Starting phenix.real_space_refine on Sun Sep 13 00:58:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ro4_4970/09_2026/6ro4_4970.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ro4_4970/09_2026/6ro4_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_4970/09_2026/6ro4_4970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ro4_4970/09_2026/6ro4_4970.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ro4_4970/09_2026/6ro4_4970.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ro4_4970/09_2026/6ro4_4970.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ro4_4970/09_2026/6ro4_4970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ro4_4970/09_2026/6ro4_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 4.28, 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: 1.78 Conformation dependent library (CDL) restraints added in 909.0 milliseconds 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: 2.20 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: 2.71 Time building geometry restraints manager: 2.27 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=" C1' DC K 38 " pdb=" N1 DC K 38 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.12e+01 bond pdb=" N9 DA J 31 " pdb=" C4 DA J 31 " ideal model delta sigma weight residual 1.374 1.351 0.023 6.00e-03 2.78e+04 1.45e+01 bond pdb=" C1' DC K 31 " pdb=" N1 DC K 31 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.39e+01 bond pdb=" C3' DA K 36 " pdb=" C2' DA K 36 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.37e+01 bond pdb=" C3' DT K 34 " pdb=" O3' DT K 34 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.23e+01 ... (remaining 20330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 26799 2.42 - 4.85: 776 4.85 - 7.27: 93 7.27 - 9.70: 31 9.70 - 12.12: 6 Bond angle restraints: 27705 Sorted by residual: angle pdb=" O4' DC K 31 " pdb=" C4' DC K 31 " pdb=" C3' DC K 31 " ideal model delta sigma weight residual 106.00 102.38 3.62 6.00e-01 2.78e+00 3.65e+01 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=" O4' DC K 31 " pdb=" C1' DC K 31 " pdb=" N1 DC K 31 " ideal model delta sigma weight residual 108.00 111.51 -3.51 7.00e-01 2.04e+00 2.51e+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 ... (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: 2398 0.062 - 0.123: 599 0.123 - 0.185: 112 0.185 - 0.247: 22 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 23.600 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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= 0.529 Angle : 1.269 52.243 27750 Z= 0.584 Chirality : 0.058 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 are 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/Z covalent geometry : bond 0.00655 / 0.38 (20335) covalent geometry : angle 0.96941 / 0.57 (27705) hydrogen bonds : bond 0.31071 / 35.39 ( 458) hydrogen bonds : angle 9.77934 / 13.04 ( 1338) metal coordination : bond 0.33171 / 22.08 ( 28) metal coordination : angle 20.34466 / 32.96 ( 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 : 0.862 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: 0.7929 (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: 0.7723 (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: 0.7617 (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: 0.8111 (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: 0.8224 (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: 0.1792 time to fit residues: 128.7011 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 : 0.841 ------------------------------------------------------------------------------- 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... 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 135 HIS B 201 HIS ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 108 ASN E 176 ASN D 60 HIS D 147 ASN D 154 GLN D 158 HIS D 279 ASN ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN C 260 ASN C 273 GLN G 119 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.132733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.096198 restraints weight = 32938.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101561 restraints weight = 17297.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.102940 restraints weight = 10296.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102953 restraints weight = 8648.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103192 restraints weight = 8619.445| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 20363 Z= 0.146 Angle : 0.768 19.271 27750 Z= 0.366 Chirality : 0.045 0.251 3137 Planarity : 0.006 0.083 3348 Dihedral : 15.021 150.704 3086 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.93 % Favored : 92.94 % Rotamer: Outliers : 2.36 % Allowed : 13.34 % Favored : 84.30 % 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 are not related in a simple way. whole: -4.42 (0.14), residues: 2309 helix: -2.83 (0.12), residues: 1008 sheet: -2.41 (0.30), residues: 288 loop : -3.09 (0.16), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 457 TYR 0.024 0.002 TYR A 581 PHE 0.019 0.001 PHE B 329 TRP 0.029 0.002 TRP C 96 HIS 0.017 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (20335) covalent geometry : angle 0.69794 / 0.36 (27705) hydrogen bonds : bond 0.05505 / 6.25 ( 458) hydrogen bonds : angle 4.81861 / 6.61 ( 1338) metal coordination : bond 0.02216 / 2.17 ( 28) metal coordination : angle 7.98260 / 12.47 ( 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 424 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 375 time to evaluate : 0.817 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: 0.8903 (tm-30) cc_final: 0.8241 (tm-30) REVERT: A 167 LYS cc_start: 0.8227 (tttt) cc_final: 0.7613 (mtmt) REVERT: A 187 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.8081 (t-90) REVERT: A 291 LEU cc_start: 0.8049 (mt) cc_final: 0.7762 (mp) REVERT: A 379 LYS cc_start: 0.8558 (mmmm) cc_final: 0.8354 (mmmm) REVERT: A 442 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7331 (mp0) REVERT: A 535 THR cc_start: 0.8200 (m) cc_final: 0.7815 (m) REVERT: F 25 GLU cc_start: 0.7783 (pt0) cc_final: 0.7492 (pm20) REVERT: F 51 ASN cc_start: 0.8159 (m-40) cc_final: 0.7747 (t0) REVERT: F 53 LEU cc_start: 0.8192 (tp) cc_final: 0.7946 (tp) REVERT: F 59 GLU cc_start: 0.7985 (tt0) cc_final: 0.7205 (tm-30) REVERT: F 64 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.7457 (p0) REVERT: B 1 MET cc_start: 0.6894 (tpt) cc_final: 0.6580 (tpp) REVERT: B 176 ASN cc_start: 0.7886 (m-40) cc_final: 0.7602 (t0) REVERT: B 438 MET cc_start: 0.8545 (mtt) cc_final: 0.8335 (mtt) REVERT: B 570 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7498 (tm-30) REVERT: B 671 LYS cc_start: 0.7994 (mttt) cc_final: 0.7705 (tttp) REVERT: E 16 ASP cc_start: 0.8199 (t0) cc_final: 0.7761 (t0) REVERT: E 68 ARG cc_start: 0.7385 (mtm-85) cc_final: 0.7044 (mtm-85) REVERT: E 114 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7291 (tp30) REVERT: E 117 ASP cc_start: 0.8444 (t0) cc_final: 0.8176 (t70) REVERT: E 158 LYS cc_start: 0.8549 (ptmt) cc_final: 0.8044 (pttp) REVERT: E 170 SER cc_start: 0.8478 (t) cc_final: 0.8232 (p) REVERT: E 251 TYR cc_start: 0.8321 (m-80) cc_final: 0.8116 (m-10) REVERT: E 266 TYR cc_start: 0.7585 (m-10) cc_final: 0.7323 (m-80) REVERT: D 103 GLN cc_start: 0.8284 (mp10) cc_final: 0.7928 (mt0) REVERT: D 142 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7985 (pt0) REVERT: D 293 GLN cc_start: 0.7924 (tp40) cc_final: 0.7509 (tt0) REVERT: D 321 SER cc_start: 0.8913 (m) cc_final: 0.8466 (t) REVERT: D 322 TYR cc_start: 0.7810 (m-80) cc_final: 0.7591 (m-80) REVERT: C 78 GLU cc_start: 0.8123 (tp30) cc_final: 0.7632 (tp30) REVERT: C 79 PHE cc_start: 0.8473 (m-80) cc_final: 0.7535 (m-80) REVERT: C 111 ASN cc_start: 0.8903 (t0) cc_final: 0.8685 (t0) REVERT: C 410 ASN cc_start: 0.4903 (t0) cc_final: 0.3454 (p0) REVERT: C 438 LYS cc_start: 0.8550 (tttt) cc_final: 0.8237 (tttp) REVERT: G 175 TRP cc_start: 0.7652 (t-100) cc_final: 0.7211 (t-100) REVERT: G 177 ASP cc_start: 0.8186 (p0) cc_final: 0.7800 (p0) REVERT: G 178 MET cc_start: 0.8476 (ttp) cc_final: 0.7697 (tmm) outliers start: 49 outliers final: 22 residues processed: 409 average time/residue: 0.1539 time to fit residues: 97.5665 Evaluate side-chains 351 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 326 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain F residue 49 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 248 SER Chi-restraints excluded: chain B residue 375 CYS 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 E residue 232 LEU Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 161 HIS 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 225 optimal weight: 0.0970 chunk 94 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 150 optimal weight: 0.3980 chunk 100 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS A 187 HIS A 677 GLN F 64 ASN ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 HIS E 176 ASN D 376 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.131632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.095357 restraints weight = 32698.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.100266 restraints weight = 16831.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.100975 restraints weight = 10684.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.101542 restraints weight = 9148.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101744 restraints weight = 8524.723| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 20363 Z= 0.140 Angle : 0.705 16.290 27750 Z= 0.339 Chirality : 0.045 0.319 3137 Planarity : 0.005 0.082 3348 Dihedral : 14.734 148.710 3083 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.10 % Favored : 92.85 % Rotamer: Outliers : 2.60 % Allowed : 14.73 % Favored : 82.67 % 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 are not related in a simple way. whole: -3.58 (0.15), residues: 2309 helix: -1.84 (0.14), residues: 1006 sheet: -2.32 (0.29), residues: 301 loop : -2.89 (0.16), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 457 TYR 0.023 0.001 TYR D 289 PHE 0.032 0.001 PHE D 326 TRP 0.023 0.001 TRP A 511 HIS 0.019 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (20335) covalent geometry : angle 0.65585 / 0.34 (27705) hydrogen bonds : bond 0.04469 / 4.95 ( 458) hydrogen bonds : angle 4.22161 / 5.81 ( 1338) metal coordination : bond 0.02407 / 2.32 ( 28) metal coordination : angle 6.44789 / 9.52 ( 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 402 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 348 time to evaluate : 0.778 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 83 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7824 (m-70) REVERT: A 97 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8236 (tm-30) REVERT: A 167 LYS cc_start: 0.8251 (tttt) cc_final: 0.7649 (mtmt) REVERT: A 187 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.8366 (t-170) REVERT: A 190 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: A 422 GLU cc_start: 0.7544 (tp30) cc_final: 0.7236 (tp30) REVERT: A 442 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7352 (mp0) REVERT: A 535 THR cc_start: 0.8406 (m) cc_final: 0.8150 (m) REVERT: A 581 TYR cc_start: 0.7865 (t80) cc_final: 0.7500 (t80) REVERT: F 25 GLU cc_start: 0.7790 (pt0) cc_final: 0.7535 (pm20) REVERT: F 51 ASN cc_start: 0.8255 (m-40) cc_final: 0.7970 (t0) REVERT: F 53 LEU cc_start: 0.8236 (tp) cc_final: 0.8026 (tp) REVERT: F 59 GLU cc_start: 0.8073 (tt0) cc_final: 0.7307 (tm-30) REVERT: F 64 ASN cc_start: 0.7914 (OUTLIER) cc_final: 0.7708 (p0) REVERT: B 1 MET cc_start: 0.6950 (tpt) cc_final: 0.6604 (tpp) REVERT: B 8 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8404 (mp) REVERT: B 176 ASN cc_start: 0.7884 (m-40) cc_final: 0.7579 (t0) REVERT: B 380 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7791 (mtt180) REVERT: B 546 GLU cc_start: 0.6272 (tm-30) cc_final: 0.6003 (tm-30) REVERT: B 570 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7759 (tm-30) REVERT: B 671 LYS cc_start: 0.8036 (mttt) cc_final: 0.7735 (tttt) REVERT: E 16 ASP cc_start: 0.8276 (t0) cc_final: 0.7825 (t0) REVERT: E 56 LYS cc_start: 0.8794 (mttt) cc_final: 0.8286 (mttp) REVERT: E 68 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.6866 (mtp180) REVERT: E 114 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7181 (tp30) REVERT: E 117 ASP cc_start: 0.8390 (t0) cc_final: 0.8079 (t0) REVERT: E 119 MET cc_start: 0.8364 (mmm) cc_final: 0.7770 (ptt) REVERT: E 147 MET cc_start: 0.8593 (tpp) cc_final: 0.8361 (mpp) REVERT: E 158 LYS cc_start: 0.8565 (ptmt) cc_final: 0.8045 (pttp) REVERT: E 170 SER cc_start: 0.8593 (t) cc_final: 0.8349 (p) REVERT: E 251 TYR cc_start: 0.8370 (m-80) cc_final: 0.8074 (m-10) REVERT: E 266 TYR cc_start: 0.7722 (m-10) cc_final: 0.7486 (m-80) REVERT: D 103 GLN cc_start: 0.8295 (mp10) cc_final: 0.8002 (mt0) REVERT: D 293 GLN cc_start: 0.7911 (tp40) cc_final: 0.7511 (tt0) REVERT: D 321 SER cc_start: 0.8893 (m) cc_final: 0.8469 (t) REVERT: C 78 GLU cc_start: 0.8143 (tp30) cc_final: 0.7589 (tp30) REVERT: C 79 PHE cc_start: 0.8539 (m-80) cc_final: 0.7542 (m-80) REVERT: C 111 ASN cc_start: 0.8877 (t0) cc_final: 0.8634 (t0) REVERT: C 163 MET cc_start: 0.8978 (mpp) cc_final: 0.8525 (mpp) REVERT: C 410 ASN cc_start: 0.4515 (t0) cc_final: 0.2994 (p0) REVERT: C 438 LYS cc_start: 0.8522 (tttt) cc_final: 0.8233 (tttp) REVERT: G 175 TRP cc_start: 0.7628 (t-100) cc_final: 0.7215 (t-100) outliers start: 54 outliers final: 30 residues processed: 389 average time/residue: 0.1511 time to fit residues: 91.4990 Evaluate side-chains 359 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 324 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 190 GLN 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 644 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 64 ASN 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 248 SER Chi-restraints excluded: chain B residue 266 LEU 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 180 VAL 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 172 SER 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 343 VAL Chi-restraints excluded: chain G residue 140 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 224 optimal weight: 0.0870 chunk 77 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 213 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 47 optimal weight: 0.0770 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS A 187 HIS A 677 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN B 148 HIS B 726 GLN E 176 ASN D 279 ASN G 119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.131887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.095085 restraints weight = 32712.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.100326 restraints weight = 17157.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101314 restraints weight = 10098.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.101517 restraints weight = 9200.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101857 restraints weight = 8753.900| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2775 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= 0.125 Angle : 0.668 14.474 27750 Z= 0.324 Chirality : 0.044 0.312 3137 Planarity : 0.004 0.075 3348 Dihedral : 14.592 148.984 3082 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.36 % Favored : 92.59 % Rotamer: Outliers : 2.74 % Allowed : 15.65 % Favored : 81.61 % 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 are not related in a simple way. whole: -3.00 (0.16), residues: 2309 helix: -1.17 (0.15), residues: 997 sheet: -2.22 (0.30), residues: 300 loop : -2.73 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 669 TYR 0.030 0.001 TYR B 410 PHE 0.028 0.001 PHE C 454 TRP 0.022 0.001 TRP C 96 HIS 0.013 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (20335) covalent geometry : angle 0.62774 / 0.32 (27705) hydrogen bonds : bond 0.03863 / 4.20 ( 458) hydrogen bonds : angle 3.95058 / 5.41 ( 1338) metal coordination : bond 0.02610 / 2.56 ( 28) metal coordination : angle 5.73230 / 8.22 ( 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 409 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 352 time to evaluate : 0.711 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: 0.8944 (tm-30) cc_final: 0.8223 (tm-30) REVERT: A 167 LYS cc_start: 0.8299 (tttt) cc_final: 0.7650 (mtpt) REVERT: A 276 MET cc_start: 0.7450 (ttm) cc_final: 0.7122 (ptm) REVERT: A 355 CYS cc_start: 0.8245 (m) cc_final: 0.7916 (m) REVERT: A 437 LEU cc_start: 0.8660 (tp) cc_final: 0.8446 (tp) REVERT: A 442 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7360 (mp0) REVERT: A 581 TYR cc_start: 0.7880 (t80) cc_final: 0.7471 (t80) REVERT: F 25 GLU cc_start: 0.7780 (pt0) cc_final: 0.7578 (pm20) REVERT: F 51 ASN cc_start: 0.8348 (m-40) cc_final: 0.7983 (t0) REVERT: F 53 LEU cc_start: 0.8328 (tp) cc_final: 0.8072 (tp) REVERT: F 63 GLN cc_start: 0.8305 (tt0) cc_final: 0.8071 (mt0) REVERT: B 8 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8431 (mp) REVERT: B 380 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7724 (mtt180) REVERT: B 438 MET cc_start: 0.8427 (mtt) cc_final: 0.8213 (mtt) REVERT: B 520 TYR cc_start: 0.8966 (m-10) cc_final: 0.8537 (m-80) REVERT: B 546 GLU cc_start: 0.6245 (tm-30) cc_final: 0.5927 (tm-30) REVERT: B 570 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7707 (tm-30) REVERT: B 671 LYS cc_start: 0.8039 (mttt) cc_final: 0.7696 (tttt) REVERT: E 16 ASP cc_start: 0.8319 (t0) cc_final: 0.7864 (t0) REVERT: E 56 LYS cc_start: 0.8810 (mttt) cc_final: 0.8306 (mttp) REVERT: E 68 ARG cc_start: 0.7421 (mtm-85) cc_final: 0.6911 (mtp180) REVERT: E 114 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7270 (tp30) REVERT: E 117 ASP cc_start: 0.8339 (t0) cc_final: 0.8059 (t0) REVERT: E 147 MET cc_start: 0.8607 (tpp) cc_final: 0.8009 (mpp) REVERT: E 158 LYS cc_start: 0.8538 (ptmt) cc_final: 0.8026 (pttp) REVERT: E 170 SER cc_start: 0.8294 (t) cc_final: 0.8072 (p) REVERT: E 226 TYR cc_start: 0.8340 (m-80) cc_final: 0.7853 (m-80) REVERT: E 266 TYR cc_start: 0.7727 (m-10) cc_final: 0.7478 (m-80) REVERT: D 103 GLN cc_start: 0.8325 (mp10) cc_final: 0.8024 (mt0) REVERT: D 321 SER cc_start: 0.8866 (m) cc_final: 0.8453 (t) REVERT: D 365 ASN cc_start: 0.6669 (m-40) cc_final: 0.6146 (m110) REVERT: C 78 GLU cc_start: 0.8151 (tp30) cc_final: 0.7791 (tp30) REVERT: C 111 ASN cc_start: 0.8875 (t0) cc_final: 0.8660 (t0) REVERT: C 393 LEU cc_start: 0.8590 (mm) cc_final: 0.8372 (mt) REVERT: C 410 ASN cc_start: 0.4455 (t0) cc_final: 0.3771 (p0) REVERT: C 438 LYS cc_start: 0.8574 (tttt) cc_final: 0.8107 (tmtt) REVERT: G 118 MET cc_start: 0.7760 (mmm) cc_final: 0.7248 (mmm) REVERT: G 122 ASP cc_start: 0.7198 (m-30) cc_final: 0.6936 (m-30) REVERT: G 175 TRP cc_start: 0.7687 (t-100) cc_final: 0.7257 (t-100) REVERT: G 178 MET cc_start: 0.8315 (ttp) cc_final: 0.7676 (tmm) REVERT: G 211 ARG cc_start: 0.8311 (ptp-110) cc_final: 0.7653 (ttm110) outliers start: 57 outliers final: 39 residues processed: 391 average time/residue: 0.1408 time to fit residues: 87.0083 Evaluate side-chains 364 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 324 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 404 SER 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 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 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 266 LEU Chi-restraints excluded: chain B residue 375 CYS 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 650 ASP Chi-restraints excluded: chain B residue 678 VAL 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 90 TYR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 174 LEU 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 G residue 129 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 109 optimal weight: 0.4980 chunk 186 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 211 optimal weight: 0.6980 chunk 58 optimal weight: 0.0030 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 677 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 GLN C 424 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.131927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.095327 restraints weight = 32520.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.100157 restraints weight = 16809.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101131 restraints weight = 10048.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.101772 restraints weight = 9254.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102133 restraints weight = 8664.319| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 20363 Z= 0.125 Angle : 0.656 16.767 27750 Z= 0.317 Chirality : 0.044 0.321 3137 Planarity : 0.004 0.073 3348 Dihedral : 14.451 148.888 3082 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.84 % Favored : 93.11 % Rotamer: Outliers : 2.74 % Allowed : 17.28 % Favored : 79.97 % 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 are not related in a simple way. whole: -2.51 (0.17), residues: 2309 helix: -0.65 (0.16), residues: 1000 sheet: -2.10 (0.30), residues: 297 loop : -2.56 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 195 TYR 0.039 0.001 TYR B 410 PHE 0.027 0.001 PHE D 326 TRP 0.022 0.001 TRP C 96 HIS 0.016 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (20335) covalent geometry : angle 0.61685 / 0.32 (27705) hydrogen bonds : bond 0.03541 / 3.77 ( 458) hydrogen bonds : angle 3.73871 / 5.14 ( 1338) metal coordination : bond 0.02534 / 2.44 ( 28) metal coordination : angle 5.55624 / 7.87 ( 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 408 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 351 time to evaluate : 0.769 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: 0.8936 (tm-30) cc_final: 0.8204 (tm-30) REVERT: A 167 LYS cc_start: 0.8290 (tttt) cc_final: 0.7619 (mtmt) REVERT: A 355 CYS cc_start: 0.8245 (m) cc_final: 0.7931 (m) REVERT: A 383 THR cc_start: 0.7928 (p) cc_final: 0.7706 (t) REVERT: A 437 LEU cc_start: 0.8560 (tp) cc_final: 0.8346 (tp) REVERT: A 442 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7355 (mp0) REVERT: F 51 ASN cc_start: 0.8372 (m-40) cc_final: 0.7993 (t0) REVERT: F 53 LEU cc_start: 0.8445 (tp) cc_final: 0.8175 (tp) REVERT: F 63 GLN cc_start: 0.8260 (tt0) cc_final: 0.7985 (mt0) REVERT: B 1 MET cc_start: 0.6699 (tpp) cc_final: 0.6407 (ttt) REVERT: B 8 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8425 (mp) REVERT: B 81 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7605 (mm-30) REVERT: B 176 ASN cc_start: 0.7838 (t0) cc_final: 0.7151 (t0) REVERT: B 380 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7708 (mtt180) REVERT: B 405 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.9086 (t) REVERT: B 520 TYR cc_start: 0.8890 (m-10) cc_final: 0.8446 (m-80) REVERT: B 570 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7635 (tm-30) REVERT: B 586 GLU cc_start: 0.8114 (tp30) cc_final: 0.7912 (tp30) REVERT: B 671 LYS cc_start: 0.8016 (mttt) cc_final: 0.7649 (tttt) REVERT: E 16 ASP cc_start: 0.8320 (t0) cc_final: 0.7898 (t0) REVERT: E 56 LYS cc_start: 0.8776 (mttt) cc_final: 0.8291 (mttp) REVERT: E 114 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7500 (tp30) REVERT: E 117 ASP cc_start: 0.8310 (t0) cc_final: 0.8098 (t0) REVERT: E 147 MET cc_start: 0.8668 (tpp) cc_final: 0.8172 (mpp) REVERT: E 158 LYS cc_start: 0.8540 (ptmt) cc_final: 0.8043 (ptmm) REVERT: E 170 SER cc_start: 0.8264 (t) cc_final: 0.8020 (p) REVERT: E 225 GLN cc_start: 0.9084 (tp-100) cc_final: 0.8816 (tp-100) REVERT: D 103 GLN cc_start: 0.8325 (mp10) cc_final: 0.8025 (mt0) REVERT: D 321 SER cc_start: 0.8812 (m) cc_final: 0.8431 (t) REVERT: D 365 ASN cc_start: 0.6675 (m-40) cc_final: 0.6125 (m110) REVERT: C 78 GLU cc_start: 0.8250 (tp30) cc_final: 0.7814 (tp30) REVERT: C 111 ASN cc_start: 0.8887 (t0) cc_final: 0.8684 (t0) REVERT: C 163 MET cc_start: 0.8997 (mpp) cc_final: 0.8342 (mpp) REVERT: C 334 MET cc_start: 0.8105 (mpp) cc_final: 0.7779 (mpp) REVERT: C 410 ASN cc_start: 0.4402 (t0) cc_final: 0.3658 (p0) REVERT: C 438 LYS cc_start: 0.8575 (tttt) cc_final: 0.8132 (tmtt) REVERT: G 118 MET cc_start: 0.7860 (mmm) cc_final: 0.7364 (mmm) REVERT: G 122 ASP cc_start: 0.7556 (m-30) cc_final: 0.7305 (m-30) REVERT: G 168 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8431 (mtpt) REVERT: G 169 ASN cc_start: 0.8375 (t0) cc_final: 0.7974 (t0) REVERT: G 175 TRP cc_start: 0.7611 (t-100) cc_final: 0.7237 (t-100) REVERT: G 178 MET cc_start: 0.8372 (ttp) cc_final: 0.7683 (tmm) REVERT: G 211 ARG cc_start: 0.8249 (ptp-110) cc_final: 0.7956 (ptp-110) outliers start: 57 outliers final: 39 residues processed: 388 average time/residue: 0.1394 time to fit residues: 84.5286 Evaluate side-chains 378 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 337 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU 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 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 266 LEU Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 405 THR 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 650 ASP Chi-restraints excluded: chain B residue 664 VAL 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 D residue 139 CYS 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 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 428 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 156 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 216 optimal weight: 0.5980 chunk 49 optimal weight: 0.0980 chunk 123 optimal weight: 0.0870 chunk 231 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS A 677 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.131744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.095162 restraints weight = 32308.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.098994 restraints weight = 16803.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101411 restraints weight = 10557.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.101720 restraints weight = 8765.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102170 restraints weight = 8422.611| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 20363 Z= 0.118 Angle : 0.641 16.570 27750 Z= 0.310 Chirality : 0.044 0.328 3137 Planarity : 0.004 0.073 3348 Dihedral : 14.321 148.942 3082 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.67 % Favored : 93.29 % Rotamer: Outliers : 3.03 % Allowed : 17.72 % Favored : 79.25 % 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 are not related in a simple way. whole: -2.20 (0.17), residues: 2309 helix: -0.31 (0.16), residues: 1000 sheet: -2.01 (0.30), residues: 299 loop : -2.46 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 669 TYR 0.034 0.001 TYR B 410 PHE 0.025 0.001 PHE D 326 TRP 0.018 0.001 TRP C 96 HIS 0.018 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (20335) covalent geometry : angle 0.60452 / 0.31 (27705) hydrogen bonds : bond 0.03371 / 3.55 ( 458) hydrogen bonds : angle 3.59356 / 4.95 ( 1338) metal coordination : bond 0.02848 / 2.80 ( 28) metal coordination : angle 5.31704 / 7.52 ( 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 406 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 343 time to evaluate : 0.624 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: A 97 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8448 (tm-30) REVERT: A 167 LYS cc_start: 0.8340 (tttt) cc_final: 0.7593 (ptpt) REVERT: A 355 CYS cc_start: 0.8206 (m) cc_final: 0.7891 (m) REVERT: A 372 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 383 THR cc_start: 0.7892 (p) cc_final: 0.7672 (t) REVERT: A 442 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7366 (mp0) REVERT: F 51 ASN cc_start: 0.8392 (m-40) cc_final: 0.7903 (t0) REVERT: F 53 LEU cc_start: 0.8429 (tp) cc_final: 0.8156 (tp) REVERT: F 55 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8123 (mm-30) REVERT: B 1 MET cc_start: 0.6781 (tpp) cc_final: 0.6442 (ttt) REVERT: B 8 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8415 (mp) REVERT: B 81 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 176 ASN cc_start: 0.7932 (t0) cc_final: 0.7311 (t0) REVERT: B 380 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7640 (mtt180) REVERT: B 405 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9136 (t) REVERT: B 546 GLU cc_start: 0.6138 (tm-30) cc_final: 0.5816 (tm-30) REVERT: B 570 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7589 (tm-30) REVERT: B 586 GLU cc_start: 0.8194 (tp30) cc_final: 0.7916 (tp30) REVERT: B 671 LYS cc_start: 0.8020 (mttt) cc_final: 0.7647 (tttt) REVERT: E 16 ASP cc_start: 0.8346 (t0) cc_final: 0.7822 (t0) REVERT: E 31 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7799 (mm-40) REVERT: E 56 LYS cc_start: 0.8809 (mttt) cc_final: 0.8326 (mttp) REVERT: E 68 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.6989 (mtm-85) REVERT: E 114 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7252 (tp30) REVERT: E 117 ASP cc_start: 0.8249 (t0) cc_final: 0.8010 (t0) REVERT: E 158 LYS cc_start: 0.8549 (ptmt) cc_final: 0.8046 (ptmm) REVERT: E 170 SER cc_start: 0.8285 (t) cc_final: 0.8073 (p) REVERT: E 225 GLN cc_start: 0.9094 (tp-100) cc_final: 0.8799 (tp-100) REVERT: D 103 GLN cc_start: 0.8304 (mp10) cc_final: 0.8021 (mt0) REVERT: D 142 GLU cc_start: 0.8303 (pt0) cc_final: 0.8087 (pt0) REVERT: D 321 SER cc_start: 0.8820 (m) cc_final: 0.8449 (t) REVERT: D 349 GLN cc_start: 0.7604 (tt0) cc_final: 0.7283 (mp10) REVERT: D 365 ASN cc_start: 0.6637 (m-40) cc_final: 0.6065 (m110) REVERT: C 163 MET cc_start: 0.8985 (mpp) cc_final: 0.8234 (mpp) REVERT: C 334 MET cc_start: 0.8052 (mpp) cc_final: 0.7801 (mpp) REVERT: C 410 ASN cc_start: 0.4051 (t0) cc_final: 0.3362 (p0) REVERT: C 438 LYS cc_start: 0.8590 (tttt) cc_final: 0.8160 (tmtt) REVERT: G 118 MET cc_start: 0.7872 (mmm) cc_final: 0.7407 (mmm) REVERT: G 122 ASP cc_start: 0.7780 (m-30) cc_final: 0.7401 (m-30) REVERT: G 168 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8409 (mtpt) REVERT: G 175 TRP cc_start: 0.7641 (t-100) cc_final: 0.7219 (t-100) REVERT: G 178 MET cc_start: 0.8345 (ttp) cc_final: 0.7683 (tmm) outliers start: 63 outliers final: 43 residues processed: 382 average time/residue: 0.1429 time to fit residues: 85.5816 Evaluate side-chains 366 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 321 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 197 CYS 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 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 266 LEU Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 405 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 589 GLU Chi-restraints excluded: chain B residue 626 VAL 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 180 VAL 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 139 CYS 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 428 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 163 optimal weight: 1.9990 chunk 209 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 221 optimal weight: 0.0050 chunk 78 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 677 GLN ** F 36 GLN ** 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 = 0.3679 r_free = 0.3679 target = 0.129629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.091348 restraints weight = 32861.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.095168 restraints weight = 17133.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.097686 restraints weight = 11625.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.099286 restraints weight = 9136.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100270 restraints weight = 7855.236| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.304 20363 Z= 0.164 Angle : 0.667 13.800 27750 Z= 0.324 Chirality : 0.045 0.333 3137 Planarity : 0.004 0.079 3348 Dihedral : 14.292 149.053 3082 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.79 % Allowed : 18.15 % Favored : 79.06 % 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 are not related in a simple way. whole: -2.00 (0.17), residues: 2309 helix: -0.09 (0.17), residues: 1009 sheet: -1.96 (0.30), residues: 296 loop : -2.43 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 146 TYR 0.026 0.001 TYR B 410 PHE 0.025 0.001 PHE D 326 TRP 0.019 0.001 TRP C 96 HIS 0.024 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (20335) covalent geometry : angle 0.63052 / 0.32 (27705) hydrogen bonds : bond 0.03421 / 3.59 ( 458) hydrogen bonds : angle 3.54981 / 4.89 ( 1338) metal coordination : bond 0.05802 / 5.78 ( 28) metal coordination : angle 5.47559 / 7.25 ( 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 381 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 323 time to evaluate : 0.842 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 97 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8409 (tm-30) REVERT: A 167 LYS cc_start: 0.8370 (tttt) cc_final: 0.7565 (ptpt) REVERT: A 355 CYS cc_start: 0.8236 (m) cc_final: 0.7917 (m) REVERT: A 372 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7510 (mm-30) REVERT: A 383 THR cc_start: 0.8044 (p) cc_final: 0.7807 (t) REVERT: A 442 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7386 (mp0) REVERT: A 700 ASP cc_start: 0.7490 (t0) cc_final: 0.7232 (t0) REVERT: F 51 ASN cc_start: 0.8318 (m-40) cc_final: 0.7903 (t0) REVERT: F 53 LEU cc_start: 0.8559 (tp) cc_final: 0.8302 (tp) REVERT: B 1 MET cc_start: 0.6778 (tpp) cc_final: 0.6502 (ttt) REVERT: B 8 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8445 (mp) REVERT: B 28 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8774 (tt) REVERT: B 81 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7709 (mm-30) REVERT: B 176 ASN cc_start: 0.7920 (t0) cc_final: 0.7316 (t0) REVERT: B 220 LEU cc_start: 0.8796 (mm) cc_final: 0.8469 (tp) REVERT: B 380 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7612 (mtt180) REVERT: B 570 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7571 (tm-30) REVERT: B 586 GLU cc_start: 0.8168 (tp30) cc_final: 0.7862 (tp30) REVERT: B 671 LYS cc_start: 0.7974 (mttt) cc_final: 0.7628 (tttp) REVERT: E 16 ASP cc_start: 0.8364 (t0) cc_final: 0.7832 (t0) REVERT: E 56 LYS cc_start: 0.8827 (mttt) cc_final: 0.8328 (mttp) REVERT: E 114 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7477 (mm-30) REVERT: E 147 MET cc_start: 0.8461 (tpp) cc_final: 0.7918 (mpp) REVERT: E 158 LYS cc_start: 0.8542 (ptmt) cc_final: 0.7986 (pttp) REVERT: E 170 SER cc_start: 0.8282 (t) cc_final: 0.8065 (p) REVERT: E 225 GLN cc_start: 0.9100 (tp-100) cc_final: 0.8802 (tp-100) REVERT: D 71 MET cc_start: 0.9140 (mmt) cc_final: 0.8922 (mmt) REVERT: D 103 GLN cc_start: 0.8304 (mp10) cc_final: 0.8029 (mt0) REVERT: D 321 SER cc_start: 0.8806 (m) cc_final: 0.8423 (t) REVERT: D 349 GLN cc_start: 0.7814 (tt0) cc_final: 0.7538 (mp10) REVERT: D 365 ASN cc_start: 0.6752 (m-40) cc_final: 0.6202 (m110) REVERT: C 163 MET cc_start: 0.8944 (mpp) cc_final: 0.8174 (mpp) REVERT: C 334 MET cc_start: 0.8079 (mpp) cc_final: 0.7876 (mpp) REVERT: C 410 ASN cc_start: 0.4025 (t0) cc_final: 0.3380 (p0) REVERT: C 438 LYS cc_start: 0.8584 (tttt) cc_final: 0.8167 (tmtt) REVERT: G 118 MET cc_start: 0.7872 (mmm) cc_final: 0.7502 (mmm) REVERT: G 122 ASP cc_start: 0.7991 (m-30) cc_final: 0.7647 (m-30) REVERT: G 175 TRP cc_start: 0.7679 (t-100) cc_final: 0.7144 (t-100) REVERT: G 178 MET cc_start: 0.8358 (ttp) cc_final: 0.7685 (tmm) outliers start: 58 outliers final: 47 residues processed: 360 average time/residue: 0.1458 time to fit residues: 81.9001 Evaluate side-chains 370 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 321 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 643 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 28 LEU Chi-restraints excluded: chain B residue 105 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 266 LEU Chi-restraints excluded: chain B residue 375 CYS 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 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 180 VAL Chi-restraints excluded: chain E residue 258 HIS 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 139 CYS 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 428 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 180 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 677 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.130424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.092180 restraints weight = 32601.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.096059 restraints weight = 16905.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.098592 restraints weight = 11426.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100115 restraints weight = 8966.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101185 restraints weight = 7726.354| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.245 20363 Z= 0.139 Angle : 0.658 14.883 27750 Z= 0.318 Chirality : 0.045 0.322 3137 Planarity : 0.004 0.076 3348 Dihedral : 14.223 149.149 3082 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.74 % Allowed : 18.54 % Favored : 78.72 % 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 are not related in a simple way. whole: -1.83 (0.17), residues: 2309 helix: 0.08 (0.17), residues: 1009 sheet: -1.89 (0.30), residues: 298 loop : -2.37 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 125 TYR 0.026 0.001 TYR B 410 PHE 0.023 0.001 PHE D 326 TRP 0.018 0.001 TRP C 96 HIS 0.023 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (20335) covalent geometry : angle 0.62194 / 0.32 (27705) hydrogen bonds : bond 0.03334 / 3.50 ( 458) hydrogen bonds : angle 3.50990 / 4.83 ( 1338) metal coordination : bond 0.04788 / 4.83 ( 28) metal coordination : angle 5.40216 / 7.08 ( 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 386 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 329 time to evaluate : 1.298 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: A 97 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8395 (tm-30) REVERT: A 167 LYS cc_start: 0.8358 (tttt) cc_final: 0.7551 (ptpt) REVERT: A 178 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7277 (tm-30) REVERT: A 355 CYS cc_start: 0.8311 (m) cc_final: 0.7965 (m) REVERT: A 372 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7487 (mm-30) REVERT: A 442 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7430 (mp0) REVERT: A 700 ASP cc_start: 0.7498 (t0) cc_final: 0.7245 (t0) REVERT: F 51 ASN cc_start: 0.8322 (m-40) cc_final: 0.7902 (t0) REVERT: F 53 LEU cc_start: 0.8560 (tp) cc_final: 0.8297 (tp) REVERT: B 1 MET cc_start: 0.6859 (tpp) cc_final: 0.6561 (ttt) REVERT: B 8 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8455 (mp) REVERT: B 28 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8755 (tt) REVERT: B 81 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 176 ASN cc_start: 0.7902 (t0) cc_final: 0.7273 (t0) REVERT: B 220 LEU cc_start: 0.8750 (mm) cc_final: 0.8441 (tp) REVERT: B 380 ARG cc_start: 0.8037 (mtt180) cc_final: 0.7593 (mtt180) REVERT: B 570 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 586 GLU cc_start: 0.8188 (tp30) cc_final: 0.7862 (tp30) REVERT: B 671 LYS cc_start: 0.8035 (mttt) cc_final: 0.7669 (tttm) REVERT: E 16 ASP cc_start: 0.8358 (t0) cc_final: 0.7806 (t0) REVERT: E 56 LYS cc_start: 0.8812 (mttt) cc_final: 0.8292 (mttp) REVERT: E 147 MET cc_start: 0.8433 (tpp) cc_final: 0.7806 (mpp) REVERT: E 150 GLU cc_start: 0.7288 (mp0) cc_final: 0.6909 (mp0) REVERT: E 158 LYS cc_start: 0.8551 (ptmt) cc_final: 0.8018 (ptmm) REVERT: E 170 SER cc_start: 0.8248 (t) cc_final: 0.8034 (p) REVERT: E 225 GLN cc_start: 0.9086 (tp-100) cc_final: 0.8768 (tp-100) REVERT: E 226 TYR cc_start: 0.8333 (m-80) cc_final: 0.7901 (m-80) REVERT: E 262 ILE cc_start: 0.8082 (mt) cc_final: 0.7700 (mt) REVERT: D 103 GLN cc_start: 0.8311 (mp10) cc_final: 0.8039 (mt0) REVERT: D 142 GLU cc_start: 0.8239 (pt0) cc_final: 0.8011 (pt0) REVERT: D 321 SER cc_start: 0.8822 (m) cc_final: 0.8411 (t) REVERT: D 365 ASN cc_start: 0.6688 (m-40) cc_final: 0.6102 (m110) REVERT: C 163 MET cc_start: 0.8924 (mpp) cc_final: 0.8140 (mpp) REVERT: C 410 ASN cc_start: 0.4115 (t0) cc_final: 0.3516 (p0) REVERT: C 438 LYS cc_start: 0.8614 (tttt) cc_final: 0.8200 (tmtt) REVERT: G 168 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8410 (mtpt) REVERT: G 175 TRP cc_start: 0.7598 (t-100) cc_final: 0.7096 (t-100) REVERT: G 178 MET cc_start: 0.8280 (ttp) cc_final: 0.7675 (tmm) outliers start: 57 outliers final: 44 residues processed: 367 average time/residue: 0.1454 time to fit residues: 83.6952 Evaluate side-chains 363 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 317 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain F residue 4 VAL 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 28 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 266 LEU 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 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 180 VAL Chi-restraints excluded: chain E residue 258 HIS 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 139 CYS Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 176 THR 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 428 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 36 optimal weight: 0.4980 chunk 150 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 228 optimal weight: 1.9990 chunk 176 optimal weight: 0.3980 chunk 212 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 chunk 156 optimal weight: 0.0670 chunk 58 optimal weight: 0.0870 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 677 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.131681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094941 restraints weight = 32212.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098962 restraints weight = 17039.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.099907 restraints weight = 10491.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.102849 restraints weight = 9650.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102598 restraints weight = 8013.775| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.241 20363 Z= 0.119 Angle : 0.659 12.524 27750 Z= 0.319 Chirality : 0.044 0.324 3137 Planarity : 0.004 0.075 3348 Dihedral : 14.137 148.901 3082 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.41 % Allowed : 19.11 % Favored : 78.48 % 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 are not related in a simple way. whole: -1.62 (0.18), residues: 2309 helix: 0.27 (0.17), residues: 1002 sheet: -1.79 (0.31), residues: 297 loop : -2.25 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 195 TYR 0.026 0.001 TYR E 143 PHE 0.024 0.001 PHE C 433 TRP 0.018 0.001 TRP C 96 HIS 0.022 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (20335) covalent geometry : angle 0.62750 / 0.32 (27705) hydrogen bonds : bond 0.03226 / 3.35 ( 458) hydrogen bonds : angle 3.43823 / 4.75 ( 1338) metal coordination : bond 0.04657 / 4.67 ( 28) metal coordination : angle 5.00262 / 7.04 ( 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 379 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 329 time to evaluate : 0.722 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: A 97 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8368 (tm-30) REVERT: A 167 LYS cc_start: 0.8334 (tttt) cc_final: 0.7529 (ptpt) REVERT: A 178 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7226 (tm-30) REVERT: A 355 CYS cc_start: 0.8314 (m) cc_final: 0.7975 (m) REVERT: A 372 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7465 (mm-30) REVERT: A 383 THR cc_start: 0.7902 (p) cc_final: 0.7676 (t) REVERT: A 442 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7471 (mp0) REVERT: A 700 ASP cc_start: 0.7474 (t0) cc_final: 0.7219 (t0) REVERT: F 51 ASN cc_start: 0.8368 (m-40) cc_final: 0.7820 (t0) REVERT: F 53 LEU cc_start: 0.8534 (tp) cc_final: 0.8272 (tp) REVERT: F 55 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7986 (mm-30) REVERT: B 1 MET cc_start: 0.6895 (tpp) cc_final: 0.6471 (ttt) REVERT: B 8 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8435 (mp) REVERT: B 28 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8796 (tt) REVERT: B 81 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7689 (mm-30) REVERT: B 176 ASN cc_start: 0.7870 (t0) cc_final: 0.7242 (t0) REVERT: B 220 LEU cc_start: 0.8695 (mm) cc_final: 0.8430 (tp) REVERT: B 238 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7888 (p0) REVERT: B 380 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7568 (mtt180) REVERT: B 570 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7469 (tm-30) REVERT: B 586 GLU cc_start: 0.8106 (tp30) cc_final: 0.7838 (tp30) REVERT: B 671 LYS cc_start: 0.8037 (mttt) cc_final: 0.7659 (tttm) REVERT: E 16 ASP cc_start: 0.8350 (t0) cc_final: 0.7790 (t0) REVERT: E 56 LYS cc_start: 0.8752 (mttt) cc_final: 0.8095 (mttp) REVERT: E 68 ARG cc_start: 0.7388 (mtm-85) cc_final: 0.6996 (mtm110) REVERT: E 147 MET cc_start: 0.8382 (tpp) cc_final: 0.7916 (mmm) REVERT: E 150 GLU cc_start: 0.7300 (mp0) cc_final: 0.6937 (mp0) REVERT: E 158 LYS cc_start: 0.8547 (ptmt) cc_final: 0.7992 (pttp) REVERT: E 170 SER cc_start: 0.8206 (t) cc_final: 0.7994 (p) REVERT: E 225 GLN cc_start: 0.9095 (tp-100) cc_final: 0.8772 (tp-100) REVERT: E 226 TYR cc_start: 0.8322 (m-80) cc_final: 0.7579 (m-80) REVERT: E 262 ILE cc_start: 0.8044 (mt) cc_final: 0.7697 (mt) REVERT: D 103 GLN cc_start: 0.8311 (mp10) cc_final: 0.8036 (mt0) REVERT: D 142 GLU cc_start: 0.8254 (pt0) cc_final: 0.8004 (pt0) REVERT: D 321 SER cc_start: 0.8749 (m) cc_final: 0.8352 (t) REVERT: D 349 GLN cc_start: 0.7843 (tt0) cc_final: 0.7498 (mp10) REVERT: D 365 ASN cc_start: 0.6521 (m-40) cc_final: 0.5926 (m110) REVERT: C 163 MET cc_start: 0.8946 (mpp) cc_final: 0.8128 (mpp) REVERT: C 410 ASN cc_start: 0.4006 (t0) cc_final: 0.3493 (p0) REVERT: C 422 LEU cc_start: 0.8632 (mt) cc_final: 0.8356 (pp) REVERT: C 438 LYS cc_start: 0.8635 (tttt) cc_final: 0.8206 (tmtt) REVERT: G 175 TRP cc_start: 0.7667 (t-100) cc_final: 0.7152 (t-100) REVERT: G 178 MET cc_start: 0.8234 (ttp) cc_final: 0.7660 (tmm) outliers start: 50 outliers final: 39 residues processed: 361 average time/residue: 0.1397 time to fit residues: 78.4322 Evaluate side-chains 359 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 317 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 316 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 644 LEU 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 B residue 8 LEU Chi-restraints excluded: chain B residue 28 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 266 LEU 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 258 HIS Chi-restraints excluded: chain E residue 276 CYS 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 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 428 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: 0.0170 chunk 10 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 ASN A 677 GLN ** F 36 GLN ** 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 = 0.3700 r_free = 0.3700 target = 0.131210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.094227 restraints weight = 32584.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099212 restraints weight = 17292.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.100124 restraints weight = 10358.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.100345 restraints weight = 9456.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100710 restraints weight = 8948.207| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.233 20363 Z= 0.129 Angle : 0.655 12.475 27750 Z= 0.317 Chirality : 0.044 0.322 3137 Planarity : 0.004 0.077 3348 Dihedral : 14.096 148.741 3082 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.17 % Allowed : 19.69 % Favored : 78.14 % 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 are not related in a simple way. whole: -1.46 (0.18), residues: 2309 helix: 0.42 (0.17), residues: 1003 sheet: -1.68 (0.31), residues: 297 loop : -2.19 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 68 TYR 0.023 0.001 TYR B 410 PHE 0.025 0.001 PHE C 79 TRP 0.019 0.001 TRP C 96 HIS 0.021 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (20335) covalent geometry : angle 0.62524 / 0.31 (27705) hydrogen bonds : bond 0.03226 / 3.32 ( 458) hydrogen bonds : angle 3.39294 / 4.68 ( 1338) metal coordination : bond 0.04493 / 4.50 ( 28) metal coordination : angle 4.90725 / 6.85 ( 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 370 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 325 time to evaluate : 0.538 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: A 97 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8332 (tm-30) REVERT: A 167 LYS cc_start: 0.8419 (tttt) cc_final: 0.7571 (ptpt) REVERT: A 178 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7234 (tm-30) REVERT: A 372 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7473 (mm-30) REVERT: A 383 THR cc_start: 0.7942 (p) cc_final: 0.7710 (t) REVERT: A 442 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7427 (mp0) REVERT: A 700 ASP cc_start: 0.7541 (t0) cc_final: 0.7267 (t0) REVERT: F 51 ASN cc_start: 0.8403 (m-40) cc_final: 0.7840 (t0) REVERT: F 53 LEU cc_start: 0.8547 (tp) cc_final: 0.8291 (tp) REVERT: F 55 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7954 (mm-30) REVERT: F 64 ASN cc_start: 0.7992 (p0) cc_final: 0.7646 (p0) REVERT: B 1 MET cc_start: 0.6877 (tpp) cc_final: 0.6453 (ttt) REVERT: B 8 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8407 (mp) REVERT: B 28 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8797 (tt) REVERT: B 81 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 176 ASN cc_start: 0.7856 (t0) cc_final: 0.7276 (t0) REVERT: B 220 LEU cc_start: 0.8638 (mm) cc_final: 0.8386 (tp) REVERT: B 238 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7896 (p0) REVERT: B 380 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7575 (mtt180) REVERT: B 570 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7369 (tm-30) REVERT: B 586 GLU cc_start: 0.8202 (tp30) cc_final: 0.7913 (tp30) REVERT: B 671 LYS cc_start: 0.8060 (mttt) cc_final: 0.7645 (tttm) REVERT: E 16 ASP cc_start: 0.8363 (t0) cc_final: 0.7788 (t0) REVERT: E 56 LYS cc_start: 0.8799 (mttt) cc_final: 0.8182 (mttp) REVERT: E 68 ARG cc_start: 0.7414 (mtm-85) cc_final: 0.6990 (mtm110) REVERT: E 147 MET cc_start: 0.8275 (tpp) cc_final: 0.7978 (mmm) REVERT: E 150 GLU cc_start: 0.7306 (mp0) cc_final: 0.6937 (mp0) REVERT: E 158 LYS cc_start: 0.8563 (ptmt) cc_final: 0.8005 (pttp) REVERT: E 170 SER cc_start: 0.8229 (t) cc_final: 0.8017 (p) REVERT: E 225 GLN cc_start: 0.9105 (tp-100) cc_final: 0.8775 (tp-100) REVERT: E 226 TYR cc_start: 0.8358 (m-80) cc_final: 0.7942 (m-80) REVERT: E 262 ILE cc_start: 0.8036 (mt) cc_final: 0.7681 (mt) REVERT: D 103 GLN cc_start: 0.8334 (mp10) cc_final: 0.8045 (mt0) REVERT: D 293 GLN cc_start: 0.7850 (tp40) cc_final: 0.7294 (tt0) REVERT: D 321 SER cc_start: 0.8799 (m) cc_final: 0.8387 (t) REVERT: D 365 ASN cc_start: 0.6517 (m-40) cc_final: 0.5899 (m110) REVERT: C 163 MET cc_start: 0.8963 (mpp) cc_final: 0.8136 (mpp) REVERT: C 272 PHE cc_start: 0.8209 (t80) cc_final: 0.7995 (t80) REVERT: C 410 ASN cc_start: 0.4188 (t0) cc_final: 0.3720 (p0) REVERT: C 422 LEU cc_start: 0.8678 (mt) cc_final: 0.8405 (pp) REVERT: C 438 LYS cc_start: 0.8666 (tttt) cc_final: 0.8227 (tmtt) REVERT: G 118 MET cc_start: 0.7365 (mmt) cc_final: 0.7064 (mmt) REVERT: G 175 TRP cc_start: 0.7705 (t-100) cc_final: 0.7220 (t-100) REVERT: G 178 MET cc_start: 0.8265 (ttp) cc_final: 0.7683 (tmm) REVERT: G 185 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8105 (mt0) outliers start: 45 outliers final: 41 residues processed: 355 average time/residue: 0.1276 time to fit residues: 71.4051 Evaluate side-chains 361 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 316 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 537 ASN 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 B residue 8 LEU Chi-restraints excluded: chain B residue 28 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 266 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 613 HIS 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 258 HIS 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 176 THR 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 428 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 177 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 222 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 ASN ** F 36 GLN ** 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 = 0.3696 r_free = 0.3696 target = 0.130897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.092506 restraints weight = 32736.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.096355 restraints weight = 17084.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098883 restraints weight = 11593.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.100464 restraints weight = 9121.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.101492 restraints weight = 7854.167| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.302 20363 Z= 0.241 Angle : 0.869 59.149 27750 Z= 0.495 Chirality : 0.052 1.431 3137 Planarity : 0.005 0.158 3348 Dihedral : 14.103 148.755 3082 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.31 % Allowed : 19.88 % Favored : 77.80 % Cbeta Deviations : 0.09 % 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 are not related in a simple way. whole: -1.49 (0.18), residues: 2309 helix: 0.37 (0.17), residues: 1003 sheet: -1.67 (0.31), residues: 297 loop : -2.19 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 68 TYR 0.021 0.001 TYR A 581 PHE 0.022 0.001 PHE D 326 TRP 0.018 0.001 TRP C 96 HIS 0.021 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.24 (20335) covalent geometry : angle 0.84726 / 0.49 (27705) hydrogen bonds : bond 0.03257 / 3.36 ( 458) hydrogen bonds : angle 3.39410 / 4.68 ( 1338) metal coordination : bond 0.04488 / 4.50 ( 28) metal coordination : angle 4.91477 / 6.87 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3651.54 seconds wall clock time: 63 minutes 45.83 seconds (3825.83 seconds total)