Starting phenix.real_space_refine on Sun Aug 24 12:07:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ro4_4970/08_2025/6ro4_4970.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ro4_4970/08_2025/6ro4_4970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ro4_4970/08_2025/6ro4_4970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ro4_4970/08_2025/6ro4_4970.map" model { file = "/net/cci-nas-00/data/ceres_data/6ro4_4970/08_2025/6ro4_4970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ro4_4970/08_2025/6ro4_4970.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 P 47 5.49 5 S 128 5.16 5 C 12543 2.51 5 N 3434 2.21 5 O 3665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19827 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 387 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "K" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 575 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "A" Number of atoms: 4648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4648 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 23, 'TRANS': 551} Chain breaks: 2 Chain: "F" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 490 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "B" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5436 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 29, 'TRANS': 645} Chain breaks: 1 Chain: "E" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1857 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2182 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 15, 'TRANS': 264} Chain breaks: 3 Chain: "C" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3109 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 366} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1129 Classifications: {'peptide': 134} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 129} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" 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 13269 SG CYS E 268 79.447 101.564 111.591 1.00 68.27 S ATOM 13288 SG CYS E 271 81.397 99.772 114.156 1.00 80.25 S ATOM 13373 SG CYS E 282 82.494 102.746 111.993 1.00 96.15 S ATOM 13393 SG CYS E 285 83.161 99.662 110.883 1.00104.31 S ATOM 13161 SG CYS E 255 79.798 107.048 122.795 1.00 92.61 S ATOM 13178 SG CYS E 257 82.768 108.902 122.336 1.00109.54 S ATOM 13327 SG CYS E 276 79.016 110.564 122.274 1.00 95.56 S ATOM 14955 SG CYS D 291 59.709 108.339 119.826 1.00106.72 S ATOM 14977 SG CYS D 294 57.270 109.821 118.417 1.00113.78 S ATOM 15066 SG CYS D 305 57.353 106.787 117.090 1.00109.45 S ATOM 15089 SG CYS D 308 59.861 110.085 116.355 1.00113.96 S ATOM 15325 SG CYS D 345 90.504 77.279 135.920 1.00 86.42 S ATOM 15347 SG CYS D 348 87.448 75.217 137.026 1.00 85.40 S ATOM 15432 SG CYS D 368 88.987 73.762 134.034 1.00 96.58 S ATOM 15453 SG CYS D 371 87.108 76.362 133.960 1.00 95.34 S ATOM 15373 SG CYS D 360 94.784 85.728 129.551 1.00107.81 S ATOM 15391 SG CYS D 363 93.933 86.677 132.644 1.00108.40 S ATOM 15540 SG CYS D 382 91.039 85.558 130.609 1.00 92.12 S ATOM 15557 SG CYS D 385 92.176 88.954 130.090 1.00 95.02 S ATOM 18698 SG CYS G 105 73.202 25.228 33.520 1.00129.00 S ATOM 18722 SG CYS G 108 72.738 24.779 30.018 1.00133.28 S ATOM 18870 SG CYS G 126 70.309 27.018 31.071 1.00133.42 S ATOM 18892 SG CYS G 129 68.909 23.951 32.347 1.00138.27 S Time building chain proxies: 4.41, per 1000 atoms: 0.22 Number of scatterers: 19827 At special positions: 0 Unit cell: (117.6, 121.8, 186.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 128 16.00 P 47 15.00 O 3665 8.00 N 3434 7.00 C 12543 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 828.2 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 294 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 308 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 291 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 305 " pdb=" ZN D 402 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 345 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 368 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 348 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 371 " pdb=" ZN D 403 " pdb="ZN ZN D 403 " - pdb=" SG CYS D 385 " pdb="ZN ZN D 403 " - pdb=" SG CYS D 360 " pdb="ZN ZN D 403 " - pdb=" SG CYS D 382 " pdb="ZN ZN D 403 " - pdb=" SG CYS D 363 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 268 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 282 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 285 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 271 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 255 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 257 " pdb="ZN ZN E 402 " - pdb=" ND1 HIS E 258 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 276 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 105 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 108 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 129 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 126 " Number of angles added : 33 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 0 sheets defined 43.9% alpha, 0.0% beta 14 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 94 through 100 removed outlier: 4.498A pdb=" N PHE A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.614A pdb=" N TYR A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 139 removed outlier: 3.686A pdb=" N THR A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 133 through 139' Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.523A pdb=" N LEU A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.502A pdb=" N GLN A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLN A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 removed outlier: 5.348A pdb=" N GLU A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 280 " --> pdb=" O MET A 276 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 346 through 357 removed outlier: 4.165A pdb=" N GLY A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.861A pdb=" N GLU A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TRP A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 432 removed outlier: 3.737A pdb=" N VAL A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 451 through 457 removed outlier: 4.879A pdb=" N LEU A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 478 through 483 removed outlier: 4.926A pdb=" N PHE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 483' Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.689A pdb=" N ARG A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 535 removed outlier: 3.890A pdb=" N LEU A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.741A pdb=" N ALA A 543 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.565A pdb=" N LYS A 569 " --> pdb=" O VAL A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 597 removed outlier: 3.557A pdb=" N GLN A 591 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 643 removed outlier: 3.899A pdb=" N LEU A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 642 " --> pdb=" O GLN A 638 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 680 removed outlier: 3.655A pdb=" N THR A 674 " --> pdb=" O MET A 670 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN A 677 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU A 680 " --> pdb=" O ARG A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 717 removed outlier: 3.645A pdb=" N GLN A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 712 " --> pdb=" O GLU A 708 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 24 removed outlier: 3.598A pdb=" N GLN F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU F 20 " --> pdb=" O MET F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 50 No H-bonds generated for 'chain 'F' and resid 48 through 50' Processing helix chain 'F' and resid 52 through 63 removed outlier: 3.817A pdb=" N ARG F 56 " --> pdb=" O VAL F 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 34 removed outlier: 4.132A pdb=" N SER B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR B 31 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 62 removed outlier: 3.629A pdb=" N ALA B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG B 61 " --> pdb=" O MET B 57 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 98 removed outlier: 3.577A pdb=" N ILE B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 138 removed outlier: 3.581A pdb=" N ASP B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 removed outlier: 3.853A pdb=" N TYR B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 147' Processing helix chain 'B' and resid 156 through 162 removed outlier: 3.729A pdb=" N ASP B 162 " --> pdb=" O TYR B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 191 through 201 removed outlier: 4.814A pdb=" N LEU B 200 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N HIS B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 215 through 221 removed outlier: 4.072A pdb=" N ASP B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.523A pdb=" N ASP B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 271 removed outlier: 3.566A pdb=" N ARG B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 269 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 271 " --> pdb=" O GLN B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 345 removed outlier: 3.559A pdb=" N GLU B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 362 removed outlier: 3.869A pdb=" N ALA B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 386 removed outlier: 4.403A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS B 375 " --> pdb=" O PRO B 371 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ALA B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 409 Proline residue: B 396 - end of helix removed outlier: 3.751A pdb=" N SER B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 409 " --> pdb=" O THR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 442 No H-bonds generated for 'chain 'B' and resid 440 through 442' Processing helix chain 'B' and resid 447 through 450 No H-bonds generated for 'chain 'B' and resid 447 through 450' Processing helix chain 'B' and resid 467 through 470 No H-bonds generated for 'chain 'B' and resid 467 through 470' Processing helix chain 'B' and resid 509 through 511 No H-bonds generated for 'chain 'B' and resid 509 through 511' Processing helix chain 'B' and resid 514 through 528 removed outlier: 4.141A pdb=" N ASN B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 523 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 554 removed outlier: 3.501A pdb=" N SER B 547 " --> pdb=" O GLN B 543 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 564 removed outlier: 3.683A pdb=" N ARG B 563 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 589 removed outlier: 3.709A pdb=" N GLU B 589 " --> pdb=" O GLN B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 607 Processing helix chain 'B' and resid 633 through 642 removed outlier: 4.041A pdb=" N GLU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 667 removed outlier: 3.745A pdb=" N LEU B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 654 " --> pdb=" O ASP B 650 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS B 659 " --> pdb=" O ASP B 655 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN B 662 " --> pdb=" O ARG B 658 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS B 663 " --> pdb=" O HIS B 659 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 664 " --> pdb=" O ALA B 660 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA B 667 " --> pdb=" O CYS B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 No H-bonds generated for 'chain 'B' and resid 682 through 685' Processing helix chain 'B' and resid 687 through 690 No H-bonds generated for 'chain 'B' and resid 687 through 690' Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 704 through 706 No H-bonds generated for 'chain 'B' and resid 704 through 706' Processing helix chain 'B' and resid 710 through 724 removed outlier: 3.507A pdb=" N VAL B 714 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN B 715 " --> pdb=" O ASP B 711 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 716 " --> pdb=" O GLU B 712 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 722 " --> pdb=" O LYS B 718 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 28 Processing helix chain 'E' and resid 35 through 51 removed outlier: 4.021A pdb=" N ALA E 40 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU E 49 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.796A pdb=" N GLU E 109 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE E 111 " --> pdb=" O ALA E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 149 removed outlier: 3.573A pdb=" N LYS E 149 " --> pdb=" O HIS E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 187 removed outlier: 5.761A pdb=" N MET E 175 " --> pdb=" O ALA E 171 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET E 178 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN E 179 " --> pdb=" O MET E 175 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL E 180 " --> pdb=" O ASN E 176 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 210 removed outlier: 4.026A pdb=" N GLN E 205 " --> pdb=" O GLY E 201 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS E 207 " --> pdb=" O LEU E 203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP E 208 " --> pdb=" O GLN E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 230 removed outlier: 6.170A pdb=" N GLN E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 240 removed outlier: 3.819A pdb=" N SER E 239 " --> pdb=" O GLN E 235 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN E 240 " --> pdb=" O ASP E 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 235 through 240' Processing helix chain 'D' and resid 69 through 72 No H-bonds generated for 'chain 'D' and resid 69 through 72' Processing helix chain 'D' and resid 80 through 98 removed outlier: 3.510A pdb=" N LEU D 87 " --> pdb=" O CYS D 83 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 131 Processing helix chain 'D' and resid 133 through 136 No H-bonds generated for 'chain 'D' and resid 133 through 136' Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.548A pdb=" N ILE D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'D' and resid 182 through 191 removed outlier: 3.501A pdb=" N ILE D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 removed outlier: 3.610A pdb=" N ALA D 212 " --> pdb=" O CYS D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 236 removed outlier: 3.584A pdb=" N GLU D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 321 removed outlier: 4.622A pdb=" N SER D 321 " --> pdb=" O HIS D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.757A pdb=" N HIS D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 379 " --> pdb=" O VAL D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 386 No H-bonds generated for 'chain 'D' and resid 383 through 386' Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 28 through 34 removed outlier: 3.653A pdb=" N ASP C 32 " --> pdb=" O PRO C 28 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 46 removed outlier: 3.523A pdb=" N PHE C 45 " --> pdb=" O CYS C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 68 through 74 removed outlier: 4.877A pdb=" N ALA C 72 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 92 removed outlier: 3.857A pdb=" N GLU C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 121 removed outlier: 3.521A pdb=" N GLN C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN C 117 " --> pdb=" O ILE C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 163 removed outlier: 4.076A pdb=" N LYS C 150 " --> pdb=" O PRO C 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL C 159 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 182 removed outlier: 3.606A pdb=" N GLN C 177 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 removed outlier: 3.515A pdb=" N GLN C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 226 removed outlier: 3.560A pdb=" N LEU C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 215 " --> pdb=" O GLN C 211 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C 218 " --> pdb=" O TYR C 214 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR C 222 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER C 225 " --> pdb=" O GLN C 221 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG C 226 " --> pdb=" O THR C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 241 Processing helix chain 'C' and resid 256 through 268 removed outlier: 4.044A pdb=" N ASN C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 268 " --> pdb=" O HIS C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 288 No H-bonds generated for 'chain 'C' and resid 285 through 288' Processing helix chain 'C' and resid 322 through 331 removed outlier: 4.326A pdb=" N PHE C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 357 removed outlier: 3.879A pdb=" N GLN C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER C 357 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 370 Processing helix chain 'C' and resid 385 through 399 removed outlier: 3.815A pdb=" N ASP C 389 " --> pdb=" O PRO C 385 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN C 390 " --> pdb=" O THR C 386 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG C 398 " --> pdb=" O TRP C 394 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 423 removed outlier: 4.142A pdb=" N ALA C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 457 removed outlier: 4.925A pdb=" N SER C 449 " --> pdb=" O PRO C 445 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASP C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL C 451 " --> pdb=" O GLY C 447 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 452 " --> pdb=" O HIS C 448 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG C 453 " --> pdb=" O SER C 449 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG C 457 " --> pdb=" O ARG C 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 148 Processing helix chain 'G' and resid 183 through 193 Processing helix chain 'G' and resid 197 through 235 removed outlier: 3.985A pdb=" N GLU G 201 " --> pdb=" O GLN G 197 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA G 203 " --> pdb=" O ALA G 199 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL G 206 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG G 207 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU G 212 " --> pdb=" O GLN G 208 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN G 216 " --> pdb=" O GLU G 212 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE G 219 " --> pdb=" O LYS G 215 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL G 223 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA G 229 " --> pdb=" O GLU G 225 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL G 230 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER G 233 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL G 234 " --> pdb=" O VAL G 230 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 8348 1.41 - 1.63: 11792 1.63 - 1.85: 183 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 20335 Sorted by residual: bond pdb=" CB ARG E 252 " pdb=" CG ARG E 252 " ideal model delta sigma weight residual 1.520 1.424 0.096 3.00e-02 1.11e+03 1.03e+01 bond pdb=" CB PRO D 282 " pdb=" CG PRO D 282 " ideal model delta sigma weight residual 1.492 1.336 0.156 5.00e-02 4.00e+02 9.72e+00 bond pdb=" N ILE E 281 " pdb=" CA ILE E 281 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.61e+00 bond pdb=" SD MET G 118 " pdb=" CE MET G 118 " ideal model delta sigma weight residual 1.791 1.719 0.072 2.50e-02 1.60e+03 8.24e+00 bond pdb=" CG LEU D 284 " pdb=" CD2 LEU D 284 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.11e+00 ... (remaining 20330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 26835 2.42 - 4.85: 741 4.85 - 7.27: 92 7.27 - 9.70: 31 9.70 - 12.12: 6 Bond angle restraints: 27705 Sorted by residual: angle pdb=" N ASN G 119 " pdb=" CA ASN G 119 " pdb=" C ASN G 119 " ideal model delta sigma weight residual 114.09 105.97 8.12 1.55e+00 4.16e-01 2.75e+01 angle pdb=" C LEU D 201 " pdb=" N SER D 202 " pdb=" CA SER D 202 " ideal model delta sigma weight residual 121.54 131.36 -9.82 1.91e+00 2.74e-01 2.64e+01 angle pdb=" C ARG G 130 " pdb=" N ASP G 131 " pdb=" CA ASP G 131 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C LYS D 77 " pdb=" N PRO D 78 " pdb=" CA PRO D 78 " ideal model delta sigma weight residual 119.84 125.75 -5.91 1.25e+00 6.40e-01 2.23e+01 angle pdb=" N PRO D 78 " pdb=" CA PRO D 78 " pdb=" C PRO D 78 " ideal model delta sigma weight residual 112.47 122.14 -9.67 2.06e+00 2.36e-01 2.20e+01 ... (remaining 27700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.44: 11542 29.44 - 58.88: 600 58.88 - 88.32: 47 88.32 - 117.76: 1 117.76 - 147.21: 4 Dihedral angle restraints: 12194 sinusoidal: 5300 harmonic: 6894 Sorted by residual: dihedral pdb=" CA ASP A 81 " pdb=" C ASP A 81 " pdb=" N GLY A 82 " pdb=" CA GLY A 82 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA PRO C 38 " pdb=" C PRO C 38 " pdb=" N ALA C 39 " pdb=" CA ALA C 39 " ideal model delta harmonic sigma weight residual 180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LEU B 693 " pdb=" C LEU B 693 " pdb=" N PRO B 694 " pdb=" CA PRO B 694 " ideal model delta harmonic sigma weight residual -180.00 -151.83 -28.17 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 12191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2429 0.062 - 0.123: 582 0.123 - 0.185: 101 0.185 - 0.247: 19 0.247 - 0.309: 6 Chirality restraints: 3137 Sorted by residual: chirality pdb=" CA PRO D 78 " pdb=" N PRO D 78 " pdb=" C PRO D 78 " pdb=" CB PRO D 78 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA SER B 462 " pdb=" N SER B 462 " pdb=" C SER B 462 " pdb=" CB SER B 462 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CG LEU G 123 " pdb=" CB LEU G 123 " pdb=" CD1 LEU G 123 " pdb=" CD2 LEU G 123 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 3134 not shown) Planarity restraints: 3348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP G 134 " -0.022 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C ASP G 134 " 0.074 2.00e-02 2.50e+03 pdb=" O ASP G 134 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS G 135 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 300 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" CD GLU D 300 " 0.066 2.00e-02 2.50e+03 pdb=" OE1 GLU D 300 " -0.023 2.00e-02 2.50e+03 pdb=" OE2 GLU D 300 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 140 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C THR G 140 " -0.062 2.00e-02 2.50e+03 pdb=" O THR G 140 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS G 141 " 0.021 2.00e-02 2.50e+03 ... (remaining 3345 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3126 2.76 - 3.29: 17605 3.29 - 3.83: 32039 3.83 - 4.36: 38015 4.36 - 4.90: 63406 Nonbonded interactions: 154191 Sorted by model distance: nonbonded pdb=" N3 DC J 18 " pdb=" NE2 HIS G 171 " model vdw 2.223 3.200 nonbonded pdb=" O ASP D 75 " pdb=" OD1 ASP D 75 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP D 73 " pdb=" N GLN D 74 " model vdw 2.284 3.120 nonbonded pdb=" O THR D 285 " pdb=" OG1 THR D 285 " model vdw 2.294 3.040 nonbonded pdb=" O THR D 176 " pdb=" OG1 THR D 176 " model vdw 2.295 3.040 ... (remaining 154186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.470 Find NCS groups from input model: 0.120 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.014 0.866 20363 Z= 0.472 Angle : 1.259 52.243 27750 Z= 0.544 Chirality : 0.057 0.309 3137 Planarity : 0.007 0.083 3348 Dihedral : 16.701 147.206 7718 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.75 % Favored : 92.03 % Rotamer: Outliers : 0.43 % Allowed : 6.74 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.70 (0.12), residues: 2309 helix: -4.49 (0.07), residues: 964 sheet: -2.68 (0.28), residues: 295 loop : -3.30 (0.15), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.001 ARG D 343 TYR 0.054 0.002 TYR G 116 PHE 0.038 0.002 PHE G 112 TRP 0.060 0.002 TRP C 96 HIS 0.016 0.001 HIS B 613 Details of bonding type rmsd covalent geometry : bond 0.00640 (20335) covalent geometry : angle 0.95638 (27705) hydrogen bonds : bond 0.31071 ( 458) hydrogen bonds : angle 9.77934 ( 1338) metal coordination : bond 0.33171 ( 28) metal coordination : angle 20.34466 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 483 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 HIS cc_start: 0.6159 (t70) cc_final: 0.5580 (m90) REVERT: A 97 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8278 (tm-30) REVERT: A 167 LYS cc_start: 0.8138 (tttt) cc_final: 0.7579 (mtmt) REVERT: A 291 LEU cc_start: 0.8018 (mt) cc_final: 0.7599 (mp) REVERT: A 318 PRO cc_start: 0.9052 (Cg_exo) cc_final: 0.8809 (Cg_endo) REVERT: A 322 LYS cc_start: 0.7412 (tptp) cc_final: 0.7206 (mttp) REVERT: F 51 ASN cc_start: 0.7930 (m-40) cc_final: 0.7586 (t0) REVERT: F 59 GLU cc_start: 0.7882 (tt0) cc_final: 0.6774 (tm-30) REVERT: B 380 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7720 (mmt180) REVERT: B 546 GLU cc_start: 0.6279 (tm-30) cc_final: 0.5953 (tm-30) REVERT: B 570 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7618 (tm-30) REVERT: B 671 LYS cc_start: 0.8053 (mttt) cc_final: 0.7660 (tttp) REVERT: E 16 ASP cc_start: 0.7788 (t0) cc_final: 0.7576 (t0) REVERT: E 114 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7294 (tp30) REVERT: E 147 MET cc_start: 0.8325 (mmm) cc_final: 0.8107 (mpp) REVERT: E 158 LYS cc_start: 0.8549 (ptmt) cc_final: 0.8316 (pttp) REVERT: E 170 SER cc_start: 0.8689 (t) cc_final: 0.8461 (p) REVERT: E 226 TYR cc_start: 0.8291 (m-80) cc_final: 0.8044 (m-80) REVERT: E 236 ASP cc_start: 0.8273 (p0) cc_final: 0.7884 (p0) REVERT: E 251 TYR cc_start: 0.8399 (m-80) cc_final: 0.8039 (m-80) REVERT: D 103 GLN cc_start: 0.8567 (mp10) cc_final: 0.8110 (mt0) REVERT: D 181 ASN cc_start: 0.8576 (t0) cc_final: 0.8158 (t0) REVERT: D 321 SER cc_start: 0.8916 (m) cc_final: 0.8416 (t) REVERT: D 365 ASN cc_start: 0.6973 (m-40) cc_final: 0.6702 (m110) REVERT: C 57 MET cc_start: 0.9088 (mmm) cc_final: 0.8755 (mmt) REVERT: C 78 GLU cc_start: 0.7812 (tp30) cc_final: 0.7603 (tp30) REVERT: C 79 PHE cc_start: 0.8230 (m-80) cc_final: 0.7853 (m-80) REVERT: C 159 VAL cc_start: 0.9122 (t) cc_final: 0.8223 (p) REVERT: C 399 ASP cc_start: 0.7725 (t70) cc_final: 0.7521 (t70) REVERT: C 438 LYS cc_start: 0.8083 (tttt) cc_final: 0.7780 (tptt) REVERT: C 454 PHE cc_start: 0.7230 (t80) cc_final: 0.6617 (t80) REVERT: C 456 LYS cc_start: 0.7899 (pttm) cc_final: 0.7460 (mtpt) REVERT: G 119 ASN cc_start: 0.6112 (m-40) cc_final: 0.5457 (m110) REVERT: G 175 TRP cc_start: 0.7272 (t-100) cc_final: 0.6489 (t-100) outliers start: 9 outliers final: 4 residues processed: 490 average time/residue: 0.1730 time to fit residues: 122.3045 Evaluate side-chains 326 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 322 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 284 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.0770 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.0060 chunk 200 optimal weight: 0.0170 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS A 498 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN F 54 GLN F 64 ASN B 60 GLN B 92 ASN B 201 HIS ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 HIS D 60 HIS D 147 ASN D 154 GLN D 158 HIS D 279 ASN D 376 HIS C 116 GLN C 181 GLN C 260 ASN C 273 GLN G 119 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.133871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.098174 restraints weight = 32620.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101977 restraints weight = 17080.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103672 restraints weight = 11199.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.104188 restraints weight = 9222.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104335 restraints weight = 9127.413| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 20363 Z= 0.130 Angle : 0.692 17.607 27750 Z= 0.336 Chirality : 0.043 0.173 3137 Planarity : 0.005 0.081 3348 Dihedral : 14.726 148.428 3086 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.67 % Favored : 93.20 % Rotamer: Outliers : 2.17 % Allowed : 13.43 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.29 (0.14), residues: 2309 helix: -2.71 (0.12), residues: 994 sheet: -2.45 (0.28), residues: 309 loop : -3.01 (0.16), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 94 TYR 0.027 0.001 TYR A 581 PHE 0.021 0.001 PHE B 329 TRP 0.028 0.001 TRP C 96 HIS 0.011 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00290 (20335) covalent geometry : angle 0.64629 (27705) hydrogen bonds : bond 0.04038 ( 458) hydrogen bonds : angle 4.54013 ( 1338) metal coordination : bond 0.02783 ( 28) metal coordination : angle 6.16250 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 389 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 167 LYS cc_start: 0.8253 (tttt) cc_final: 0.7614 (mttt) REVERT: A 189 LEU cc_start: 0.8567 (mp) cc_final: 0.8233 (mp) REVERT: A 276 MET cc_start: 0.7540 (ttm) cc_final: 0.7309 (ttm) REVERT: A 284 CYS cc_start: 0.7786 (m) cc_final: 0.7581 (m) REVERT: A 291 LEU cc_start: 0.7981 (mt) cc_final: 0.7704 (mp) REVERT: A 442 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7331 (mp0) REVERT: A 535 THR cc_start: 0.8232 (m) cc_final: 0.7916 (m) REVERT: A 581 TYR cc_start: 0.7791 (t80) cc_final: 0.7369 (t80) REVERT: F 25 GLU cc_start: 0.7795 (pt0) cc_final: 0.7535 (pm20) REVERT: F 51 ASN cc_start: 0.8240 (m-40) cc_final: 0.7808 (t0) REVERT: F 53 LEU cc_start: 0.8116 (tp) cc_final: 0.7894 (tp) REVERT: F 59 GLU cc_start: 0.8099 (tt0) cc_final: 0.7275 (tm-30) REVERT: F 64 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7454 (p0) REVERT: B 1 MET cc_start: 0.6872 (tpt) cc_final: 0.6560 (tpp) REVERT: B 8 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8436 (mp) REVERT: B 125 ARG cc_start: 0.7833 (tpt90) cc_final: 0.7605 (ttp80) REVERT: B 380 ARG cc_start: 0.8224 (mtt180) cc_final: 0.7824 (mmt180) REVERT: B 405 THR cc_start: 0.9273 (t) cc_final: 0.9019 (t) REVERT: B 410 TYR cc_start: 0.8090 (m-80) cc_final: 0.7801 (m-80) REVERT: B 570 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7455 (tm-30) REVERT: B 671 LYS cc_start: 0.8031 (mttt) cc_final: 0.7733 (tttp) REVERT: E 16 ASP cc_start: 0.8214 (t0) cc_final: 0.7816 (t0) REVERT: E 33 THR cc_start: 0.9172 (t) cc_final: 0.8846 (p) REVERT: E 56 LYS cc_start: 0.8770 (mttt) cc_final: 0.8261 (mttp) REVERT: E 68 ARG cc_start: 0.7420 (mtm-85) cc_final: 0.7119 (mtm-85) REVERT: E 114 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7309 (tp30) REVERT: E 117 ASP cc_start: 0.8422 (t0) cc_final: 0.8175 (t70) REVERT: E 158 LYS cc_start: 0.8542 (ptmt) cc_final: 0.8020 (pttp) REVERT: E 170 SER cc_start: 0.8548 (t) cc_final: 0.8335 (p) REVERT: E 251 TYR cc_start: 0.8460 (m-80) cc_final: 0.8196 (m-10) REVERT: E 256 PHE cc_start: 0.8457 (m-10) cc_final: 0.8199 (m-10) REVERT: E 266 TYR cc_start: 0.7736 (m-10) cc_final: 0.7417 (m-80) REVERT: D 66 ASP cc_start: 0.8429 (t0) cc_final: 0.8189 (t0) REVERT: D 103 GLN cc_start: 0.8237 (mp10) cc_final: 0.7917 (mt0) REVERT: D 293 GLN cc_start: 0.7985 (tp40) cc_final: 0.7574 (tt0) REVERT: D 321 SER cc_start: 0.8878 (m) cc_final: 0.8482 (t) REVERT: C 78 GLU cc_start: 0.8130 (tp30) cc_final: 0.7788 (tp30) REVERT: C 393 LEU cc_start: 0.8610 (mm) cc_final: 0.8381 (mt) REVERT: C 410 ASN cc_start: 0.4313 (t0) cc_final: 0.2960 (p0) REVERT: C 438 LYS cc_start: 0.8442 (tttt) cc_final: 0.8197 (tttp) REVERT: G 175 TRP cc_start: 0.7621 (t-100) cc_final: 0.7178 (t-100) REVERT: G 177 ASP cc_start: 0.8248 (p0) cc_final: 0.7867 (p0) REVERT: G 178 MET cc_start: 0.8333 (ttp) cc_final: 0.7560 (tmm) REVERT: G 211 ARG cc_start: 0.8140 (ptp-110) cc_final: 0.7522 (ttm110) outliers start: 45 outliers final: 18 residues processed: 420 average time/residue: 0.1331 time to fit residues: 85.7609 Evaluate side-chains 351 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 331 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain G residue 186 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 225 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 chunk 156 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 150 optimal weight: 0.0000 chunk 100 optimal weight: 0.8980 chunk 231 optimal weight: 0.0020 chunk 140 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 564 ASN A 677 GLN B 148 HIS B 726 GLN C 424 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.097015 restraints weight = 32989.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100894 restraints weight = 17901.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.102859 restraints weight = 11292.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103048 restraints weight = 10127.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.103540 restraints weight = 9386.136| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 20363 Z= 0.118 Angle : 0.647 13.722 27750 Z= 0.311 Chirality : 0.042 0.165 3137 Planarity : 0.004 0.076 3348 Dihedral : 14.347 148.268 3082 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.24 % Favored : 93.72 % Rotamer: Outliers : 2.17 % Allowed : 15.21 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (0.16), residues: 2309 helix: -1.56 (0.15), residues: 984 sheet: -2.28 (0.30), residues: 298 loop : -2.68 (0.17), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 343 TYR 0.021 0.001 TYR A 534 PHE 0.020 0.001 PHE B 329 TRP 0.022 0.001 TRP C 96 HIS 0.010 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00266 (20335) covalent geometry : angle 0.61137 (27705) hydrogen bonds : bond 0.03482 ( 458) hydrogen bonds : angle 3.92090 ( 1338) metal coordination : bond 0.02572 ( 28) metal coordination : angle 5.29411 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 368 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7878 (m-70) REVERT: A 97 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8177 (tm-30) REVERT: A 167 LYS cc_start: 0.8212 (tttt) cc_final: 0.7579 (mtpt) REVERT: A 276 MET cc_start: 0.7632 (ttm) cc_final: 0.7314 (ttm) REVERT: A 284 CYS cc_start: 0.8049 (m) cc_final: 0.7837 (m) REVERT: A 291 LEU cc_start: 0.8119 (mt) cc_final: 0.7847 (mp) REVERT: A 442 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7355 (mp0) REVERT: F 25 GLU cc_start: 0.7800 (pt0) cc_final: 0.7558 (pm20) REVERT: F 51 ASN cc_start: 0.8244 (m-40) cc_final: 0.7981 (t0) REVERT: F 53 LEU cc_start: 0.8178 (tp) cc_final: 0.7955 (tp) REVERT: F 59 GLU cc_start: 0.8064 (tt0) cc_final: 0.7859 (tt0) REVERT: F 63 GLN cc_start: 0.8330 (tt0) cc_final: 0.8068 (mt0) REVERT: B 1 MET cc_start: 0.6943 (tpt) cc_final: 0.6571 (tpp) REVERT: B 8 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8438 (mp) REVERT: B 125 ARG cc_start: 0.7875 (tpt90) cc_final: 0.7610 (ttp80) REVERT: B 380 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7808 (mmt180) REVERT: B 410 TYR cc_start: 0.8061 (m-80) cc_final: 0.7720 (m-80) REVERT: B 570 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7690 (tm-30) REVERT: B 606 GLU cc_start: 0.8369 (pm20) cc_final: 0.8003 (pm20) REVERT: B 671 LYS cc_start: 0.7995 (mttt) cc_final: 0.7642 (tttt) REVERT: E 16 ASP cc_start: 0.8329 (t0) cc_final: 0.7894 (t0) REVERT: E 33 THR cc_start: 0.9179 (t) cc_final: 0.8843 (p) REVERT: E 56 LYS cc_start: 0.8737 (mttt) cc_final: 0.8249 (mttp) REVERT: E 114 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7450 (tp30) REVERT: E 117 ASP cc_start: 0.8276 (t0) cc_final: 0.8010 (t0) REVERT: E 158 LYS cc_start: 0.8525 (ptmt) cc_final: 0.8029 (ptmm) REVERT: E 170 SER cc_start: 0.8538 (t) cc_final: 0.8255 (p) REVERT: E 226 TYR cc_start: 0.8342 (m-80) cc_final: 0.7827 (m-80) REVERT: E 266 TYR cc_start: 0.7705 (m-10) cc_final: 0.7473 (m-80) REVERT: D 73 ASP cc_start: 0.7984 (t70) cc_final: 0.7741 (t70) REVERT: D 103 GLN cc_start: 0.8243 (mp10) cc_final: 0.7971 (mt0) REVERT: D 282 PRO cc_start: 0.7747 (Cg_endo) cc_final: 0.7520 (Cg_exo) REVERT: D 321 SER cc_start: 0.8791 (m) cc_final: 0.8442 (t) REVERT: C 163 MET cc_start: 0.8978 (mpp) cc_final: 0.8509 (mpp) REVERT: C 410 ASN cc_start: 0.4353 (t0) cc_final: 0.3494 (p0) REVERT: C 438 LYS cc_start: 0.8482 (tttt) cc_final: 0.8058 (tmtt) REVERT: C 454 PHE cc_start: 0.7179 (t80) cc_final: 0.6976 (t80) REVERT: G 175 TRP cc_start: 0.7562 (t-100) cc_final: 0.7134 (t-100) REVERT: G 178 MET cc_start: 0.8188 (ttp) cc_final: 0.7583 (tmm) outliers start: 45 outliers final: 27 residues processed: 398 average time/residue: 0.1360 time to fit residues: 84.5233 Evaluate side-chains 364 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 335 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 187 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 224 optimal weight: 0.0570 chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 0.1980 chunk 213 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 677 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN G 119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.129641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.093162 restraints weight = 32755.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.097581 restraints weight = 19172.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098118 restraints weight = 12027.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.098620 restraints weight = 10819.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.098745 restraints weight = 10230.339| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 20363 Z= 0.175 Angle : 0.662 12.515 27750 Z= 0.323 Chirality : 0.044 0.198 3137 Planarity : 0.004 0.083 3348 Dihedral : 14.263 149.053 3082 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.41 % Favored : 92.55 % Rotamer: Outliers : 2.70 % Allowed : 16.23 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.16), residues: 2309 helix: -0.93 (0.16), residues: 1003 sheet: -2.11 (0.30), residues: 302 loop : -2.54 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 195 TYR 0.025 0.001 TYR A 581 PHE 0.021 0.001 PHE B 329 TRP 0.024 0.001 TRP C 96 HIS 0.021 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00408 (20335) covalent geometry : angle 0.63063 (27705) hydrogen bonds : bond 0.03403 ( 458) hydrogen bonds : angle 3.70597 ( 1338) metal coordination : bond 0.03238 ( 28) metal coordination : angle 5.05292 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 346 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 167 LYS cc_start: 0.8310 (tttt) cc_final: 0.7488 (ptpt) REVERT: A 276 MET cc_start: 0.7618 (ttm) cc_final: 0.7282 (ttm) REVERT: A 284 CYS cc_start: 0.8266 (m) cc_final: 0.7964 (m) REVERT: A 442 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7281 (mp0) REVERT: A 700 ASP cc_start: 0.7622 (t0) cc_final: 0.7359 (t0) REVERT: F 51 ASN cc_start: 0.8394 (m-40) cc_final: 0.7895 (t0) REVERT: F 53 LEU cc_start: 0.8457 (tp) cc_final: 0.8205 (tp) REVERT: F 55 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8116 (mm-30) REVERT: B 8 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8463 (mp) REVERT: B 220 LEU cc_start: 0.8887 (mm) cc_final: 0.8626 (tp) REVERT: B 380 ARG cc_start: 0.8135 (mtt180) cc_final: 0.7768 (mmt180) REVERT: B 410 TYR cc_start: 0.8166 (m-80) cc_final: 0.7919 (m-80) REVERT: B 570 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7634 (tm-30) REVERT: B 606 GLU cc_start: 0.8412 (pm20) cc_final: 0.8013 (pm20) REVERT: B 671 LYS cc_start: 0.8070 (mttt) cc_final: 0.7675 (tttt) REVERT: E 16 ASP cc_start: 0.8391 (t0) cc_final: 0.7949 (t0) REVERT: E 56 LYS cc_start: 0.8864 (mttt) cc_final: 0.8604 (mttp) REVERT: E 68 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.6891 (mtp180) REVERT: E 114 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7237 (tp30) REVERT: E 117 ASP cc_start: 0.8286 (t0) cc_final: 0.8007 (t0) REVERT: E 133 LEU cc_start: 0.8547 (tp) cc_final: 0.8216 (tt) REVERT: E 158 LYS cc_start: 0.8551 (ptmt) cc_final: 0.8044 (ptmm) REVERT: E 170 SER cc_start: 0.8403 (t) cc_final: 0.8121 (p) REVERT: E 266 TYR cc_start: 0.7597 (m-10) cc_final: 0.7384 (m-80) REVERT: D 73 ASP cc_start: 0.8229 (t70) cc_final: 0.7968 (t70) REVERT: D 103 GLN cc_start: 0.8311 (mp10) cc_final: 0.8040 (mt0) REVERT: D 113 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7777 (mtm110) REVERT: D 136 ASP cc_start: 0.7971 (p0) cc_final: 0.7653 (p0) REVERT: D 293 GLN cc_start: 0.7929 (tp40) cc_final: 0.7465 (tt0) REVERT: D 321 SER cc_start: 0.8838 (m) cc_final: 0.8441 (t) REVERT: D 364 GLN cc_start: 0.7639 (mp10) cc_final: 0.7432 (pp30) REVERT: C 78 GLU cc_start: 0.8267 (tp30) cc_final: 0.7817 (tp30) REVERT: C 334 MET cc_start: 0.8156 (mpp) cc_final: 0.7836 (mpp) REVERT: C 410 ASN cc_start: 0.4034 (t0) cc_final: 0.3234 (p0) REVERT: C 438 LYS cc_start: 0.8561 (tttt) cc_final: 0.8120 (tmtt) REVERT: G 118 MET cc_start: 0.7687 (mmm) cc_final: 0.7250 (mmm) REVERT: G 122 ASP cc_start: 0.7722 (m-30) cc_final: 0.7276 (m-30) REVERT: G 175 TRP cc_start: 0.7525 (t-100) cc_final: 0.7022 (t-100) REVERT: G 178 MET cc_start: 0.8192 (ttp) cc_final: 0.7521 (tmm) REVERT: G 211 ARG cc_start: 0.7732 (ptp-110) cc_final: 0.7373 (ttm110) outliers start: 56 outliers final: 41 residues processed: 381 average time/residue: 0.1307 time to fit residues: 77.3326 Evaluate side-chains 358 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 316 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 276 CYS Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 206 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 180 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 211 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 GLN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 GLN G 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.130503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.094282 restraints weight = 32489.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098084 restraints weight = 18484.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099717 restraints weight = 11657.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.100052 restraints weight = 9643.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.100602 restraints weight = 10103.153| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.146 20363 Z= 0.133 Angle : 0.632 14.432 27750 Z= 0.305 Chirality : 0.043 0.170 3137 Planarity : 0.004 0.080 3348 Dihedral : 14.093 148.771 3082 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.99 % Allowed : 17.24 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.17), residues: 2309 helix: -0.44 (0.16), residues: 1008 sheet: -2.00 (0.30), residues: 294 loop : -2.42 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 487 TYR 0.023 0.001 TYR A 581 PHE 0.022 0.001 PHE B 329 TRP 0.023 0.001 TRP C 96 HIS 0.012 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00307 (20335) covalent geometry : angle 0.60030 (27705) hydrogen bonds : bond 0.03080 ( 458) hydrogen bonds : angle 3.51565 ( 1338) metal coordination : bond 0.02908 ( 28) metal coordination : angle 4.95501 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 334 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8360 (tm-30) REVERT: A 167 LYS cc_start: 0.8309 (tttt) cc_final: 0.7452 (ptpt) REVERT: A 279 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 442 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7456 (mp0) REVERT: A 514 MET cc_start: 0.9031 (mmm) cc_final: 0.8137 (tpt) REVERT: A 537 ASN cc_start: 0.9116 (t0) cc_final: 0.8910 (t0) REVERT: A 700 ASP cc_start: 0.7480 (t0) cc_final: 0.7235 (t0) REVERT: F 51 ASN cc_start: 0.8454 (m-40) cc_final: 0.7959 (t0) REVERT: F 53 LEU cc_start: 0.8505 (tp) cc_final: 0.8267 (tp) REVERT: B 8 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8436 (mp) REVERT: B 220 LEU cc_start: 0.8835 (mm) cc_final: 0.8569 (tp) REVERT: B 238 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.7987 (p0) REVERT: B 380 ARG cc_start: 0.8139 (mtt180) cc_final: 0.7774 (mmt180) REVERT: B 410 TYR cc_start: 0.8122 (m-80) cc_final: 0.7855 (m-10) REVERT: B 570 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7542 (tm-30) REVERT: B 606 GLU cc_start: 0.8372 (pm20) cc_final: 0.8099 (pm20) REVERT: B 671 LYS cc_start: 0.8112 (mttt) cc_final: 0.7675 (tttp) REVERT: E 16 ASP cc_start: 0.8440 (t0) cc_final: 0.7891 (t0) REVERT: E 31 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7905 (mm-40) REVERT: E 56 LYS cc_start: 0.8816 (mttt) cc_final: 0.8306 (mttp) REVERT: E 68 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7335 (mtm-85) REVERT: E 114 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7479 (tp30) REVERT: E 117 ASP cc_start: 0.8270 (t0) cc_final: 0.8049 (t0) REVERT: E 147 MET cc_start: 0.8237 (tpp) cc_final: 0.7719 (mpp) REVERT: E 158 LYS cc_start: 0.8544 (ptmt) cc_final: 0.7978 (pttp) REVERT: E 170 SER cc_start: 0.8215 (t) cc_final: 0.7931 (p) REVERT: E 226 TYR cc_start: 0.8279 (m-80) cc_final: 0.7637 (m-80) REVERT: D 103 GLN cc_start: 0.8264 (mp10) cc_final: 0.8008 (mt0) REVERT: D 113 ARG cc_start: 0.8010 (mtm110) cc_final: 0.7775 (mtm110) REVERT: D 321 SER cc_start: 0.8782 (m) cc_final: 0.8399 (t) REVERT: D 349 GLN cc_start: 0.7730 (tt0) cc_final: 0.7383 (mp10) REVERT: C 408 LEU cc_start: 0.8351 (tp) cc_final: 0.8130 (tp) REVERT: C 410 ASN cc_start: 0.4059 (t0) cc_final: 0.3417 (p0) REVERT: C 438 LYS cc_start: 0.8637 (tttt) cc_final: 0.8172 (tmtt) REVERT: G 175 TRP cc_start: 0.7505 (t-100) cc_final: 0.6964 (t-100) REVERT: G 178 MET cc_start: 0.8126 (ttp) cc_final: 0.7437 (tmm) outliers start: 62 outliers final: 43 residues processed: 373 average time/residue: 0.1272 time to fit residues: 73.5293 Evaluate side-chains 369 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 324 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 166 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 156 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN C 181 GLN C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.128125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.089540 restraints weight = 32625.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.093319 restraints weight = 17037.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.095770 restraints weight = 11585.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.097346 restraints weight = 9130.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.098222 restraints weight = 7880.530| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.218 20363 Z= 0.178 Angle : 0.673 18.914 27750 Z= 0.322 Chirality : 0.044 0.159 3137 Planarity : 0.004 0.082 3348 Dihedral : 14.109 148.814 3082 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.27 % Allowed : 17.43 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.17), residues: 2309 helix: -0.22 (0.17), residues: 1021 sheet: -1.93 (0.30), residues: 297 loop : -2.37 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 487 TYR 0.025 0.001 TYR A 581 PHE 0.022 0.001 PHE B 329 TRP 0.022 0.001 TRP C 96 HIS 0.024 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00415 (20335) covalent geometry : angle 0.63184 (27705) hydrogen bonds : bond 0.03256 ( 458) hydrogen bonds : angle 3.50481 ( 1338) metal coordination : bond 0.04288 ( 28) metal coordination : angle 5.76369 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 328 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8349 (tm-30) REVERT: A 167 LYS cc_start: 0.8372 (tttt) cc_final: 0.7556 (ptpt) REVERT: A 279 GLU cc_start: 0.8296 (tm-30) cc_final: 0.8086 (tm-30) REVERT: A 700 ASP cc_start: 0.7427 (t0) cc_final: 0.7191 (t0) REVERT: F 13 ASP cc_start: 0.8048 (t70) cc_final: 0.7697 (t0) REVERT: F 44 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6531 (t80) REVERT: F 51 ASN cc_start: 0.8348 (m-40) cc_final: 0.7903 (t0) REVERT: F 53 LEU cc_start: 0.8669 (tp) cc_final: 0.8453 (tp) REVERT: F 64 ASN cc_start: 0.7953 (p0) cc_final: 0.7718 (m-40) REVERT: B 1 MET cc_start: 0.6461 (tpp) cc_final: 0.6210 (ttt) REVERT: B 8 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8469 (mp) REVERT: B 220 LEU cc_start: 0.8845 (mm) cc_final: 0.8542 (tp) REVERT: B 238 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8091 (p0) REVERT: B 380 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7751 (mmt180) REVERT: B 410 TYR cc_start: 0.8164 (m-80) cc_final: 0.7920 (m-10) REVERT: B 546 GLU cc_start: 0.6071 (tm-30) cc_final: 0.5706 (tm-30) REVERT: B 554 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7258 (tp30) REVERT: B 570 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7503 (tm-30) REVERT: B 606 GLU cc_start: 0.8286 (pm20) cc_final: 0.8065 (pm20) REVERT: B 657 MET cc_start: 0.9160 (mmm) cc_final: 0.8901 (mmm) REVERT: B 671 LYS cc_start: 0.8052 (mttt) cc_final: 0.7662 (tttm) REVERT: E 16 ASP cc_start: 0.8432 (t0) cc_final: 0.7858 (t0) REVERT: E 68 ARG cc_start: 0.7571 (mtm-85) cc_final: 0.7173 (mtp180) REVERT: E 114 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7537 (tp30) REVERT: E 117 ASP cc_start: 0.8213 (t0) cc_final: 0.7993 (t0) REVERT: E 150 GLU cc_start: 0.7345 (mp0) cc_final: 0.6949 (mp0) REVERT: E 158 LYS cc_start: 0.8524 (ptmt) cc_final: 0.7929 (pttp) REVERT: E 170 SER cc_start: 0.8222 (t) cc_final: 0.7975 (p) REVERT: E 262 ILE cc_start: 0.8102 (mt) cc_final: 0.7666 (mt) REVERT: D 103 GLN cc_start: 0.8326 (mp10) cc_final: 0.8078 (mt0) REVERT: D 113 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7762 (mtm110) REVERT: D 321 SER cc_start: 0.8866 (m) cc_final: 0.8435 (t) REVERT: D 349 GLN cc_start: 0.7826 (tt0) cc_final: 0.7522 (mp10) REVERT: C 78 GLU cc_start: 0.8249 (tp30) cc_final: 0.7937 (tp30) REVERT: C 408 LEU cc_start: 0.8151 (tp) cc_final: 0.7807 (mt) REVERT: C 410 ASN cc_start: 0.4120 (t0) cc_final: 0.3512 (p0) REVERT: C 438 LYS cc_start: 0.8621 (tttt) cc_final: 0.8178 (tmtt) REVERT: G 118 MET cc_start: 0.7702 (mmm) cc_final: 0.7264 (mmt) REVERT: G 122 ASP cc_start: 0.8034 (m-30) cc_final: 0.7790 (m-30) REVERT: G 175 TRP cc_start: 0.7580 (t-100) cc_final: 0.6959 (t-100) REVERT: G 178 MET cc_start: 0.8228 (ttp) cc_final: 0.7507 (tmm) REVERT: G 211 ARG cc_start: 0.7758 (ptp-110) cc_final: 0.7416 (ttm110) outliers start: 68 outliers final: 52 residues processed: 373 average time/residue: 0.1272 time to fit residues: 73.6598 Evaluate side-chains 369 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 314 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 276 CYS Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 206 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 163 optimal weight: 0.9990 chunk 209 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 221 optimal weight: 0.0870 chunk 78 optimal weight: 0.0870 chunk 137 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.130445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.092013 restraints weight = 32706.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.095914 restraints weight = 16881.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098429 restraints weight = 11389.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100022 restraints weight = 8959.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100899 restraints weight = 7701.247| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.212 20363 Z= 0.123 Angle : 0.643 14.764 27750 Z= 0.306 Chirality : 0.043 0.155 3137 Planarity : 0.004 0.077 3348 Dihedral : 13.928 148.123 3082 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.03 % Allowed : 18.44 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.18), residues: 2309 helix: 0.11 (0.17), residues: 1010 sheet: -1.85 (0.30), residues: 294 loop : -2.27 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 487 TYR 0.021 0.001 TYR A 534 PHE 0.022 0.001 PHE B 93 TRP 0.019 0.001 TRP C 96 HIS 0.019 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00277 (20335) covalent geometry : angle 0.60589 (27705) hydrogen bonds : bond 0.02932 ( 458) hydrogen bonds : angle 3.37447 ( 1338) metal coordination : bond 0.04140 ( 28) metal coordination : angle 5.35935 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 326 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8304 (tm-30) REVERT: A 167 LYS cc_start: 0.8351 (tttt) cc_final: 0.7517 (ptpt) REVERT: A 279 GLU cc_start: 0.8233 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 427 MET cc_start: 0.8732 (tpp) cc_final: 0.8338 (tpp) REVERT: A 700 ASP cc_start: 0.7422 (t0) cc_final: 0.7200 (t0) REVERT: F 9 LEU cc_start: 0.8024 (tt) cc_final: 0.7706 (tt) REVERT: F 44 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6484 (t80) REVERT: F 51 ASN cc_start: 0.8317 (m-40) cc_final: 0.7842 (t0) REVERT: F 53 LEU cc_start: 0.8634 (tp) cc_final: 0.8423 (tp) REVERT: F 64 ASN cc_start: 0.7872 (p0) cc_final: 0.7597 (m-40) REVERT: B 1 MET cc_start: 0.6420 (tpp) cc_final: 0.6156 (ttt) REVERT: B 8 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8402 (mp) REVERT: B 28 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8752 (tt) REVERT: B 220 LEU cc_start: 0.8796 (mm) cc_final: 0.8530 (tp) REVERT: B 238 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7944 (p0) REVERT: B 380 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7830 (mtt180) REVERT: B 410 TYR cc_start: 0.8092 (m-80) cc_final: 0.7876 (m-10) REVERT: B 546 GLU cc_start: 0.5922 (tm-30) cc_final: 0.5576 (tm-30) REVERT: B 570 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7275 (tm-30) REVERT: B 657 MET cc_start: 0.9152 (mmm) cc_final: 0.8949 (tpp) REVERT: B 671 LYS cc_start: 0.8001 (mttt) cc_final: 0.7588 (tttm) REVERT: E 16 ASP cc_start: 0.8418 (t0) cc_final: 0.7825 (t0) REVERT: E 68 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.6756 (mtp180) REVERT: E 114 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7165 (tp30) REVERT: E 117 ASP cc_start: 0.8170 (t0) cc_final: 0.7899 (t0) REVERT: E 150 GLU cc_start: 0.7365 (mp0) cc_final: 0.6976 (mp0) REVERT: E 158 LYS cc_start: 0.8536 (ptmt) cc_final: 0.7932 (pttp) REVERT: E 170 SER cc_start: 0.8197 (t) cc_final: 0.7943 (p) REVERT: E 197 ASP cc_start: 0.7958 (p0) cc_final: 0.7729 (p0) REVERT: E 226 TYR cc_start: 0.8396 (m-80) cc_final: 0.7590 (m-80) REVERT: E 262 ILE cc_start: 0.8084 (mt) cc_final: 0.7751 (mt) REVERT: D 103 GLN cc_start: 0.8324 (mp10) cc_final: 0.8059 (mt0) REVERT: D 113 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7748 (mtm110) REVERT: D 321 SER cc_start: 0.8811 (m) cc_final: 0.8398 (t) REVERT: C 78 GLU cc_start: 0.8240 (tp30) cc_final: 0.8014 (tp30) REVERT: C 163 MET cc_start: 0.8933 (mpp) cc_final: 0.8212 (mpp) REVERT: C 408 LEU cc_start: 0.8130 (tp) cc_final: 0.7812 (mt) REVERT: C 410 ASN cc_start: 0.4127 (t0) cc_final: 0.3645 (p0) REVERT: C 438 LYS cc_start: 0.8630 (tttt) cc_final: 0.8207 (tmtt) REVERT: G 175 TRP cc_start: 0.7569 (t-100) cc_final: 0.7047 (t-100) REVERT: G 178 MET cc_start: 0.8147 (ttp) cc_final: 0.7512 (tmm) REVERT: G 185 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8185 (mt0) outliers start: 63 outliers final: 45 residues processed: 367 average time/residue: 0.1283 time to fit residues: 72.3305 Evaluate side-chains 368 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 318 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 276 CYS Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 185 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 180 optimal weight: 7.9990 chunk 201 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 161 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.129446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.090937 restraints weight = 32782.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094785 restraints weight = 17045.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.097288 restraints weight = 11569.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.098834 restraints weight = 9113.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099839 restraints weight = 7883.805| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.205 20363 Z= 0.143 Angle : 0.655 12.601 27750 Z= 0.314 Chirality : 0.043 0.159 3137 Planarity : 0.004 0.078 3348 Dihedral : 13.915 147.900 3082 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.99 % Allowed : 19.16 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.18), residues: 2309 helix: 0.20 (0.17), residues: 1019 sheet: -1.78 (0.31), residues: 294 loop : -2.20 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 487 TYR 0.023 0.001 TYR E 143 PHE 0.021 0.001 PHE B 93 TRP 0.019 0.001 TRP C 96 HIS 0.019 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00332 (20335) covalent geometry : angle 0.62140 (27705) hydrogen bonds : bond 0.03037 ( 458) hydrogen bonds : angle 3.36058 ( 1338) metal coordination : bond 0.03979 ( 28) metal coordination : angle 5.19973 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 323 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 167 LYS cc_start: 0.8430 (tttt) cc_final: 0.7617 (ptpt) REVERT: A 427 MET cc_start: 0.8762 (tpp) cc_final: 0.8385 (tpp) REVERT: A 700 ASP cc_start: 0.7454 (t0) cc_final: 0.7232 (t0) REVERT: F 9 LEU cc_start: 0.8161 (tt) cc_final: 0.7849 (tt) REVERT: F 44 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6477 (t80) REVERT: F 51 ASN cc_start: 0.8288 (m-40) cc_final: 0.7822 (t0) REVERT: F 53 LEU cc_start: 0.8621 (tp) cc_final: 0.8409 (tp) REVERT: F 64 ASN cc_start: 0.7898 (p0) cc_final: 0.7695 (m-40) REVERT: B 1 MET cc_start: 0.6478 (tpp) cc_final: 0.6175 (ttt) REVERT: B 8 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8394 (mp) REVERT: B 28 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8786 (tt) REVERT: B 81 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 220 LEU cc_start: 0.8797 (mm) cc_final: 0.8515 (tp) REVERT: B 238 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.7951 (p0) REVERT: B 380 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7825 (mtt180) REVERT: B 546 GLU cc_start: 0.6099 (tm-30) cc_final: 0.5720 (tm-30) REVERT: B 554 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7260 (tp30) REVERT: B 570 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7241 (tm-30) REVERT: B 657 MET cc_start: 0.9158 (mmm) cc_final: 0.8951 (tpp) REVERT: B 671 LYS cc_start: 0.8012 (mttt) cc_final: 0.7599 (tttm) REVERT: E 16 ASP cc_start: 0.8420 (t0) cc_final: 0.7815 (t0) REVERT: E 68 ARG cc_start: 0.7565 (mtm-85) cc_final: 0.7140 (mtm180) REVERT: E 114 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7483 (tp30) REVERT: E 117 ASP cc_start: 0.8169 (t0) cc_final: 0.7899 (t0) REVERT: E 150 GLU cc_start: 0.7411 (mp0) cc_final: 0.7023 (mp0) REVERT: E 158 LYS cc_start: 0.8512 (ptmt) cc_final: 0.7908 (pttp) REVERT: E 170 SER cc_start: 0.8223 (t) cc_final: 0.7945 (p) REVERT: E 226 TYR cc_start: 0.8399 (m-80) cc_final: 0.7985 (m-80) REVERT: E 262 ILE cc_start: 0.8094 (mt) cc_final: 0.7702 (mt) REVERT: D 103 GLN cc_start: 0.8353 (mp10) cc_final: 0.8081 (mt0) REVERT: D 113 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7711 (mtm110) REVERT: D 321 SER cc_start: 0.8864 (m) cc_final: 0.8429 (t) REVERT: D 349 GLN cc_start: 0.7863 (tt0) cc_final: 0.7532 (mp10) REVERT: C 55 TRP cc_start: 0.7727 (m100) cc_final: 0.7400 (m100) REVERT: C 163 MET cc_start: 0.8947 (mpp) cc_final: 0.8242 (mpp) REVERT: C 408 LEU cc_start: 0.8114 (tp) cc_final: 0.7814 (mt) REVERT: C 410 ASN cc_start: 0.4004 (t0) cc_final: 0.3557 (p0) REVERT: C 438 LYS cc_start: 0.8641 (tttt) cc_final: 0.8223 (tmtt) REVERT: G 175 TRP cc_start: 0.7571 (t-100) cc_final: 0.6991 (t-100) REVERT: G 178 MET cc_start: 0.8172 (ttp) cc_final: 0.7521 (tmm) REVERT: G 185 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8288 (mt0) REVERT: G 197 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8587 (tm-30) outliers start: 62 outliers final: 52 residues processed: 367 average time/residue: 0.1214 time to fit residues: 68.8566 Evaluate side-chains 368 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 311 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 276 CYS Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 185 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 36 optimal weight: 1.9990 chunk 150 optimal weight: 0.3980 chunk 126 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 176 optimal weight: 0.1980 chunk 212 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.129277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.090874 restraints weight = 32491.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.094670 restraints weight = 16967.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.097181 restraints weight = 11559.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098754 restraints weight = 9098.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.099646 restraints weight = 7839.745| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 20363 Z= 0.148 Angle : 0.661 12.175 27750 Z= 0.318 Chirality : 0.044 0.227 3137 Planarity : 0.004 0.078 3348 Dihedral : 13.898 147.436 3082 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.89 % Allowed : 19.45 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.18), residues: 2309 helix: 0.33 (0.17), residues: 1022 sheet: -1.72 (0.30), residues: 300 loop : -2.14 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 487 TYR 0.022 0.001 TYR A 534 PHE 0.022 0.001 PHE B 93 TRP 0.020 0.001 TRP C 96 HIS 0.019 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00345 (20335) covalent geometry : angle 0.62897 (27705) hydrogen bonds : bond 0.03058 ( 458) hydrogen bonds : angle 3.36462 ( 1338) metal coordination : bond 0.03898 ( 28) metal coordination : angle 5.11241 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 320 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8344 (tm-30) REVERT: A 167 LYS cc_start: 0.8501 (tttt) cc_final: 0.7623 (ptpt) REVERT: A 427 MET cc_start: 0.8758 (tpp) cc_final: 0.8380 (tpp) REVERT: A 442 GLU cc_start: 0.7822 (mp0) cc_final: 0.7453 (mm-30) REVERT: F 13 ASP cc_start: 0.8137 (t70) cc_final: 0.7769 (t0) REVERT: F 51 ASN cc_start: 0.8295 (m-40) cc_final: 0.7804 (t0) REVERT: F 53 LEU cc_start: 0.8645 (tp) cc_final: 0.8443 (tp) REVERT: B 1 MET cc_start: 0.6585 (tpp) cc_final: 0.6241 (ttt) REVERT: B 8 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8410 (mp) REVERT: B 28 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8783 (tt) REVERT: B 81 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8007 (mm-30) REVERT: B 220 LEU cc_start: 0.8751 (mm) cc_final: 0.8476 (tp) REVERT: B 238 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.7956 (p0) REVERT: B 380 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7818 (mtt180) REVERT: B 546 GLU cc_start: 0.6253 (tm-30) cc_final: 0.5633 (tm-30) REVERT: B 554 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7287 (tp30) REVERT: B 570 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7212 (tm-30) REVERT: B 657 MET cc_start: 0.9159 (mmm) cc_final: 0.8937 (tpp) REVERT: B 671 LYS cc_start: 0.7995 (mttt) cc_final: 0.7585 (tttm) REVERT: B 711 ASP cc_start: 0.8134 (t0) cc_final: 0.7781 (t0) REVERT: E 16 ASP cc_start: 0.8444 (t0) cc_final: 0.7838 (t0) REVERT: E 68 ARG cc_start: 0.7547 (mtm-85) cc_final: 0.7098 (mtm180) REVERT: E 114 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7407 (tp30) REVERT: E 117 ASP cc_start: 0.8151 (t0) cc_final: 0.7911 (t0) REVERT: E 147 MET cc_start: 0.8220 (mtp) cc_final: 0.7635 (mtp) REVERT: E 150 GLU cc_start: 0.7439 (mp0) cc_final: 0.7052 (mp0) REVERT: E 158 LYS cc_start: 0.8525 (ptmt) cc_final: 0.7917 (pttp) REVERT: E 170 SER cc_start: 0.8228 (t) cc_final: 0.7956 (p) REVERT: E 226 TYR cc_start: 0.8410 (m-80) cc_final: 0.8000 (m-80) REVERT: E 262 ILE cc_start: 0.8110 (mt) cc_final: 0.7732 (mt) REVERT: D 103 GLN cc_start: 0.8361 (mp10) cc_final: 0.8070 (mt0) REVERT: D 113 ARG cc_start: 0.7971 (mtm110) cc_final: 0.7735 (mtm110) REVERT: D 321 SER cc_start: 0.8885 (m) cc_final: 0.8446 (t) REVERT: D 322 TYR cc_start: 0.8174 (m-80) cc_final: 0.7958 (m-80) REVERT: C 55 TRP cc_start: 0.7713 (m100) cc_final: 0.7436 (m100) REVERT: C 163 MET cc_start: 0.8935 (mpp) cc_final: 0.8208 (mpp) REVERT: C 332 SER cc_start: 0.8885 (t) cc_final: 0.8682 (m) REVERT: C 410 ASN cc_start: 0.3938 (t0) cc_final: 0.3504 (p0) REVERT: C 422 LEU cc_start: 0.8697 (mt) cc_final: 0.8390 (pp) REVERT: C 438 LYS cc_start: 0.8659 (tttt) cc_final: 0.8243 (tmtt) REVERT: G 113 MET cc_start: 0.6136 (mmp) cc_final: 0.5921 (mmp) REVERT: G 175 TRP cc_start: 0.7590 (t-100) cc_final: 0.7006 (t-100) REVERT: G 178 MET cc_start: 0.8174 (ttp) cc_final: 0.7487 (tmm) REVERT: G 197 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8531 (tm-30) REVERT: G 211 ARG cc_start: 0.7752 (ptp-110) cc_final: 0.7469 (ttm110) outliers start: 60 outliers final: 53 residues processed: 359 average time/residue: 0.1295 time to fit residues: 71.8094 Evaluate side-chains 370 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 314 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 276 CYS Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 143 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 201 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 185 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.130427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.092048 restraints weight = 32745.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.095911 restraints weight = 16931.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098354 restraints weight = 11457.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.099929 restraints weight = 9065.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100800 restraints weight = 7811.332| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.198 20363 Z= 0.131 Angle : 0.663 12.001 27750 Z= 0.319 Chirality : 0.043 0.204 3137 Planarity : 0.004 0.077 3348 Dihedral : 13.842 146.918 3082 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.99 % Allowed : 19.79 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.18), residues: 2309 helix: 0.51 (0.17), residues: 1018 sheet: -1.63 (0.31), residues: 300 loop : -2.04 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 487 TYR 0.021 0.001 TYR A 534 PHE 0.023 0.001 PHE B 93 TRP 0.020 0.001 TRP C 96 HIS 0.018 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00304 (20335) covalent geometry : angle 0.63307 (27705) hydrogen bonds : bond 0.02942 ( 458) hydrogen bonds : angle 3.31127 ( 1338) metal coordination : bond 0.03820 ( 28) metal coordination : angle 4.96403 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 325 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8342 (tm-30) REVERT: A 167 LYS cc_start: 0.8495 (tttt) cc_final: 0.7642 (ptpt) REVERT: A 427 MET cc_start: 0.8722 (tpp) cc_final: 0.8355 (tpp) REVERT: A 442 GLU cc_start: 0.7802 (mp0) cc_final: 0.7393 (mp0) REVERT: F 51 ASN cc_start: 0.8284 (m-40) cc_final: 0.7665 (t0) REVERT: F 53 LEU cc_start: 0.8636 (tp) cc_final: 0.8434 (tp) REVERT: F 55 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7866 (mm-30) REVERT: B 1 MET cc_start: 0.6623 (tpp) cc_final: 0.6242 (ttt) REVERT: B 8 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8400 (mp) REVERT: B 28 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8779 (tt) REVERT: B 81 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8007 (mm-30) REVERT: B 220 LEU cc_start: 0.8734 (mm) cc_final: 0.8466 (tp) REVERT: B 238 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7950 (p0) REVERT: B 380 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7809 (mtt180) REVERT: B 546 GLU cc_start: 0.6253 (tm-30) cc_final: 0.5315 (tm-30) REVERT: B 554 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7268 (tp30) REVERT: B 570 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7228 (tm-30) REVERT: B 657 MET cc_start: 0.9147 (mmm) cc_final: 0.8932 (tpp) REVERT: B 669 ARG cc_start: 0.7455 (mmm-85) cc_final: 0.7206 (mtp180) REVERT: B 671 LYS cc_start: 0.7994 (mttt) cc_final: 0.7573 (tttm) REVERT: B 711 ASP cc_start: 0.8112 (t0) cc_final: 0.7765 (t0) REVERT: E 16 ASP cc_start: 0.8439 (t0) cc_final: 0.7831 (t0) REVERT: E 68 ARG cc_start: 0.7556 (mtm-85) cc_final: 0.7098 (mtm180) REVERT: E 114 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7408 (tp30) REVERT: E 117 ASP cc_start: 0.8140 (t0) cc_final: 0.7896 (t0) REVERT: E 150 GLU cc_start: 0.7478 (mp0) cc_final: 0.7099 (mp0) REVERT: E 158 LYS cc_start: 0.8540 (ptmt) cc_final: 0.7935 (pttp) REVERT: E 170 SER cc_start: 0.8226 (t) cc_final: 0.7942 (p) REVERT: E 197 ASP cc_start: 0.7897 (p0) cc_final: 0.7696 (p0) REVERT: E 226 TYR cc_start: 0.8433 (m-80) cc_final: 0.8052 (m-80) REVERT: E 262 ILE cc_start: 0.8107 (mt) cc_final: 0.7729 (mt) REVERT: D 103 GLN cc_start: 0.8370 (mp10) cc_final: 0.8088 (mt0) REVERT: D 113 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7712 (mtm110) REVERT: D 321 SER cc_start: 0.8884 (m) cc_final: 0.8430 (t) REVERT: C 55 TRP cc_start: 0.7686 (m100) cc_final: 0.7434 (m100) REVERT: C 163 MET cc_start: 0.8933 (mpp) cc_final: 0.8203 (mpp) REVERT: C 332 SER cc_start: 0.8875 (t) cc_final: 0.8657 (m) REVERT: C 410 ASN cc_start: 0.3880 (t0) cc_final: 0.3574 (p0) REVERT: C 422 LEU cc_start: 0.8677 (mt) cc_final: 0.8375 (pp) REVERT: C 438 LYS cc_start: 0.8689 (tttt) cc_final: 0.8247 (tmtt) REVERT: G 118 MET cc_start: 0.6040 (mmt) cc_final: 0.5487 (ttp) REVERT: G 168 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8335 (mtpt) REVERT: G 175 TRP cc_start: 0.7606 (t-100) cc_final: 0.7031 (t-100) REVERT: G 197 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8530 (tm-30) REVERT: G 211 ARG cc_start: 0.7767 (ptp-110) cc_final: 0.7395 (ttm110) outliers start: 62 outliers final: 52 residues processed: 367 average time/residue: 0.1298 time to fit residues: 73.5828 Evaluate side-chains 369 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 314 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 276 CYS Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 166 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 177 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 5 optimal weight: 0.0010 chunk 204 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN G 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.092060 restraints weight = 32858.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.095259 restraints weight = 18723.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.095747 restraints weight = 12723.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096168 restraints weight = 11583.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.096466 restraints weight = 10422.030| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.195 20363 Z= 0.175 Angle : 0.682 13.179 27750 Z= 0.330 Chirality : 0.045 0.203 3137 Planarity : 0.004 0.079 3348 Dihedral : 13.922 146.737 3082 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.94 % Allowed : 20.17 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.18), residues: 2309 helix: 0.51 (0.17), residues: 1018 sheet: -1.65 (0.31), residues: 300 loop : -2.01 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 487 TYR 0.024 0.001 TYR A 534 PHE 0.021 0.001 PHE C 433 TRP 0.021 0.001 TRP C 96 HIS 0.018 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00413 (20335) covalent geometry : angle 0.65186 (27705) hydrogen bonds : bond 0.03149 ( 458) hydrogen bonds : angle 3.37603 ( 1338) metal coordination : bond 0.03776 ( 28) metal coordination : angle 5.04499 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3249.48 seconds wall clock time: 56 minutes 52.61 seconds (3412.61 seconds total)