532 / 2.53 ( 3480) metal coordination : bond 0.01061 / 0.68 ( 15) metal coordination : angle 3.82742 / 2.22 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 395 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 87 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7981 (tp30) REVERT: A 92 HIS cc_start: 0.8296 (m90) cc_final: 0.8010 (m90) REVERT: A 98 ASP cc_start: 0.8458 (p0) cc_final: 0.8183 (p0) REVERT: A 107 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7550 (mt-10) REVERT: A 170 ARG cc_start: 0.8407 (mtp180) cc_final: 0.7264 (mtm-85) REVERT: A 242 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7557 (mm-30) REVERT: A 324 ARG cc_start: 0.1566 (OUTLIER) cc_final: 0.1195 (tpp80) REVERT: A 343 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7864 (ttm) REVERT: A 380 MET cc_start: 0.8611 (mtp) cc_final: 0.8407 (mtt) REVERT: B 71 ARG cc_start: 0.7320 (mtm110) cc_final: 0.6272 (mtm-85) REVERT: B 108 VAL cc_start: 0.8707 (p) cc_final: 0.8430 (m) REVERT: B 160 LEU cc_start: 0.8485 (mp) cc_final: 0.8137 (mp) REVERT: B 189 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8507 (p) REVERT: B 237 PHE cc_start: 0.8551 (m-80) cc_final: 0.8240 (m-80) REVERT: B 240 GLU cc_start: 0.7843 (mp0) cc_final: 0.7502 (mp0) REVERT: B 304 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: B 406 MET cc_start: 0.6733 (ptp) cc_final: 0.6225 (mmp) REVERT: B 521 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8144 (tp) REVERT: B 545 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7505 (mtm-85) REVERT: B 551 ASN cc_start: 0.8467 (t0) cc_final: 0.8115 (t0) REVERT: B 722 LYS cc_start: 0.8922 (ttpt) cc_final: 0.8671 (ttpp) REVERT: C 79 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6889 (mm-30) REVERT: C 81 GLU cc_start: 0.8160 (pm20) cc_final: 0.7439 (pm20) REVERT: C 98 ASP cc_start: 0.7969 (t0) cc_final: 0.7652 (t0) REVERT: C 102 TYR cc_start: 0.8399 (m-80) cc_final: 0.8024 (m-80) REVERT: C 222 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8302 (ttp80) REVERT: C 396 GLN cc_start: 0.8115 (mt0) cc_final: 0.7864 (mt0) REVERT: C 638 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: C 653 GLU cc_start: 0.7040 (mp0) cc_final: 0.6763 (mp0) REVERT: C 662 ASN cc_start: 0.8216 (t0) cc_final: 0.7767 (t0) REVERT: C 722 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8826 (mtpp) REVERT: D 228 LYS cc_start: 0.8384 (tppt) cc_final: 0.7400 (ttpp) REVERT: D 267 ILE cc_start: 0.8872 (mm) cc_final: 0.8584 (mt) REVERT: D 335 MET cc_start: 0.6722 (mmm) cc_final: 0.6336 (mmm) REVERT: D 350 ILE cc_start: 0.6494 (OUTLIER) cc_final: 0.6013 (tt) REVERT: D 361 LYS cc_start: 0.7569 (mttp) cc_final: 0.7101 (mtmm) REVERT: D 468 GLU cc_start: 0.8110 (mp0) cc_final: 0.7777 (mp0) REVERT: D 471 MET cc_start: 0.8605 (ttp) cc_final: 0.8325 (ttp) outliers start: 88 outliers final: 71 residues processed: 450 average time/residue: 0.1453 time to fit residues: 99.6804 Evaluate side-chains 471 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 389 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 640 LYS Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 562 ASN Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 202 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.132536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.096973 restraints weight = 20144.065| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.94 r_work: 0.2774 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19328 Z= 0.157 Angle : 0.547 14.426 26198 Z= 0.272 Chirality : 0.039 0.251 2973 Planarity : 0.004 0.054 3239 Dihedral : 4.348 48.765 2493 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.29 % Rotamer: Outliers : 4.39 % Allowed : 24.09 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.53 (0.18), residues: 2265 helix: 2.28 (0.12), residues: 1678 sheet: None (None), residues: 0 loop : -0.07 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 545 TYR 0.023 0.001 TYR C 348 PHE 0.018 0.001 PHE A 319 TRP 0.019 0.001 TRP B 315 HIS 0.002 0.000 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (19309) covalent geometry : angle 0.54226 / 0.27 (26181) SS BOND : bond 0.00148 / 0.07 ( 4) SS BOND : angle 0.33083 / 0.24 ( 8) hydrogen bonds : bond 0.04207 / 2.88 ( 1200) hydrogen bonds : angle 3.60111 / 2.55 ( 3480) metal coordination : bond 0.01365 / 0.83 ( 15) metal coordination : angle 3.98869 / 2.32 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 397 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8286 (m90) cc_final: 0.7986 (m90) REVERT: A 107 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7540 (mt-10) REVERT: A 170 ARG cc_start: 0.8417 (mtp180) cc_final: 0.7238 (mtm-85) REVERT: A 242 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: A 324 ARG cc_start: 0.1480 (OUTLIER) cc_final: 0.1170 (tpp80) REVERT: A 343 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7854 (ttm) REVERT: A 380 MET cc_start: 0.8634 (mtp) cc_final: 0.8427 (mtt) REVERT: A 519 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8035 (mtmm) REVERT: B 108 VAL cc_start: 0.8687 (p) cc_final: 0.8425 (m) REVERT: B 189 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8477 (p) REVERT: B 240 GLU cc_start: 0.7832 (mp0) cc_final: 0.7465 (mp0) REVERT: B 304 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: B 406 MET cc_start: 0.6736 (ptp) cc_final: 0.6187 (mmp) REVERT: B 521 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8096 (tp) REVERT: B 545 ARG cc_start: 0.8000 (mtm-85) cc_final: 0.7453 (mtm-85) REVERT: B 551 ASN cc_start: 0.8587 (t0) cc_final: 0.8361 (t0) REVERT: B 722 LYS cc_start: 0.8880 (ttpt) cc_final: 0.8635 (ttpp) REVERT: C 81 GLU cc_start: 0.8146 (pm20) cc_final: 0.7410 (pm20) REVERT: C 98 ASP cc_start: 0.7983 (t0) cc_final: 0.7652 (t0) REVERT: C 102 TYR cc_start: 0.8393 (m-80) cc_final: 0.7968 (m-80) REVERT: C 222 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8290 (ttp80) REVERT: C 638 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: C 653 GLU cc_start: 0.7029 (mp0) cc_final: 0.6736 (mp0) REVERT: C 662 ASN cc_start: 0.8222 (t0) cc_final: 0.7764 (t0) REVERT: C 722 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8802 (mtpp) REVERT: D 228 LYS cc_start: 0.8359 (tppt) cc_final: 0.7301 (ttpp) REVERT: D 242 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7809 (mm-30) REVERT: D 267 ILE cc_start: 0.8834 (mm) cc_final: 0.8548 (mt) REVERT: D 335 MET cc_start: 0.6688 (mmm) cc_final: 0.6250 (mmm) REVERT: D 350 ILE cc_start: 0.6445 (OUTLIER) cc_final: 0.5982 (tt) REVERT: D 361 LYS cc_start: 0.7585 (mttp) cc_final: 0.7104 (mtmm) REVERT: D 468 GLU cc_start: 0.8111 (mp0) cc_final: 0.7747 (mp0) REVERT: D 471 MET cc_start: 0.8602 (ttp) cc_final: 0.8314 (ttp) REVERT: D 623 MET cc_start: 0.5911 (mpp) cc_final: 0.4985 (mpt) REVERT: D 711 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7696 (tm-30) outliers start: 91 outliers final: 68 residues processed: 455 average time/residue: 0.1493 time to fit residues: 102.2863 Evaluate side-chains 469 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 390 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 640 LYS Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 562 ASN Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 147 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 28 optimal weight: 0.0030 chunk 223 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 GLN B 552 ASN B 625 ASN D 443 ASN D 625 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.133812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.098100 restraints weight = 20422.237| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.94 r_work: 0.2802 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19328 Z= 0.139 Angle : 0.541 14.449 26198 Z= 0.269 Chirality : 0.038 0.267 2973 Planarity : 0.004 0.054 3239 Dihedral : 4.340 49.059 2493 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.29 % Rotamer: Outliers : 4.10 % Allowed : 24.34 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.55 (0.18), residues: 2265 helix: 2.31 (0.12), residues: 1677 sheet: None (None), residues: 0 loop : -0.13 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 545 TYR 0.023 0.001 TYR C 348 PHE 0.032 0.001 PHE A 319 TRP 0.018 0.001 TRP B 315 HIS 0.008 0.000 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (19309) covalent geometry : angle 0.53594 / 0.27 (26181) SS BOND : bond 0.00171 / 0.09 ( 4) SS BOND : angle 0.31207 / 0.21 ( 8) hydrogen bonds : bond 0.04069 / 2.78 ( 1200) hydrogen bonds : angle 3.58695 / 2.54 ( 3480) metal coordination : bond 0.01385 / 0.87 ( 15) metal coordination : angle 4.09251 / 2.36 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 399 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8290 (m90) cc_final: 0.8002 (m90) REVERT: A 98 ASP cc_start: 0.8429 (p0) cc_final: 0.8154 (p0) REVERT: A 107 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7512 (mt-10) REVERT: A 170 ARG cc_start: 0.8399 (mtp180) cc_final: 0.7268 (mtm-85) REVERT: A 242 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7513 (mm-30) REVERT: A 324 ARG cc_start: 0.1677 (OUTLIER) cc_final: 0.1332 (tpp80) REVERT: A 343 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7816 (ttm) REVERT: A 380 MET cc_start: 0.8633 (mtp) cc_final: 0.8428 (mtt) REVERT: A 468 GLU cc_start: 0.8279 (pt0) cc_final: 0.7893 (pt0) REVERT: A 519 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8067 (mtmm) REVERT: B 108 VAL cc_start: 0.8693 (p) cc_final: 0.8439 (m) REVERT: B 160 LEU cc_start: 0.8453 (mp) cc_final: 0.8124 (mp) REVERT: B 189 SER cc_start: 0.8737 (t) cc_final: 0.8472 (p) REVERT: B 240 GLU cc_start: 0.7821 (mp0) cc_final: 0.7483 (mp0) REVERT: B 304 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: B 406 MET cc_start: 0.6762 (ptp) cc_final: 0.6200 (mmp) REVERT: B 521 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8113 (tp) REVERT: B 545 ARG cc_start: 0.8045 (mtm-85) cc_final: 0.7528 (mtm-85) REVERT: B 551 ASN cc_start: 0.8628 (t0) cc_final: 0.8406 (t0) REVERT: B 722 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8640 (ttpp) REVERT: C 81 GLU cc_start: 0.8146 (pm20) cc_final: 0.7409 (pm20) REVERT: C 222 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8264 (ttp80) REVERT: C 638 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8167 (mt-10) REVERT: C 653 GLU cc_start: 0.7001 (mp0) cc_final: 0.6710 (mp0) REVERT: C 662 ASN cc_start: 0.8193 (t0) cc_final: 0.7819 (t0) REVERT: C 722 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8801 (mtpp) REVERT: D 228 LYS cc_start: 0.8365 (tppt) cc_final: 0.7364 (ttpp) REVERT: D 267 ILE cc_start: 0.8846 (mm) cc_final: 0.8558 (mt) REVERT: D 335 MET cc_start: 0.6739 (mmm) cc_final: 0.6350 (mmm) REVERT: D 350 ILE cc_start: 0.6457 (OUTLIER) cc_final: 0.6005 (tt) REVERT: D 361 LYS cc_start: 0.7586 (mttp) cc_final: 0.7110 (mtmm) REVERT: D 468 GLU cc_start: 0.8083 (mp0) cc_final: 0.7740 (mp0) REVERT: D 471 MET cc_start: 0.8602 (ttp) cc_final: 0.8317 (ttp) REVERT: D 623 MET cc_start: 0.5893 (mpp) cc_final: 0.5050 (mpt) REVERT: D 711 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7692 (tm-30) outliers start: 85 outliers final: 71 residues processed: 454 average time/residue: 0.1464 time to fit residues: 101.1719 Evaluate side-chains 471 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 390 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 640 LYS Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 562 ASN Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 106 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 169 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 160 optimal weight: 0.1980 chunk 124 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 GLN B 552 ASN D 443 ASN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.134009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.098345 restraints weight = 20449.348| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.94 r_work: 0.2796 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19328 Z= 0.128 Angle : 0.539 14.321 26198 Z= 0.268 Chirality : 0.038 0.266 2973 Planarity : 0.004 0.053 3239 Dihedral : 4.326 49.296 2493 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 3.81 % Allowed : 24.87 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.59 (0.18), residues: 2265 helix: 2.34 (0.12), residues: 1677 sheet: None (None), residues: 0 loop : -0.12 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 545 TYR 0.022 0.001 TYR C 348 PHE 0.023 0.001 PHE A 319 TRP 0.018 0.001 TRP B 315 HIS 0.008 0.000 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (19309) covalent geometry : angle 0.53414 / 0.27 (26181) SS BOND : bond 0.00206 / 0.10 ( 4) SS BOND : angle 0.27986 / 0.18 ( 8) hydrogen bonds : bond 0.03982 / 2.72 ( 1200) hydrogen bonds : angle 3.57822 / 2.53 ( 3480) metal coordination : bond 0.01259 / 0.79 ( 15) metal coordination : angle 4.08132 / 2.34 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5380.98 seconds wall clock time: 92 minutes 50.97 seconds (5570.97 seconds total)