Starting phenix.real_space_refine on Mon Jul 6 01:27:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28js_56551/07_2026/28js_56551.cif Found real_map, /net/cci-nas-00/data/ceres_data/28js_56551/07_2026/28js_56551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28js_56551/07_2026/28js_56551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28js_56551/07_2026/28js_56551.map" model { file = "/net/cci-nas-00/data/ceres_data/28js_56551/07_2026/28js_56551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28js_56551/07_2026/28js_56551.cif" } resolution = 3.32 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= 0.095 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 Zn 5 6.06 5 P 69 5.49 5 S 165 5.16 5 C 19429 2.51 5 N 5348 2.21 5 O 5806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30828 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5131 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 25, 'TRANS': 610} Chain breaks: 2 Chain: "B" Number of atoms: 6080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6080 Classifications: {'peptide': 755} Link IDs: {'PTRANS': 31, 'TRANS': 723} Chain breaks: 1 Chain: "C" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3014 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 358} Chain breaks: 5 Chain: "D" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3600 Classifications: {'peptide': 449} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 426} Chain breaks: 1 Chain: "E" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2828 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 18, 'TRANS': 341} Chain breaks: 1 Chain: "F" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2049 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 2 Chain: "G" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 556 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "H" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 659 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "I" Number of atoms: 4383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4383 Classifications: {'peptide': 534} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 508} Chain breaks: 3 Chain: "J" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 504 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 6, 'TRANS': 54} Chain: "K" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 578 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "L" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 375 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "L" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 315 Unusual residues: {'VM6': 1} Classifications: {'DNA': 14, 'undetermined': 1} Link IDs: {'rna3p': 13, None: 1} Not linked: pdbres="VM6 L 24 " pdbres=" DT L 25 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "M" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 741 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" 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: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6074 SG CYS B 116 95.385 29.515 113.884 1.00132.99 S ATOM 6383 SG CYS B 155 93.527 22.949 115.457 1.00137.48 S ATOM 6214 SG CYS B 134 98.620 26.125 117.857 1.00132.45 S ATOM 6672 SG CYS B 190 98.100 24.408 111.443 1.00100.14 S ATOM 20331 SG CYS E 345 101.283 81.317 44.371 1.00112.25 S ATOM 20353 SG CYS E 348 100.305 85.419 44.952 1.00117.35 S ATOM 20510 SG CYS E 368 101.876 82.844 48.319 1.00122.04 S ATOM 20531 SG CYS E 371 98.467 81.906 46.551 1.00116.28 S ATOM 20451 SG CYS E 360 99.158 68.961 44.052 1.00134.04 S ATOM 20469 SG CYS E 363 99.386 70.781 40.379 1.00134.52 S ATOM 20618 SG CYS E 382 96.814 72.489 43.166 1.00108.10 S ATOM 20635 SG CYS E 385 95.960 68.889 41.326 1.00111.04 S ATOM 19895 SG CYS E 291 55.769 67.142 51.420 1.00 93.02 S ATOM 19917 SG CYS E 294 52.386 66.867 53.577 1.00106.90 S ATOM 20006 SG CYS E 305 55.612 68.591 55.083 1.00 91.05 S ATOM 20029 SG CYS E 308 55.573 64.729 54.224 1.00 96.00 S ATOM 22523 SG CYS F 268 75.455 55.622 51.393 1.00 73.00 S ATOM 22542 SG CYS F 271 77.639 57.182 48.399 1.00 83.22 S ATOM 22627 SG CYS F 282 75.875 53.662 48.123 1.00 82.32 S ATOM 22647 SG CYS F 285 78.939 54.266 50.714 1.00108.34 S ATOM 22415 SG CYS F 255 68.183 59.510 38.127 1.00104.70 S ATOM 22432 SG CYS F 257 70.070 56.175 38.962 1.00 98.71 S ATOM 22581 SG CYS F 276 66.149 56.314 39.485 1.00 97.48 S Time building chain proxies: 6.43, per 1000 atoms: 0.21 Number of scatterers: 30828 At special positions: 0 Unit cell: (151.42, 178.22, 219.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 5 29.99 Fe 4 26.01 Ca 2 19.99 S 165 16.00 P 69 15.00 O 5806 8.00 N 5348 7.00 C 19429 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 345 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 368 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 348 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 363 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 382 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 294 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 291 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb=" ZN F 402 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 257 " pdb="ZN ZN F 402 " - pdb=" ND1 HIS F 258 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 276 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 255 " Number of angles added : 27 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6938 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 26 sheets defined 52.3% alpha, 8.9% beta 31 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.572A pdb=" N GLY A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 149 through 160 Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.677A pdb=" N ARG A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N CYS A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 287 Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 345 through 358 removed outlier: 3.508A pdb=" N VAL A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.250A pdb=" N ARG A 425 " --> pdb=" O TRP A 421 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 446 removed outlier: 3.558A pdb=" N ILE A 446 " --> pdb=" O VAL A 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 443 through 446' Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 492 through 498 removed outlier: 3.657A pdb=" N ASN A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.294A pdb=" N ALA A 524 " --> pdb=" O ARG A 520 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS A 526 " --> pdb=" O TYR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 536 Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.868A pdb=" N ARG A 554 " --> pdb=" O PHE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 576 removed outlier: 3.584A pdb=" N LEU A 575 " --> pdb=" O TYR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 598 Processing helix chain 'A' and resid 632 through 641 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 667 through 672 removed outlier: 4.074A pdb=" N ALA A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 684 Processing helix chain 'A' and resid 705 through 717 Processing helix chain 'A' and resid 774 through 780 Processing helix chain 'B' and resid 18 through 34 removed outlier: 3.582A pdb=" N PHE B 22 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 63 Processing helix chain 'B' and resid 76 through 98 Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 139 through 149 Processing helix chain 'B' and resid 155 through 164 removed outlier: 3.854A pdb=" N GLU B 159 " --> pdb=" O CYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 238 through 247 removed outlier: 4.083A pdb=" N VAL B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 274 Processing helix chain 'B' and resid 277 through 291 removed outlier: 4.600A pdb=" N LEU B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 325 through 345 removed outlier: 3.650A pdb=" N PHE B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 365 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.819A pdb=" N LEU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 386 removed outlier: 3.660A pdb=" N LEU B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 394 through 408 removed outlier: 3.626A pdb=" N ALA B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 450 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.758A pdb=" N LYS B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 512 Processing helix chain 'B' and resid 513 through 531 removed outlier: 3.783A pdb=" N ILE B 517 " --> pdb=" O ASP B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 555 removed outlier: 3.755A pdb=" N MET B 545 " --> pdb=" O SER B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.825A pdb=" N ASN B 560 " --> pdb=" O GLY B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 590 removed outlier: 4.051A pdb=" N VAL B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 580 " --> pdb=" O GLU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 608 removed outlier: 3.647A pdb=" N GLU B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 630 through 643 Processing helix chain 'B' and resid 647 through 665 Processing helix chain 'B' and resid 681 through 685 Processing helix chain 'B' and resid 686 through 692 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 709 through 725 Processing helix chain 'B' and resid 733 through 738 removed outlier: 3.532A pdb=" N LEU B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 removed outlier: 3.790A pdb=" N GLU B 745 " --> pdb=" O LEU B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 121 through 132 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 169 through 174 removed outlier: 3.599A pdb=" N ASP C 173 " --> pdb=" O PHE C 170 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 174 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 199 removed outlier: 3.859A pdb=" N SER C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 215 Proline residue: C 212 - end of helix removed outlier: 4.075A pdb=" N MET C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 226 removed outlier: 3.663A pdb=" N THR C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 261 removed outlier: 4.347A pdb=" N GLU C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ALA C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY C 261 " --> pdb=" O MET C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 320 Processing helix chain 'C' and resid 347 through 357 Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'C' and resid 397 through 413 removed outlier: 3.551A pdb=" N ILE C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 457 through 477 Processing helix chain 'C' and resid 483 through 504 Processing helix chain 'C' and resid 509 through 516 Processing helix chain 'C' and resid 522 through 546 removed outlier: 3.503A pdb=" N GLU C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N MET C 545 " --> pdb=" O SER C 541 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 546 " --> pdb=" O ARG C 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 37 through 47 removed outlier: 3.808A pdb=" N GLU D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 59 Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 111 through 123 removed outlier: 3.857A pdb=" N GLN D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN D 117 " --> pdb=" O ILE D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 144 through 164 removed outlier: 3.618A pdb=" N TRP D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 197 through 204 removed outlier: 3.749A pdb=" N PHE D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 222 removed outlier: 3.562A pdb=" N THR D 222 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 227 Processing helix chain 'D' and resid 229 through 242 removed outlier: 3.507A pdb=" N SER D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE D 242 " --> pdb=" O PHE D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.669A pdb=" N ILE D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 284 through 289' Processing helix chain 'D' and resid 321 through 329 removed outlier: 3.758A pdb=" N ILE D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 347 through 356 removed outlier: 3.677A pdb=" N GLN D 353 " --> pdb=" O GLU D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 removed outlier: 3.729A pdb=" N ARG D 371 " --> pdb=" O PHE D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 377 Processing helix chain 'D' and resid 384 through 396 removed outlier: 3.643A pdb=" N THR D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 429 Processing helix chain 'D' and resid 446 through 462 removed outlier: 3.881A pdb=" N ASP D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS D 452 " --> pdb=" O HIS D 448 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 79 through 99 removed outlier: 3.525A pdb=" N ASP E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 134 Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 144 through 157 removed outlier: 3.645A pdb=" N SER E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 192 removed outlier: 3.838A pdb=" N LEU E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 215 Processing helix chain 'E' and resid 224 through 235 Processing helix chain 'E' and resid 314 through 319 removed outlier: 3.942A pdb=" N LEU E 318 " --> pdb=" O SER E 314 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA E 319 " --> pdb=" O ALA E 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 314 through 319' Processing helix chain 'E' and resid 321 through 326 removed outlier: 4.199A pdb=" N LEU E 325 " --> pdb=" O SER E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 378 Processing helix chain 'E' and resid 382 through 387 removed outlier: 3.560A pdb=" N ILE E 386 " --> pdb=" O CYS E 382 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS E 387 " --> pdb=" O PRO E 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 382 through 387' Processing helix chain 'F' and resid 18 through 28 Processing helix chain 'F' and resid 33 through 52 removed outlier: 3.522A pdb=" N CYS F 37 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN F 52 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 121 removed outlier: 3.795A pdb=" N VAL F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE F 111 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL F 112 " --> pdb=" O ASN F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 151 Processing helix chain 'F' and resid 173 through 187 Processing helix chain 'F' and resid 200 through 211 Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 234 through 240 removed outlier: 3.809A pdb=" N GLN F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 27 Processing helix chain 'G' and resid 49 through 62 Processing helix chain 'H' and resid 65 through 82 Processing helix chain 'H' and resid 92 through 112 removed outlier: 3.559A pdb=" N ASN H 112 " --> pdb=" O ASN H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 128 Processing helix chain 'H' and resid 131 through 140 removed outlier: 3.864A pdb=" N LYS H 135 " --> pdb=" O ASP H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 225 removed outlier: 4.072A pdb=" N ALA I 173 " --> pdb=" O THR I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 237 removed outlier: 3.627A pdb=" N HIS I 230 " --> pdb=" O GLN I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 243 Processing helix chain 'I' and resid 245 through 249 Processing helix chain 'I' and resid 250 through 265 Processing helix chain 'I' and resid 278 through 289 Processing helix chain 'I' and resid 294 through 307 Processing helix chain 'I' and resid 554 through 561 Processing helix chain 'I' and resid 581 through 586 removed outlier: 4.190A pdb=" N TYR I 585 " --> pdb=" O VAL I 581 " (cutoff:3.500A) Processing helix chain 'I' and resid 599 through 606 removed outlier: 3.621A pdb=" N TRP I 603 " --> pdb=" O ASP I 599 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR I 606 " --> pdb=" O TRP I 602 " (cutoff:3.500A) Processing helix chain 'I' and resid 607 through 611 removed outlier: 3.830A pdb=" N GLN I 611 " --> pdb=" O ARG I 608 " (cutoff:3.500A) Processing helix chain 'I' and resid 614 through 631 removed outlier: 3.626A pdb=" N GLU I 618 " --> pdb=" O PHE I 614 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS I 619 " --> pdb=" O MET I 615 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS I 620 " --> pdb=" O ASP I 616 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP I 631 " --> pdb=" O ALA I 627 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 642 Processing helix chain 'I' and resid 686 through 693 Processing helix chain 'I' and resid 713 through 721 Processing helix chain 'I' and resid 722 through 727 removed outlier: 4.330A pdb=" N GLU I 726 " --> pdb=" O PRO I 722 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU I 727 " --> pdb=" O GLN I 723 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 722 through 727' Processing helix chain 'I' and resid 734 through 736 No H-bonds generated for 'chain 'I' and resid 734 through 736' Processing helix chain 'I' and resid 778 through 786 removed outlier: 4.631A pdb=" N VAL I 782 " --> pdb=" O ASN I 778 " (cutoff:3.500A) Processing helix chain 'I' and resid 817 through 866 Processing helix chain 'I' and resid 890 through 902 Processing helix chain 'I' and resid 903 through 913 removed outlier: 4.059A pdb=" N ARG I 908 " --> pdb=" O TRP I 904 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU I 909 " --> pdb=" O PRO I 905 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 282 removed outlier: 3.689A pdb=" N ARG J 280 " --> pdb=" O LEU J 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 295 removed outlier: 3.554A pdb=" N GLN J 286 " --> pdb=" O GLN J 282 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN J 295 " --> pdb=" O ILE J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 307 removed outlier: 3.764A pdb=" N GLN J 305 " --> pdb=" O ALA J 301 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 318 removed outlier: 3.594A pdb=" N LEU J 314 " --> pdb=" O ASN J 310 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER J 318 " --> pdb=" O LEU J 314 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 330 removed outlier: 3.556A pdb=" N PHE J 324 " --> pdb=" O HIS J 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 114 removed outlier: 3.808A pdb=" N ASP K 114 " --> pdb=" O PHE K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 134 Processing helix chain 'K' and resid 138 through 150 Processing helix chain 'K' and resid 158 through 167 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 4.600A pdb=" N LYS A 52 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL D 343 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 87 removed outlier: 6.793A pdb=" N GLU A 115 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 171 Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 391 removed outlier: 6.357A pdb=" N LEU A 362 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP A 441 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU A 364 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY A 436 " --> pdb=" O CYS A 462 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU A 464 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N MET A 438 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU A 466 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 440 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 337 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU A 490 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 339 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 579 through 580 removed outlier: 6.620A pdb=" N ILE A 558 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE A 607 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A 623 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU A 662 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN A 625 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N SER A 664 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLN A 506 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N SER A 661 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA A 508 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL A 663 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL A 510 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 688 " --> pdb=" O CYS A 507 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 174 through 175 removed outlier: 6.751A pdb=" N GLY B 106 " --> pdb=" O TYR B 175 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 229 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ILE B 455 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 231 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR B 457 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE B 233 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 458 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N HIS B 37 " --> pdb=" O PRO B 475 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 477 " --> pdb=" O HIS B 37 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 249 through 251 Processing sheet with id=AA9, first strand: chain 'B' and resid 491 through 494 removed outlier: 6.454A pdb=" N CYS B 491 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE B 679 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET B 493 " --> pdb=" O PHE B 679 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 536 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 186 through 188 removed outlier: 3.686A pdb=" N VAL I 163 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AB3, first strand: chain 'D' and resid 185 through 186 removed outlier: 3.509A pdb=" N LYS D 186 " --> pdb=" O CYS D 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 271 through 272 Processing sheet with id=AB5, first strand: chain 'D' and resid 431 through 433 removed outlier: 6.853A pdb=" N VAL D 442 " --> pdb=" O VAL D 432 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG D 402 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU G 11 " --> pdb=" O ARG D 402 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN G 36 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 113 through 121 removed outlier: 6.685A pdb=" N ILE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLU E 119 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE E 104 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 303 through 304 removed outlier: 3.619A pdb=" N VAL E 303 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 312 " --> pdb=" O VAL E 303 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR E 311 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 289 through 290 Processing sheet with id=AB9, first strand: chain 'E' and resid 332 through 335 Processing sheet with id=AC1, first strand: chain 'F' and resid 67 through 71 removed outlier: 6.839A pdb=" N VAL F 59 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU F 8 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG F 160 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU F 10 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU F 162 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL F 12 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE F 164 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL F 14 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N LEU F 190 " --> pdb=" O MET F 157 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER F 159 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASP F 192 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE F 161 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N CYS F 194 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL F 163 " --> pdb=" O CYS F 194 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU F 215 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA F 193 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 551 through 552 Processing sheet with id=AC3, first strand: chain 'I' and resid 647 through 648 removed outlier: 3.880A pdb=" N TYR I 676 " --> pdb=" O ALA I 648 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL I 675 " --> pdb=" O GLY I 668 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY I 668 " --> pdb=" O VAL I 675 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 657 through 659 Processing sheet with id=AC5, first strand: chain 'I' and resid 696 through 697 removed outlier: 3.771A pdb=" N VAL I 696 " --> pdb=" O GLU I 739 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 705 through 707 removed outlier: 3.734A pdb=" N LYS I 705 " --> pdb=" O LEU I 732 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 759 through 760 removed outlier: 6.326A pdb=" N VAL I 759 " --> pdb=" O ILE I 794 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 771 through 773 1347 hydrogen bonds defined for protein. 3867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 6.45 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 13304 1.43 - 1.64: 18038 1.64 - 1.86: 246 1.86 - 2.07: 0 2.07 - 2.29: 12 Bond restraints: 31600 Sorted by residual: bond pdb=" C14 VM6 L 24 " pdb=" N1 VM6 L 24 " ideal model delta sigma weight residual 1.376 1.548 -0.172 2.00e-02 2.50e+03 7.43e+01 bond pdb=" C26 VM6 L 24 " pdb=" N2 VM6 L 24 " ideal model delta sigma weight residual 1.381 1.541 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" C10 VM6 L 24 " pdb=" C20 VM6 L 24 " ideal model delta sigma weight residual 1.534 1.393 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C7 VM6 L 24 " pdb=" C8 VM6 L 24 " ideal model delta sigma weight residual 1.502 1.399 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C8 VM6 L 24 " pdb=" C9 VM6 L 24 " ideal model delta sigma weight residual 1.504 1.403 0.101 2.00e-02 2.50e+03 2.58e+01 ... (remaining 31595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 42786 3.26 - 6.52: 187 6.52 - 9.79: 31 9.79 - 13.05: 4 13.05 - 16.31: 1 Bond angle restraints: 43009 Sorted by residual: angle pdb=" CB MET J 288 " pdb=" CG MET J 288 " pdb=" SD MET J 288 " ideal model delta sigma weight residual 112.70 129.01 -16.31 3.00e+00 1.11e-01 2.96e+01 angle pdb=" C LYS H 80 " pdb=" N ILE H 81 " pdb=" CA ILE H 81 " ideal model delta sigma weight residual 121.85 116.47 5.38 1.19e+00 7.06e-01 2.04e+01 angle pdb=" O4' DA M 20 " pdb=" C4' DA M 20 " pdb=" C3' DA M 20 " ideal model delta sigma weight residual 106.00 103.34 2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT L 14 " pdb=" C4 DT L 14 " pdb=" O4 DT L 14 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" O4' DA L 28 " pdb=" C4' DA L 28 " pdb=" C3' DA L 28 " ideal model delta sigma weight residual 106.00 103.44 2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 43004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 18039 35.39 - 70.78: 933 70.78 - 106.17: 47 106.17 - 141.56: 9 141.56 - 176.96: 5 Dihedral angle restraints: 19033 sinusoidal: 8339 harmonic: 10694 Sorted by residual: dihedral pdb=" CA ASP H 131 " pdb=" C ASP H 131 " pdb=" N VAL H 132 " pdb=" CA VAL H 132 " ideal model delta harmonic sigma weight residual -180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" C13 VM6 L 24 " pdb=" C11 VM6 L 24 " pdb=" C12 VM6 L 24 " pdb=" N1 VM6 L 24 " ideal model delta sinusoidal sigma weight residual 181.09 34.07 147.02 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C1 VM6 L 24 " pdb=" C2 VM6 L 24 " pdb=" C4 VM6 L 24 " pdb=" N2 VM6 L 24 " ideal model delta sinusoidal sigma weight residual 246.92 116.09 130.83 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 19030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4025 0.055 - 0.111: 681 0.111 - 0.166: 88 0.166 - 0.222: 2 0.222 - 0.277: 1 Chirality restraints: 4797 Sorted by residual: chirality pdb=" CA MET J 288 " pdb=" N MET J 288 " pdb=" C MET J 288 " pdb=" CB MET J 288 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA LYS H 120 " pdb=" N LYS H 120 " pdb=" C LYS H 120 " pdb=" CB LYS H 120 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CB THR H 110 " pdb=" CA THR H 110 " pdb=" OG1 THR H 110 " pdb=" CG2 THR H 110 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.54e-01 ... (remaining 4794 not shown) Planarity restraints: 5272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 77 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C LYS H 77 " 0.063 2.00e-02 2.50e+03 pdb=" O LYS H 77 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL H 78 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 VM6 L 24 " -0.004 2.00e-02 2.50e+03 2.18e-02 5.92e+00 pdb=" C4 VM6 L 24 " -0.007 2.00e-02 2.50e+03 pdb=" C5 VM6 L 24 " -0.035 2.00e-02 2.50e+03 pdb=" C6 VM6 L 24 " 0.026 2.00e-02 2.50e+03 pdb=" N2 VM6 L 24 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 VM6 L 24 " -0.023 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C6 VM6 L 24 " 0.023 2.00e-02 2.50e+03 pdb=" C7 VM6 L 24 " 0.022 2.00e-02 2.50e+03 pdb=" C8 VM6 L 24 " -0.023 2.00e-02 2.50e+03 ... (remaining 5269 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 8029 2.81 - 3.33: 29268 3.33 - 3.86: 50509 3.86 - 4.38: 56409 4.38 - 4.90: 94930 Nonbonded interactions: 239145 Sorted by model distance: nonbonded pdb=" O ASN D 312 " pdb=" OD1 ASN D 312 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASP K 150 " pdb="CA CA K1001 " model vdw 2.300 3.250 nonbonded pdb=" OD1 ASN K 125 " pdb="CA CA K1002 " model vdw 2.306 3.250 nonbonded pdb=" OD1 ASP K 152 " pdb="CA CA K1001 " model vdw 2.394 3.250 nonbonded pdb=" O LYS K 120 " pdb="CA CA K1002 " model vdw 2.397 3.250 ... (remaining 239140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 37.170 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.006 0.565 31626 Z= 0.281 Angle : 0.651 16.309 43048 Z= 0.368 Chirality : 0.042 0.277 4797 Planarity : 0.004 0.049 5272 Dihedral : 19.387 176.955 12095 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.15 % Allowed : 23.83 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3596 helix: 1.15 (0.13), residues: 1692 sheet: -0.30 (0.28), residues: 359 loop : -0.95 (0.17), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 289 TYR 0.022 0.001 TYR H 95 PHE 0.027 0.001 PHE K 113 TRP 0.026 0.001 TRP C 539 HIS 0.007 0.001 HIS B 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.22 (31600) covalent geometry : angle 0.63229 / 0.37 (43009) hydrogen bonds : bond 0.13587 / 9.12 ( 1424) hydrogen bonds : angle 5.53733 / 3.91 ( 4021) metal coordination : bond 0.18260 / 12.72 ( 24) metal coordination : angle 5.17214 / 3.30 ( 39) Misc. bond : bond 0.04176 / 2.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 315 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 THR cc_start: 0.9071 (p) cc_final: 0.8788 (t) REVERT: A 306 ILE cc_start: 0.8765 (mm) cc_final: 0.8556 (mt) REVERT: A 380 MET cc_start: 0.8938 (tmm) cc_final: 0.8581 (tmm) REVERT: A 450 MET cc_start: 0.6911 (mpp) cc_final: 0.6480 (mtp) REVERT: A 714 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: B 9 LEU cc_start: 0.8080 (tp) cc_final: 0.7424 (tp) REVERT: B 12 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.6203 (m-80) REVERT: B 27 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: B 95 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8074 (mt-10) REVERT: B 268 LYS cc_start: 0.8087 (mptt) cc_final: 0.7774 (mmtm) REVERT: B 342 TRP cc_start: 0.8708 (t60) cc_final: 0.8378 (t60) REVERT: B 350 VAL cc_start: 0.8220 (p) cc_final: 0.8008 (m) REVERT: B 363 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7900 (tm-30) REVERT: B 657 MET cc_start: 0.8501 (mmm) cc_final: 0.8216 (mmm) REVERT: B 707 ASN cc_start: 0.7581 (t0) cc_final: 0.7196 (t0) REVERT: B 745 GLU cc_start: 0.7389 (pm20) cc_final: 0.7022 (pm20) REVERT: C 117 MET cc_start: 0.4031 (pmm) cc_final: 0.3665 (mtp) REVERT: C 384 HIS cc_start: 0.7000 (p-80) cc_final: 0.6372 (p90) REVERT: C 521 LEU cc_start: 0.5325 (tt) cc_final: 0.4997 (mt) REVERT: C 539 TRP cc_start: 0.7280 (t60) cc_final: 0.7008 (t60) REVERT: C 545 MET cc_start: 0.5066 (pmm) cc_final: 0.4309 (ppp) REVERT: D 260 ASN cc_start: 0.9093 (m-40) cc_final: 0.8775 (m110) REVERT: D 321 SER cc_start: 0.8157 (OUTLIER) cc_final: 0.7784 (p) REVERT: E 50 HIS cc_start: 0.6157 (OUTLIER) cc_final: 0.5763 (t-90) REVERT: E 62 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: E 250 ILE cc_start: 0.7761 (mt) cc_final: 0.7468 (tt) REVERT: E 303 VAL cc_start: 0.8810 (p) cc_final: 0.8418 (m) REVERT: E 336 LEU cc_start: 0.7286 (mt) cc_final: 0.6908 (tp) REVERT: G 36 GLN cc_start: 0.7645 (tp-100) cc_final: 0.7442 (tp-100) REVERT: G 37 ASP cc_start: 0.8018 (p0) cc_final: 0.7672 (p0) REVERT: G 61 MET cc_start: 0.7508 (mmp) cc_final: 0.7306 (mmm) REVERT: H 76 LYS cc_start: 0.8187 (ptmt) cc_final: 0.7572 (mmtt) REVERT: H 93 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7302 (mtp85) REVERT: H 97 ASP cc_start: 0.8918 (m-30) cc_final: 0.8644 (m-30) REVERT: H 122 MET cc_start: 0.8577 (mtt) cc_final: 0.8214 (mtt) REVERT: I 194 MET cc_start: 0.5032 (mmm) cc_final: 0.3302 (tmm) REVERT: I 209 HIS cc_start: 0.0463 (OUTLIER) cc_final: -0.0188 (t70) REVERT: I 605 GLU cc_start: 0.8653 (tp30) cc_final: 0.7875 (mt-10) REVERT: I 615 MET cc_start: 0.7025 (ptt) cc_final: 0.6520 (ppp) REVERT: I 643 ASN cc_start: 0.9065 (t0) cc_final: 0.8325 (t0) REVERT: I 686 SER cc_start: 0.4089 (OUTLIER) cc_final: 0.2546 (m) REVERT: I 741 TYR cc_start: 0.7495 (t80) cc_final: 0.7136 (t80) REVERT: I 766 MET cc_start: 0.7450 (ptp) cc_final: 0.7234 (ptp) REVERT: I 840 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8607 (mtmm) REVERT: K 103 LYS cc_start: 0.8404 (pttp) cc_final: 0.8144 (pttp) REVERT: K 141 GLU cc_start: 0.7546 (pt0) cc_final: 0.7287 (pm20) outliers start: 37 outliers final: 27 residues processed: 342 average time/residue: 0.1808 time to fit residues: 100.2962 Evaluate side-chains 342 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 307 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain I residue 686 SER Chi-restraints excluded: chain I residue 710 PHE Chi-restraints excluded: chain I residue 767 MET Chi-restraints excluded: chain K residue 126 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.0020 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS A 299 ASN A 444 HIS ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN A 665 GLN B 21 GLN B 97 GLN B 135 HIS B 164 HIS B 210 HIS B 260 GLN B 662 GLN B 733 GLN B 758 GLN ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN C 534 ASN D 20 GLN D 97 HIS D 302 HIS E 220 HIS E 317 HIS F 63 HIS F 205 GLN F 235 GLN F 240 GLN G 18 GLN H 136 ASN I 202 HIS I 206 HIS I 538 GLN ** I 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 758 ASN I 780 HIS I 800 HIS I 907 ASN J 329 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.119733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.091917 restraints weight = 88604.138| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.61 r_work: 0.3348 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 31626 Z= 0.246 Angle : 0.674 27.002 43048 Z= 0.338 Chirality : 0.045 0.234 4797 Planarity : 0.005 0.050 5272 Dihedral : 15.759 172.316 4838 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.90 % Allowed : 22.07 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3596 helix: 1.10 (0.13), residues: 1722 sheet: -0.79 (0.27), residues: 367 loop : -1.18 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 195 TYR 0.027 0.002 TYR A 534 PHE 0.023 0.002 PHE B 448 TRP 0.013 0.002 TRP C 539 HIS 0.008 0.001 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 (31600) covalent geometry : angle 0.64234 / 0.34 (43009) hydrogen bonds : bond 0.05161 / 3.41 ( 1424) hydrogen bonds : angle 4.83200 / 3.40 ( 4021) metal coordination : bond 0.02376 / 1.60 ( 24) metal coordination : angle 6.82351 / 4.22 ( 39) Misc. bond : bond 0.00422 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 311 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 THR cc_start: 0.9088 (p) cc_final: 0.8811 (t) REVERT: A 276 MET cc_start: 0.8591 (mpp) cc_final: 0.8224 (mmp) REVERT: A 306 ILE cc_start: 0.8944 (mm) cc_final: 0.8723 (mt) REVERT: A 380 MET cc_start: 0.8906 (tmm) cc_final: 0.8597 (tmm) REVERT: A 450 MET cc_start: 0.7177 (mpp) cc_final: 0.6903 (mtp) REVERT: A 714 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7090 (tm-30) REVERT: B 9 LEU cc_start: 0.8179 (tp) cc_final: 0.7571 (tp) REVERT: B 12 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.6597 (m-80) REVERT: B 27 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6969 (tt0) REVERT: B 42 MET cc_start: 0.7173 (ttt) cc_final: 0.6952 (ttt) REVERT: B 95 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8105 (mt-10) REVERT: B 363 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 707 ASN cc_start: 0.7552 (t0) cc_final: 0.7167 (t0) REVERT: C 117 MET cc_start: 0.4403 (pmm) cc_final: 0.3739 (mtp) REVERT: C 415 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8650 (p) REVERT: C 521 LEU cc_start: 0.5593 (OUTLIER) cc_final: 0.5381 (mp) REVERT: C 529 LEU cc_start: 0.8396 (mm) cc_final: 0.8131 (tp) REVERT: C 545 MET cc_start: 0.4782 (pmm) cc_final: 0.4324 (ppp) REVERT: D 259 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8737 (mm) REVERT: D 260 ASN cc_start: 0.8928 (m-40) cc_final: 0.8616 (m110) REVERT: D 371 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7516 (mtt-85) REVERT: D 441 MET cc_start: 0.6452 (pmm) cc_final: 0.5023 (pmm) REVERT: E 12 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6096 (pt0) REVERT: E 50 HIS cc_start: 0.6162 (OUTLIER) cc_final: 0.5775 (t-90) REVERT: E 62 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: E 140 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7988 (t-90) REVERT: E 244 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8400 (p) REVERT: E 250 ILE cc_start: 0.8159 (mt) cc_final: 0.7795 (tt) REVERT: E 336 LEU cc_start: 0.7116 (mt) cc_final: 0.6775 (tp) REVERT: F 7 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: G 37 ASP cc_start: 0.7956 (p0) cc_final: 0.7486 (p0) REVERT: H 76 LYS cc_start: 0.8273 (ptmt) cc_final: 0.7687 (mmtt) REVERT: H 93 ARG cc_start: 0.8047 (mtp85) cc_final: 0.7775 (mtp85) REVERT: H 97 ASP cc_start: 0.8851 (m-30) cc_final: 0.8583 (m-30) REVERT: H 122 MET cc_start: 0.8566 (mtt) cc_final: 0.8266 (mtt) REVERT: I 194 MET cc_start: 0.5018 (mmm) cc_final: 0.3342 (tmm) REVERT: I 209 HIS cc_start: 0.0225 (OUTLIER) cc_final: -0.0276 (t70) REVERT: I 542 TRP cc_start: 0.8637 (m100) cc_final: 0.8383 (m100) REVERT: I 566 MET cc_start: 0.0568 (tpp) cc_final: 0.0304 (tpp) REVERT: I 615 MET cc_start: 0.7071 (ptt) cc_final: 0.6545 (ppp) REVERT: I 643 ASN cc_start: 0.9221 (t0) cc_final: 0.8477 (t0) REVERT: I 686 SER cc_start: 0.4838 (OUTLIER) cc_final: 0.1640 (t) REVERT: I 741 TYR cc_start: 0.7472 (t80) cc_final: 0.7111 (t80) REVERT: J 294 GLN cc_start: 0.7166 (pt0) cc_final: 0.5830 (tp40) REVERT: J 305 GLN cc_start: 0.5415 (OUTLIER) cc_final: 0.4980 (mt0) REVERT: J 309 GLU cc_start: 0.8204 (tp30) cc_final: 0.7895 (tp30) outliers start: 126 outliers final: 80 residues processed: 413 average time/residue: 0.1736 time to fit residues: 117.9847 Evaluate side-chains 389 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 294 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 575 ASP Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 686 SER Chi-restraints excluded: chain I residue 710 PHE Chi-restraints excluded: chain I residue 786 LEU Chi-restraints excluded: chain I residue 807 VAL Chi-restraints excluded: chain J residue 305 GLN Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 163 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 242 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 276 optimal weight: 0.1980 chunk 321 optimal weight: 3.9990 chunk 290 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 296 optimal weight: 9.9990 chunk 310 optimal weight: 30.0000 chunk 170 optimal weight: 9.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS B 572 GLN B 723 GLN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN F 176 ASN I 206 HIS ** I 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 780 HIS ** J 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.118723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.091213 restraints weight = 88316.484| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.69 r_work: 0.3320 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 31626 Z= 0.268 Angle : 0.693 28.622 43048 Z= 0.349 Chirality : 0.045 0.273 4797 Planarity : 0.005 0.049 5272 Dihedral : 15.774 173.209 4814 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.14 % Allowed : 22.28 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.14), residues: 3596 helix: 0.91 (0.13), residues: 1721 sheet: -1.05 (0.27), residues: 368 loop : -1.35 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 647 TYR 0.028 0.002 TYR A 534 PHE 0.023 0.002 PHE F 50 TRP 0.015 0.002 TRP C 539 HIS 0.022 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.27 (31600) covalent geometry : angle 0.65738 / 0.35 (43009) hydrogen bonds : bond 0.05358 / 3.57 ( 1424) hydrogen bonds : angle 4.83039 / 3.41 ( 4021) metal coordination : bond 0.01618 / 0.94 ( 24) metal coordination : angle 7.31568 / 4.57 ( 39) Misc. bond : bond 0.00128 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 308 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8776 (m) REVERT: A 146 THR cc_start: 0.9135 (p) cc_final: 0.8855 (t) REVERT: A 306 ILE cc_start: 0.8960 (mm) cc_final: 0.8757 (mt) REVERT: A 380 MET cc_start: 0.8848 (tmm) cc_final: 0.8571 (tmm) REVERT: A 450 MET cc_start: 0.7153 (mpp) cc_final: 0.6563 (mtp) REVERT: A 533 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7109 (tp) REVERT: A 627 SER cc_start: 0.8566 (t) cc_final: 0.8280 (t) REVERT: A 714 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7108 (tm-30) REVERT: B 9 LEU cc_start: 0.8196 (tp) cc_final: 0.7562 (tp) REVERT: B 20 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6207 (tm-30) REVERT: B 247 MET cc_start: 0.8512 (mmm) cc_final: 0.8176 (mmm) REVERT: B 268 LYS cc_start: 0.8054 (mptt) cc_final: 0.7668 (mmtm) REVERT: B 363 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8021 (tm-30) REVERT: B 707 ASN cc_start: 0.7580 (t0) cc_final: 0.7175 (t0) REVERT: C 117 MET cc_start: 0.4423 (pmm) cc_final: 0.3801 (mtp) REVERT: C 521 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5327 (mp) REVERT: C 541 SER cc_start: 0.7201 (OUTLIER) cc_final: 0.6914 (t) REVERT: D 259 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8751 (mm) REVERT: D 260 ASN cc_start: 0.8836 (m-40) cc_final: 0.8499 (m110) REVERT: D 280 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6897 (ptm160) REVERT: D 371 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7324 (mtt-85) REVERT: D 441 MET cc_start: 0.6387 (pmm) cc_final: 0.4911 (pmm) REVERT: E 12 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6100 (pt0) REVERT: E 50 HIS cc_start: 0.5912 (OUTLIER) cc_final: 0.5620 (t-90) REVERT: E 211 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8186 (tp) REVERT: E 244 SER cc_start: 0.8639 (OUTLIER) cc_final: 0.8403 (p) REVERT: E 317 HIS cc_start: 0.8727 (OUTLIER) cc_final: 0.8479 (m90) REVERT: E 336 LEU cc_start: 0.7154 (mt) cc_final: 0.6792 (tp) REVERT: F 7 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7991 (pm20) REVERT: F 129 THR cc_start: 0.7633 (OUTLIER) cc_final: 0.7284 (t) REVERT: F 241 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8316 (mp) REVERT: H 76 LYS cc_start: 0.8360 (ptmt) cc_final: 0.7814 (mmtt) REVERT: H 93 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7731 (mtp85) REVERT: H 97 ASP cc_start: 0.8872 (m-30) cc_final: 0.8641 (m-30) REVERT: H 122 MET cc_start: 0.8604 (mtt) cc_final: 0.8345 (mtt) REVERT: I 194 MET cc_start: 0.4977 (mmm) cc_final: 0.3347 (tmm) REVERT: I 209 HIS cc_start: 0.0126 (OUTLIER) cc_final: -0.0351 (t70) REVERT: I 542 TRP cc_start: 0.8629 (m100) cc_final: 0.8276 (m100) REVERT: I 615 MET cc_start: 0.6995 (ptt) cc_final: 0.6445 (ppp) REVERT: I 643 ASN cc_start: 0.9231 (t0) cc_final: 0.8548 (t0) REVERT: I 686 SER cc_start: 0.4863 (OUTLIER) cc_final: 0.1622 (t) REVERT: I 716 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7518 (ptpp) REVERT: I 893 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7520 (pp30) REVERT: J 305 GLN cc_start: 0.5541 (OUTLIER) cc_final: 0.5197 (mt0) REVERT: J 309 GLU cc_start: 0.8348 (tp30) cc_final: 0.7965 (tp30) outliers start: 166 outliers final: 102 residues processed: 447 average time/residue: 0.1803 time to fit residues: 132.6239 Evaluate side-chains 421 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 299 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 302 HIS Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 575 ASP Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 686 SER Chi-restraints excluded: chain I residue 710 PHE Chi-restraints excluded: chain I residue 716 LYS Chi-restraints excluded: chain I residue 767 MET Chi-restraints excluded: chain I residue 786 LEU Chi-restraints excluded: chain I residue 807 VAL Chi-restraints excluded: chain I residue 893 GLN Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain J residue 305 GLN Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 163 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 123 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 213 optimal weight: 0.0980 chunk 244 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN I 206 HIS I 256 ASN I 737 GLN I 780 HIS ** J 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.120153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.092647 restraints weight = 88020.179| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.68 r_work: 0.3366 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31626 Z= 0.150 Angle : 0.612 26.962 43048 Z= 0.302 Chirality : 0.042 0.264 4797 Planarity : 0.004 0.047 5272 Dihedral : 15.666 172.891 4809 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.93 % Allowed : 23.71 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3596 helix: 1.12 (0.13), residues: 1721 sheet: -0.87 (0.27), residues: 373 loop : -1.28 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 198 TYR 0.026 0.001 TYR A 534 PHE 0.022 0.001 PHE F 50 TRP 0.025 0.001 TRP I 848 HIS 0.025 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (31600) covalent geometry : angle 0.57699 / 0.30 (43009) hydrogen bonds : bond 0.04297 / 2.88 ( 1424) hydrogen bonds : angle 4.52225 / 3.20 ( 4021) metal coordination : bond 0.01357 / 0.83 ( 24) metal coordination : angle 6.83830 / 4.25 ( 39) Misc. bond : bond 0.00024 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 312 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 THR cc_start: 0.9122 (p) cc_final: 0.8834 (t) REVERT: A 276 MET cc_start: 0.8633 (tpp) cc_final: 0.8161 (mmp) REVERT: A 306 ILE cc_start: 0.8932 (mm) cc_final: 0.8720 (mt) REVERT: A 335 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8579 (m) REVERT: A 380 MET cc_start: 0.8886 (tmm) cc_final: 0.8397 (tmm) REVERT: A 450 MET cc_start: 0.7120 (mpp) cc_final: 0.6764 (mtp) REVERT: A 627 SER cc_start: 0.8517 (t) cc_final: 0.8225 (t) REVERT: A 714 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7030 (tm-30) REVERT: B 9 LEU cc_start: 0.8196 (tp) cc_final: 0.7559 (tp) REVERT: B 20 GLU cc_start: 0.6511 (tm-30) cc_final: 0.6202 (tm-30) REVERT: B 27 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6805 (tt0) REVERT: B 365 VAL cc_start: 0.7670 (t) cc_final: 0.7438 (m) REVERT: B 707 ASN cc_start: 0.7522 (t0) cc_final: 0.7124 (t0) REVERT: C 117 MET cc_start: 0.4574 (pmm) cc_final: 0.4117 (mtp) REVERT: C 143 TRP cc_start: 0.7250 (m-90) cc_final: 0.6880 (m100) REVERT: C 521 LEU cc_start: 0.5520 (OUTLIER) cc_final: 0.5266 (mp) REVERT: C 529 LEU cc_start: 0.8352 (mm) cc_final: 0.8083 (tp) REVERT: C 542 ARG cc_start: 0.7333 (ttp-170) cc_final: 0.7087 (tmm160) REVERT: C 545 MET cc_start: 0.4982 (pmm) cc_final: 0.4254 (ppp) REVERT: D 259 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8760 (mm) REVERT: D 260 ASN cc_start: 0.8802 (m-40) cc_final: 0.8472 (m110) REVERT: D 280 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7078 (ptm160) REVERT: D 371 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7303 (mtt-85) REVERT: D 398 ARG cc_start: 0.7835 (mpt-90) cc_final: 0.7400 (mtt90) REVERT: D 441 MET cc_start: 0.6445 (pmm) cc_final: 0.4998 (pmm) REVERT: E 12 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6128 (pt0) REVERT: E 50 HIS cc_start: 0.5905 (OUTLIER) cc_final: 0.5616 (t-90) REVERT: E 303 VAL cc_start: 0.8981 (p) cc_final: 0.8517 (m) REVERT: E 317 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.8414 (m90) REVERT: E 336 LEU cc_start: 0.7133 (mt) cc_final: 0.6766 (tp) REVERT: F 7 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: F 129 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.7197 (t) REVERT: F 241 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8222 (mp) REVERT: G 37 ASP cc_start: 0.7757 (p0) cc_final: 0.7299 (p0) REVERT: H 76 LYS cc_start: 0.8332 (ptmt) cc_final: 0.7907 (ptmt) REVERT: H 93 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7738 (mtp85) REVERT: H 97 ASP cc_start: 0.8901 (m-30) cc_final: 0.8699 (m-30) REVERT: H 122 MET cc_start: 0.8573 (mtt) cc_final: 0.8296 (mtt) REVERT: I 194 MET cc_start: 0.4950 (mmm) cc_final: 0.3345 (tmm) REVERT: I 209 HIS cc_start: 0.0193 (OUTLIER) cc_final: -0.0296 (t70) REVERT: I 542 TRP cc_start: 0.8608 (m100) cc_final: 0.8249 (m100) REVERT: I 615 MET cc_start: 0.6834 (ptt) cc_final: 0.6255 (ppp) REVERT: I 643 ASN cc_start: 0.9258 (t0) cc_final: 0.8549 (t0) REVERT: I 686 SER cc_start: 0.4267 (OUTLIER) cc_final: 0.2831 (m) REVERT: I 741 TYR cc_start: 0.7349 (t80) cc_final: 0.6992 (t80) REVERT: I 840 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8582 (mtmm) REVERT: I 908 ARG cc_start: 0.8477 (mmt-90) cc_final: 0.8267 (mmt180) REVERT: J 294 GLN cc_start: 0.7212 (pt0) cc_final: 0.6035 (tp40) REVERT: J 305 GLN cc_start: 0.5411 (OUTLIER) cc_final: 0.5146 (mt0) REVERT: J 309 GLU cc_start: 0.8284 (tp30) cc_final: 0.7921 (tp30) REVERT: K 144 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7974 (pt0) outliers start: 127 outliers final: 81 residues processed: 417 average time/residue: 0.1900 time to fit residues: 129.4943 Evaluate side-chains 397 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 301 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 302 HIS Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 686 SER Chi-restraints excluded: chain I residue 710 PHE Chi-restraints excluded: chain I residue 767 MET Chi-restraints excluded: chain I residue 786 LEU Chi-restraints excluded: chain I residue 807 VAL Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain J residue 305 GLN Chi-restraints excluded: chain K residue 126 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 249 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 321 optimal weight: 0.0270 chunk 348 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 326 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN I 206 HIS I 780 HIS ** J 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.119558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092032 restraints weight = 87652.378| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.65 r_work: 0.3354 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31626 Z= 0.191 Angle : 0.634 26.886 43048 Z= 0.314 Chirality : 0.043 0.302 4797 Planarity : 0.004 0.047 5272 Dihedral : 15.676 172.960 4803 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.55 % Allowed : 23.68 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3596 helix: 1.09 (0.13), residues: 1722 sheet: -0.89 (0.27), residues: 373 loop : -1.33 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 198 TYR 0.024 0.002 TYR A 534 PHE 0.022 0.002 PHE B 448 TRP 0.020 0.001 TRP C 539 HIS 0.010 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (31600) covalent geometry : angle 0.59975 / 0.31 (43009) hydrogen bonds : bond 0.04515 / 3.01 ( 1424) hydrogen bonds : angle 4.52256 / 3.20 ( 4021) metal coordination : bond 0.01298 / 0.74 ( 24) metal coordination : angle 6.80506 / 4.22 ( 39) Misc. bond : bond 0.00031 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 311 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 THR cc_start: 0.9133 (p) cc_final: 0.8845 (t) REVERT: A 335 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8604 (m) REVERT: A 380 MET cc_start: 0.8869 (tmm) cc_final: 0.8354 (tmm) REVERT: A 450 MET cc_start: 0.7149 (mpp) cc_final: 0.6761 (mtp) REVERT: A 589 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7879 (mtm180) REVERT: A 627 SER cc_start: 0.8543 (t) cc_final: 0.8250 (t) REVERT: A 714 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7044 (tm-30) REVERT: B 9 LEU cc_start: 0.8125 (tp) cc_final: 0.7509 (tp) REVERT: B 20 GLU cc_start: 0.6469 (tm-30) cc_final: 0.6047 (tm-30) REVERT: B 223 LYS cc_start: 0.8252 (mmmt) cc_final: 0.8011 (mmmt) REVERT: B 268 LYS cc_start: 0.8044 (mptt) cc_final: 0.7716 (mmtm) REVERT: B 363 GLN cc_start: 0.8336 (tm-30) cc_final: 0.8022 (tm-30) REVERT: B 707 ASN cc_start: 0.7524 (t0) cc_final: 0.7126 (t0) REVERT: B 748 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7874 (tm-30) REVERT: C 117 MET cc_start: 0.4571 (pmm) cc_final: 0.4112 (mtp) REVERT: C 143 TRP cc_start: 0.7259 (m-90) cc_final: 0.6886 (m100) REVERT: C 361 GLU cc_start: 0.6823 (tp30) cc_final: 0.6618 (tp30) REVERT: C 521 LEU cc_start: 0.5592 (OUTLIER) cc_final: 0.5360 (mp) REVERT: C 529 LEU cc_start: 0.8345 (mm) cc_final: 0.8088 (tp) REVERT: C 545 MET cc_start: 0.4977 (pmm) cc_final: 0.4295 (ppp) REVERT: D 109 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8533 (tp) REVERT: D 259 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8752 (mm) REVERT: D 260 ASN cc_start: 0.8822 (m-40) cc_final: 0.8492 (m110) REVERT: D 280 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7064 (ptm160) REVERT: D 371 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7392 (mtt-85) REVERT: D 441 MET cc_start: 0.6304 (pmm) cc_final: 0.4915 (pmm) REVERT: E 12 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6195 (pt0) REVERT: E 50 HIS cc_start: 0.5904 (OUTLIER) cc_final: 0.5633 (t-90) REVERT: E 244 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8433 (p) REVERT: E 303 VAL cc_start: 0.8976 (p) cc_final: 0.8509 (m) REVERT: E 317 HIS cc_start: 0.8690 (OUTLIER) cc_final: 0.8469 (m90) REVERT: E 336 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6822 (tp) REVERT: F 7 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: F 129 THR cc_start: 0.7492 (OUTLIER) cc_final: 0.7080 (t) REVERT: F 241 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8280 (mp) REVERT: G 37 ASP cc_start: 0.7829 (p0) cc_final: 0.7392 (p0) REVERT: H 76 LYS cc_start: 0.8279 (ptmt) cc_final: 0.7733 (mmtt) REVERT: H 93 ARG cc_start: 0.7967 (mtp85) cc_final: 0.7741 (mtp85) REVERT: H 122 MET cc_start: 0.8536 (mtt) cc_final: 0.8246 (mtt) REVERT: I 194 MET cc_start: 0.4926 (mmm) cc_final: 0.3342 (tmm) REVERT: I 209 HIS cc_start: 0.0023 (OUTLIER) cc_final: -0.0436 (t70) REVERT: I 542 TRP cc_start: 0.8630 (m100) cc_final: 0.8265 (m100) REVERT: I 615 MET cc_start: 0.6779 (ptt) cc_final: 0.6216 (ppp) REVERT: I 643 ASN cc_start: 0.9283 (t0) cc_final: 0.8580 (t0) REVERT: I 686 SER cc_start: 0.4546 (OUTLIER) cc_final: 0.3230 (m) REVERT: I 716 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7535 (ptpp) REVERT: I 741 TYR cc_start: 0.7323 (t80) cc_final: 0.6953 (t80) REVERT: I 840 LYS cc_start: 0.8812 (mtpt) cc_final: 0.8586 (mtmm) REVERT: I 893 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7553 (pp30) REVERT: J 305 GLN cc_start: 0.5458 (OUTLIER) cc_final: 0.5245 (mt0) REVERT: J 309 GLU cc_start: 0.8378 (tp30) cc_final: 0.8041 (tp30) outliers start: 147 outliers final: 105 residues processed: 434 average time/residue: 0.1805 time to fit residues: 127.7769 Evaluate side-chains 432 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 307 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 302 HIS Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 575 ASP Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 686 SER Chi-restraints excluded: chain I residue 710 PHE Chi-restraints excluded: chain I residue 716 LYS Chi-restraints excluded: chain I residue 767 MET Chi-restraints excluded: chain I residue 786 LEU Chi-restraints excluded: chain I residue 807 VAL Chi-restraints excluded: chain I residue 893 GLN Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain J residue 305 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 38 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 285 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN C 496 ASN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 HIS I 780 HIS ** J 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.119989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.092490 restraints weight = 88246.697| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.64 r_work: 0.3368 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31626 Z= 0.156 Angle : 0.608 25.607 43048 Z= 0.300 Chirality : 0.042 0.267 4797 Planarity : 0.004 0.047 5272 Dihedral : 15.616 172.950 4796 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.46 % Allowed : 24.14 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3596 helix: 1.16 (0.13), residues: 1722 sheet: -0.84 (0.27), residues: 379 loop : -1.31 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 56 TYR 0.025 0.001 TYR A 534 PHE 0.022 0.001 PHE F 50 TRP 0.020 0.001 TRP C 539 HIS 0.006 0.001 HIS I 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (31600) covalent geometry : angle 0.57460 / 0.30 (43009) hydrogen bonds : bond 0.04180 / 2.80 ( 1424) hydrogen bonds : angle 4.42087 / 3.13 ( 4021) metal coordination : bond 0.01204 / 0.72 ( 24) metal coordination : angle 6.65885 / 4.12 ( 39) Misc. bond : bond 0.00025 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 316 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 THR cc_start: 0.9128 (p) cc_final: 0.8841 (t) REVERT: A 205 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: A 335 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8609 (m) REVERT: A 380 MET cc_start: 0.8885 (tmm) cc_final: 0.8381 (tmm) REVERT: A 450 MET cc_start: 0.7181 (mpp) cc_final: 0.6788 (mtp) REVERT: A 589 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7925 (mtm180) REVERT: A 627 SER cc_start: 0.8519 (t) cc_final: 0.8225 (t) REVERT: A 714 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7004 (tm-30) REVERT: B 9 LEU cc_start: 0.8092 (tp) cc_final: 0.7390 (tp) REVERT: B 20 GLU cc_start: 0.6380 (tm-30) cc_final: 0.6004 (tm-30) REVERT: B 27 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6803 (tt0) REVERT: B 268 LYS cc_start: 0.8093 (mptt) cc_final: 0.7667 (mmtm) REVERT: B 363 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7977 (tm-30) REVERT: B 707 ASN cc_start: 0.7508 (t0) cc_final: 0.7115 (t0) REVERT: C 117 MET cc_start: 0.4639 (pmm) cc_final: 0.4139 (mtp) REVERT: C 143 TRP cc_start: 0.7177 (m-90) cc_final: 0.6767 (m100) REVERT: C 361 GLU cc_start: 0.6839 (tp30) cc_final: 0.6601 (tp30) REVERT: C 529 LEU cc_start: 0.8428 (mm) cc_final: 0.8155 (tp) REVERT: C 542 ARG cc_start: 0.7066 (tmm160) cc_final: 0.6856 (tmm-80) REVERT: C 545 MET cc_start: 0.4996 (pmm) cc_final: 0.4298 (ppp) REVERT: D 109 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8572 (tp) REVERT: D 259 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8791 (mm) REVERT: D 260 ASN cc_start: 0.8806 (m-40) cc_final: 0.8522 (m-40) REVERT: D 280 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7110 (ptm160) REVERT: D 312 ASN cc_start: 0.8331 (t0) cc_final: 0.7904 (t0) REVERT: D 371 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7323 (mtt-85) REVERT: D 441 MET cc_start: 0.6619 (pmm) cc_final: 0.5200 (pmm) REVERT: E 12 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6175 (pt0) REVERT: E 50 HIS cc_start: 0.5894 (OUTLIER) cc_final: 0.5609 (t-90) REVERT: E 244 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8537 (p) REVERT: E 252 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8179 (mtt) REVERT: E 303 VAL cc_start: 0.8977 (p) cc_final: 0.8514 (m) REVERT: E 317 HIS cc_start: 0.8662 (OUTLIER) cc_final: 0.8428 (m90) REVERT: E 336 LEU cc_start: 0.7231 (mt) cc_final: 0.6820 (tp) REVERT: F 7 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7924 (pm20) REVERT: F 129 THR cc_start: 0.7510 (OUTLIER) cc_final: 0.7095 (t) REVERT: F 241 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8273 (mp) REVERT: H 70 LYS cc_start: 0.7551 (mmtm) cc_final: 0.6587 (tppp) REVERT: H 76 LYS cc_start: 0.8323 (ptmt) cc_final: 0.7984 (ptmt) REVERT: H 119 LYS cc_start: 0.7212 (mmmt) cc_final: 0.6745 (mmmt) REVERT: H 122 MET cc_start: 0.8526 (mtt) cc_final: 0.7906 (mtt) REVERT: H 135 LYS cc_start: 0.6204 (pttt) cc_final: 0.5916 (mmtm) REVERT: I 194 MET cc_start: 0.4991 (mmm) cc_final: 0.3346 (tmm) REVERT: I 209 HIS cc_start: 0.0367 (OUTLIER) cc_final: -0.0203 (t70) REVERT: I 542 TRP cc_start: 0.8638 (m100) cc_final: 0.8314 (m100) REVERT: I 615 MET cc_start: 0.6805 (ptt) cc_final: 0.6215 (ppp) REVERT: I 643 ASN cc_start: 0.9310 (t0) cc_final: 0.8600 (t0) REVERT: I 686 SER cc_start: 0.4316 (OUTLIER) cc_final: 0.2843 (m) REVERT: I 716 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7607 (ptpp) REVERT: I 741 TYR cc_start: 0.7429 (t80) cc_final: 0.7061 (t80) REVERT: I 840 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8576 (mtmm) REVERT: J 309 GLU cc_start: 0.8248 (tp30) cc_final: 0.7939 (tp30) outliers start: 144 outliers final: 104 residues processed: 437 average time/residue: 0.1918 time to fit residues: 136.8991 Evaluate side-chains 426 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 303 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 302 HIS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 575 ASP Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 686 SER Chi-restraints excluded: chain I residue 710 PHE Chi-restraints excluded: chain I residue 716 LYS Chi-restraints excluded: chain I residue 751 VAL Chi-restraints excluded: chain I residue 767 MET Chi-restraints excluded: chain I residue 786 LEU Chi-restraints excluded: chain I residue 807 VAL Chi-restraints excluded: chain J residue 302 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 307 optimal weight: 30.0000 chunk 94 optimal weight: 7.9990 chunk 204 optimal weight: 0.3980 chunk 290 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 327 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 250 optimal weight: 0.3980 chunk 239 optimal weight: 4.9990 chunk 262 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN H 108 ASN I 206 HIS ** I 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 780 HIS ** J 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 305 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.119254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.091729 restraints weight = 88041.075| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.70 r_work: 0.3341 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 31626 Z= 0.203 Angle : 0.656 27.146 43048 Z= 0.323 Chirality : 0.044 0.317 4797 Planarity : 0.004 0.047 5272 Dihedral : 15.665 172.683 4796 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.70 % Allowed : 24.20 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3596 helix: 1.08 (0.13), residues: 1716 sheet: -1.01 (0.26), residues: 394 loop : -1.32 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 75 TYR 0.024 0.002 TYR A 534 PHE 0.025 0.002 PHE B 448 TRP 0.024 0.001 TRP I 577 HIS 0.008 0.001 HIS I 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (31600) covalent geometry : angle 0.62275 / 0.32 (43009) hydrogen bonds : bond 0.04553 / 3.03 ( 1424) hydrogen bonds : angle 4.50296 / 3.19 ( 4021) metal coordination : bond 0.01407 / 0.83 ( 24) metal coordination : angle 6.84266 / 4.24 ( 39) Misc. bond : bond 0.00026 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 315 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 THR cc_start: 0.9138 (p) cc_final: 0.8846 (t) REVERT: A 205 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: A 335 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8712 (m) REVERT: A 380 MET cc_start: 0.8879 (tmm) cc_final: 0.8348 (tmm) REVERT: A 450 MET cc_start: 0.7170 (mpp) cc_final: 0.6865 (mtp) REVERT: A 627 SER cc_start: 0.8535 (t) cc_final: 0.8241 (t) REVERT: A 714 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7025 (tm-30) REVERT: B 9 LEU cc_start: 0.8124 (tp) cc_final: 0.7527 (tp) REVERT: B 20 GLU cc_start: 0.6340 (tm-30) cc_final: 0.5945 (tm-30) REVERT: B 223 LYS cc_start: 0.8246 (mmmt) cc_final: 0.8021 (mmmt) REVERT: B 268 LYS cc_start: 0.8024 (mptt) cc_final: 0.7567 (mmtm) REVERT: B 707 ASN cc_start: 0.7541 (t0) cc_final: 0.7137 (t0) REVERT: C 117 MET cc_start: 0.4656 (pmm) cc_final: 0.4163 (mtp) REVERT: C 143 TRP cc_start: 0.7164 (m-90) cc_final: 0.6742 (m100) REVERT: C 361 GLU cc_start: 0.6721 (tp30) cc_final: 0.6467 (tp30) REVERT: C 542 ARG cc_start: 0.7228 (tmm160) cc_final: 0.6777 (tmm-80) REVERT: C 545 MET cc_start: 0.4997 (pmm) cc_final: 0.4310 (ppp) REVERT: D 109 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8598 (tp) REVERT: D 259 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8772 (mm) REVERT: D 260 ASN cc_start: 0.8827 (m-40) cc_final: 0.8541 (m-40) REVERT: D 280 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7064 (ptm160) REVERT: D 312 ASN cc_start: 0.8386 (t0) cc_final: 0.7974 (t0) REVERT: D 371 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7391 (mtt-85) REVERT: D 441 MET cc_start: 0.6569 (pmm) cc_final: 0.5220 (pmm) REVERT: E 12 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6193 (pt0) REVERT: E 50 HIS cc_start: 0.5917 (OUTLIER) cc_final: 0.5638 (t-90) REVERT: E 244 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8429 (p) REVERT: E 250 ILE cc_start: 0.8108 (mt) cc_final: 0.7707 (tt) REVERT: E 303 VAL cc_start: 0.8978 (p) cc_final: 0.8503 (m) REVERT: E 317 HIS cc_start: 0.8704 (OUTLIER) cc_final: 0.8466 (m90) REVERT: E 336 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6830 (tp) REVERT: F 7 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: F 129 THR cc_start: 0.7517 (OUTLIER) cc_final: 0.7091 (t) REVERT: F 241 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8283 (mp) REVERT: H 70 LYS cc_start: 0.7528 (mmtm) cc_final: 0.6625 (tppp) REVERT: H 76 LYS cc_start: 0.8287 (ptmt) cc_final: 0.7921 (ptmt) REVERT: H 119 LYS cc_start: 0.7157 (mmmt) cc_final: 0.6822 (mmmt) REVERT: H 122 MET cc_start: 0.8516 (mtt) cc_final: 0.7916 (mtt) REVERT: H 135 LYS cc_start: 0.6333 (pttt) cc_final: 0.6053 (mmtm) REVERT: I 194 MET cc_start: 0.5012 (mmm) cc_final: 0.3328 (tmm) REVERT: I 209 HIS cc_start: -0.0178 (OUTLIER) cc_final: -0.0584 (t70) REVERT: I 542 TRP cc_start: 0.8682 (m100) cc_final: 0.8425 (m100) REVERT: I 615 MET cc_start: 0.6816 (ptt) cc_final: 0.6177 (ppp) REVERT: I 643 ASN cc_start: 0.9302 (t0) cc_final: 0.8606 (t0) REVERT: I 686 SER cc_start: 0.4643 (OUTLIER) cc_final: 0.3318 (m) REVERT: I 716 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7578 (ptpp) REVERT: I 741 TYR cc_start: 0.7493 (t80) cc_final: 0.7106 (t80) REVERT: I 840 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8572 (mtmm) REVERT: I 893 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7566 (pp30) outliers start: 152 outliers final: 118 residues processed: 441 average time/residue: 0.1927 time to fit residues: 139.3888 Evaluate side-chains 433 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 297 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 302 HIS Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 575 ASP Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 686 SER Chi-restraints excluded: chain I residue 710 PHE Chi-restraints excluded: chain I residue 716 LYS Chi-restraints excluded: chain I residue 751 VAL Chi-restraints excluded: chain I residue 767 MET Chi-restraints excluded: chain I residue 786 LEU Chi-restraints excluded: chain I residue 807 VAL Chi-restraints excluded: chain I residue 893 GLN Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 267 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 0.3980 chunk 258 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 354 optimal weight: 4.9990 chunk 316 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 255 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 GLN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN I 206 HIS I 780 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.120444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.093008 restraints weight = 88756.928| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.67 r_work: 0.3376 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31626 Z= 0.130 Angle : 0.618 24.765 43048 Z= 0.301 Chirality : 0.042 0.439 4797 Planarity : 0.004 0.046 5272 Dihedral : 15.611 172.713 4796 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.65 % Allowed : 25.47 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3596 helix: 1.25 (0.13), residues: 1715 sheet: -0.83 (0.27), residues: 381 loop : -1.26 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 56 TYR 0.024 0.001 TYR A 534 PHE 0.022 0.001 PHE B 448 TRP 0.024 0.001 TRP C 539 HIS 0.005 0.001 HIS J 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (31600) covalent geometry : angle 0.58604 / 0.30 (43009) hydrogen bonds : bond 0.03918 / 2.63 ( 1424) hydrogen bonds : angle 4.33065 / 3.07 ( 4021) metal coordination : bond 0.01077 / 0.65 ( 24) metal coordination : angle 6.58635 / 4.07 ( 39) Misc. bond : bond 0.00022 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 312 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 THR cc_start: 0.9122 (p) cc_final: 0.8826 (t) REVERT: A 205 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: A 335 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8687 (m) REVERT: A 380 MET cc_start: 0.8866 (tmm) cc_final: 0.8350 (tmm) REVERT: A 450 MET cc_start: 0.7170 (mpp) cc_final: 0.6913 (mtp) REVERT: A 627 SER cc_start: 0.8507 (t) cc_final: 0.8148 (t) REVERT: A 714 GLN cc_start: 0.7959 (tm-30) cc_final: 0.6978 (tm-30) REVERT: B 9 LEU cc_start: 0.8092 (tp) cc_final: 0.7392 (tp) REVERT: B 20 GLU cc_start: 0.6383 (tm-30) cc_final: 0.6030 (tm-30) REVERT: B 27 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: B 223 LYS cc_start: 0.8377 (mmmt) cc_final: 0.8032 (mmmt) REVERT: B 268 LYS cc_start: 0.8017 (mptt) cc_final: 0.7550 (mmtm) REVERT: B 363 GLN cc_start: 0.8336 (tm-30) cc_final: 0.8054 (tm-30) REVERT: B 707 ASN cc_start: 0.7506 (t0) cc_final: 0.7106 (t0) REVERT: C 117 MET cc_start: 0.4617 (pmm) cc_final: 0.4133 (mtp) REVERT: C 143 TRP cc_start: 0.7188 (m-90) cc_final: 0.6764 (m100) REVERT: C 361 GLU cc_start: 0.6834 (tp30) cc_final: 0.6593 (tp30) REVERT: C 529 LEU cc_start: 0.8358 (mm) cc_final: 0.8083 (tp) REVERT: C 542 ARG cc_start: 0.7096 (tmm160) cc_final: 0.6719 (tmm-80) REVERT: C 545 MET cc_start: 0.4984 (pmm) cc_final: 0.4317 (ppp) REVERT: D 109 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8566 (tp) REVERT: D 259 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8794 (mm) REVERT: D 260 ASN cc_start: 0.8824 (m-40) cc_final: 0.8531 (m-40) REVERT: D 280 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7101 (ptm160) REVERT: D 312 ASN cc_start: 0.8301 (t0) cc_final: 0.7913 (t0) REVERT: D 371 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7395 (mtt-85) REVERT: D 398 ARG cc_start: 0.7790 (mpt-90) cc_final: 0.7420 (mtt90) REVERT: D 441 MET cc_start: 0.6585 (pmm) cc_final: 0.5200 (pmm) REVERT: E 12 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6177 (pt0) REVERT: E 50 HIS cc_start: 0.5894 (OUTLIER) cc_final: 0.5617 (t-90) REVERT: E 303 VAL cc_start: 0.8962 (p) cc_final: 0.8512 (m) REVERT: E 317 HIS cc_start: 0.8651 (OUTLIER) cc_final: 0.8420 (m90) REVERT: E 336 LEU cc_start: 0.7196 (mt) cc_final: 0.6772 (tp) REVERT: F 7 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: F 129 THR cc_start: 0.7463 (OUTLIER) cc_final: 0.7038 (t) REVERT: F 241 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8276 (mp) REVERT: H 76 LYS cc_start: 0.8260 (ptmt) cc_final: 0.7688 (mmtt) REVERT: H 120 LYS cc_start: 0.8212 (mmtm) cc_final: 0.7976 (pttm) REVERT: H 122 MET cc_start: 0.8488 (mtt) cc_final: 0.8212 (mtt) REVERT: I 194 MET cc_start: 0.4945 (mmm) cc_final: 0.3342 (tmm) REVERT: I 209 HIS cc_start: 0.0340 (OUTLIER) cc_final: -0.0228 (t70) REVERT: I 542 TRP cc_start: 0.8693 (m100) cc_final: 0.8403 (m100) REVERT: I 615 MET cc_start: 0.6893 (ptt) cc_final: 0.6192 (ppp) REVERT: I 643 ASN cc_start: 0.9280 (t0) cc_final: 0.8553 (t0) REVERT: I 686 SER cc_start: 0.3990 (OUTLIER) cc_final: 0.2425 (m) REVERT: I 716 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7596 (ptpp) REVERT: I 741 TYR cc_start: 0.7442 (t80) cc_final: 0.7061 (t80) REVERT: I 893 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7541 (pp30) REVERT: J 294 GLN cc_start: 0.7103 (pt0) cc_final: 0.5826 (tp40) outliers start: 118 outliers final: 88 residues processed: 412 average time/residue: 0.1782 time to fit residues: 120.8103 Evaluate side-chains 410 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 305 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 302 HIS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 686 SER Chi-restraints excluded: chain I residue 710 PHE Chi-restraints excluded: chain I residue 716 LYS Chi-restraints excluded: chain I residue 751 VAL Chi-restraints excluded: chain I residue 786 LEU Chi-restraints excluded: chain I residue 807 VAL Chi-restraints excluded: chain I residue 893 GLN Chi-restraints excluded: chain J residue 302 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 311 optimal weight: 4.9990 chunk 309 optimal weight: 20.0000 chunk 340 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 337 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 GLN C 228 HIS C 236 ASN ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** I 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 780 HIS ** J 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.116900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.088388 restraints weight = 87842.923| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.16 r_work: 0.3313 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 31626 Z= 0.384 Angle : 0.828 33.458 43048 Z= 0.413 Chirality : 0.050 0.351 4797 Planarity : 0.006 0.055 5272 Dihedral : 15.868 173.066 4795 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.52 % Allowed : 25.01 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3596 helix: 0.63 (0.12), residues: 1719 sheet: -1.26 (0.26), residues: 379 loop : -1.58 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 272 TYR 0.026 0.003 TYR B 141 PHE 0.038 0.003 PHE B 448 TRP 0.037 0.003 TRP C 539 HIS 0.018 0.002 HIS I 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00889 / 0.38 (31600) covalent geometry : angle 0.79433 / 0.41 (43009) hydrogen bonds : bond 0.05983 / 3.95 ( 1424) hydrogen bonds : angle 4.94704 / 3.51 ( 4021) metal coordination : bond 0.02118 / 1.23 ( 24) metal coordination : angle 7.84959 / 4.87 ( 39) Misc. bond : bond 0.00032 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 304 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 SER cc_start: 0.9192 (OUTLIER) cc_final: 0.8927 (m) REVERT: A 205 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: A 380 MET cc_start: 0.8880 (tmm) cc_final: 0.8327 (tmm) REVERT: A 627 SER cc_start: 0.8590 (t) cc_final: 0.8318 (t) REVERT: A 692 LYS cc_start: 0.8872 (tttp) cc_final: 0.8369 (tttp) REVERT: A 714 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7007 (tm-30) REVERT: B 9 LEU cc_start: 0.8032 (tp) cc_final: 0.7499 (tp) REVERT: B 20 GLU cc_start: 0.6472 (tm-30) cc_final: 0.6049 (tm-30) REVERT: B 363 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7995 (tm-30) REVERT: B 707 ASN cc_start: 0.7567 (t0) cc_final: 0.7172 (t0) REVERT: B 748 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7861 (tm-30) REVERT: C 117 MET cc_start: 0.4508 (pmm) cc_final: 0.4012 (mtp) REVERT: C 143 TRP cc_start: 0.7243 (m-90) cc_final: 0.6812 (m100) REVERT: C 252 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7470 (ttmm) REVERT: C 361 GLU cc_start: 0.6803 (tp30) cc_final: 0.6534 (tp30) REVERT: C 545 MET cc_start: 0.4987 (pmm) cc_final: 0.4307 (ppp) REVERT: D 109 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8658 (tp) REVERT: D 259 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8796 (mm) REVERT: D 260 ASN cc_start: 0.8832 (m-40) cc_final: 0.8556 (m-40) REVERT: D 280 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7084 (ptm160) REVERT: D 371 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7255 (mtt-85) REVERT: D 441 MET cc_start: 0.6631 (pmm) cc_final: 0.5584 (pmm) REVERT: E 50 HIS cc_start: 0.5797 (OUTLIER) cc_final: 0.5558 (t-90) REVERT: E 317 HIS cc_start: 0.8743 (OUTLIER) cc_final: 0.8493 (m90) REVERT: E 336 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6836 (tp) REVERT: F 7 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7954 (pm20) REVERT: F 129 THR cc_start: 0.7602 (OUTLIER) cc_final: 0.7152 (t) REVERT: F 177 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: H 76 LYS cc_start: 0.8263 (ptmt) cc_final: 0.7713 (ptmt) REVERT: H 77 LYS cc_start: 0.8066 (pttm) cc_final: 0.7248 (mmtt) REVERT: I 194 MET cc_start: 0.5153 (mmm) cc_final: 0.3390 (tmm) REVERT: I 209 HIS cc_start: 0.0256 (OUTLIER) cc_final: -0.0266 (t70) REVERT: I 542 TRP cc_start: 0.8637 (m100) cc_final: 0.8351 (m100) REVERT: I 615 MET cc_start: 0.7226 (ptt) cc_final: 0.6560 (ppp) REVERT: I 643 ASN cc_start: 0.9278 (t0) cc_final: 0.8797 (t0) REVERT: I 686 SER cc_start: 0.5195 (OUTLIER) cc_final: 0.1831 (t) REVERT: I 716 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7607 (ptpp) REVERT: I 840 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8322 (pttp) REVERT: I 893 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7291 (tp40) outliers start: 146 outliers final: 112 residues processed: 424 average time/residue: 0.1868 time to fit residues: 130.0184 Evaluate side-chains 427 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 298 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 302 HIS Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 177 PHE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 686 SER Chi-restraints excluded: chain I residue 710 PHE Chi-restraints excluded: chain I residue 716 LYS Chi-restraints excluded: chain I residue 751 VAL Chi-restraints excluded: chain I residue 786 LEU Chi-restraints excluded: chain I residue 807 VAL Chi-restraints excluded: chain I residue 893 GLN Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 163 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 237 optimal weight: 0.9990 chunk 352 optimal weight: 8.9990 chunk 140 optimal weight: 0.3980 chunk 262 optimal weight: 3.9990 chunk 349 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 222 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 252 optimal weight: 9.9990 chunk 203 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 GLN ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 HIS I 780 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.120525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.092345 restraints weight = 88034.981| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.21 r_work: 0.3399 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31626 Z= 0.123 Angle : 0.651 26.802 43048 Z= 0.317 Chirality : 0.043 0.344 4797 Planarity : 0.004 0.046 5272 Dihedral : 15.691 174.897 4795 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.48 % Allowed : 27.08 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3596 helix: 1.13 (0.13), residues: 1714 sheet: -0.89 (0.27), residues: 366 loop : -1.33 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 272 TYR 0.023 0.001 TYR A 534 PHE 0.021 0.001 PHE F 50 TRP 0.031 0.001 TRP C 539 HIS 0.005 0.001 HIS J 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (31600) covalent geometry : angle 0.61747 / 0.32 (43009) hydrogen bonds : bond 0.03908 / 2.64 ( 1424) hydrogen bonds : angle 4.38723 / 3.11 ( 4021) metal coordination : bond 0.01079 / 0.65 ( 24) metal coordination : angle 6.90341 / 4.28 ( 39) Misc. bond : bond 0.00018 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7192 Ramachandran restraints generated. 3596 Oldfield, 0 Emsley, 3596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 308 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 THR cc_start: 0.9191 (p) cc_final: 0.8858 (t) REVERT: A 380 MET cc_start: 0.8877 (tmm) cc_final: 0.8381 (tmm) REVERT: A 589 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7736 (mtm180) REVERT: A 627 SER cc_start: 0.8472 (t) cc_final: 0.8115 (t) REVERT: A 714 GLN cc_start: 0.7911 (tm-30) cc_final: 0.6935 (tm-30) REVERT: B 9 LEU cc_start: 0.8064 (tp) cc_final: 0.7361 (tp) REVERT: B 247 MET cc_start: 0.8493 (mmm) cc_final: 0.8171 (mmm) REVERT: B 268 LYS cc_start: 0.7946 (mptt) cc_final: 0.7557 (mmtm) REVERT: B 363 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7953 (tm-30) REVERT: B 707 ASN cc_start: 0.7485 (t0) cc_final: 0.7092 (t0) REVERT: C 117 MET cc_start: 0.4646 (pmm) cc_final: 0.4202 (mtp) REVERT: C 143 TRP cc_start: 0.7253 (m-90) cc_final: 0.6897 (m100) REVERT: C 361 GLU cc_start: 0.6741 (tp30) cc_final: 0.6497 (tp30) REVERT: C 529 LEU cc_start: 0.8415 (mm) cc_final: 0.8145 (tp) REVERT: C 545 MET cc_start: 0.4987 (pmm) cc_final: 0.4309 (ppp) REVERT: D 109 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8608 (tp) REVERT: D 259 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8823 (mm) REVERT: D 260 ASN cc_start: 0.8781 (m-40) cc_final: 0.8479 (m-40) REVERT: D 312 ASN cc_start: 0.8347 (t0) cc_final: 0.7981 (t0) REVERT: D 371 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7428 (mtt-85) REVERT: D 441 MET cc_start: 0.7369 (pmm) cc_final: 0.5835 (pmm) REVERT: E 50 HIS cc_start: 0.5898 (OUTLIER) cc_final: 0.5658 (t-90) REVERT: E 77 LYS cc_start: 0.7430 (mmmt) cc_final: 0.7119 (mtpp) REVERT: E 211 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8115 (tp) REVERT: E 303 VAL cc_start: 0.9009 (p) cc_final: 0.8539 (m) REVERT: E 317 HIS cc_start: 0.8608 (OUTLIER) cc_final: 0.8381 (m90) REVERT: E 336 LEU cc_start: 0.7027 (mt) cc_final: 0.6612 (tp) REVERT: F 7 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: F 146 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8596 (ttp80) REVERT: H 70 LYS cc_start: 0.7503 (mmtm) cc_final: 0.7020 (mmmm) REVERT: H 76 LYS cc_start: 0.8352 (ptmt) cc_final: 0.7728 (mmtt) REVERT: H 77 LYS cc_start: 0.7993 (pttm) cc_final: 0.7401 (mmtt) REVERT: I 194 MET cc_start: 0.5010 (mmm) cc_final: 0.3309 (tmm) REVERT: I 209 HIS cc_start: 0.0319 (OUTLIER) cc_final: -0.0253 (t70) REVERT: I 615 MET cc_start: 0.7229 (ptt) cc_final: 0.6544 (ppp) REVERT: I 643 ASN cc_start: 0.9236 (t0) cc_final: 0.8724 (t0) REVERT: I 686 SER cc_start: 0.3802 (OUTLIER) cc_final: 0.2508 (m) REVERT: I 716 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7501 (pttm) REVERT: I 840 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8328 (pttp) outliers start: 80 outliers final: 61 residues processed: 374 average time/residue: 0.1868 time to fit residues: 113.9498 Evaluate side-chains 373 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 300 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 HIS Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 209 HIS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 686 SER Chi-restraints excluded: chain I residue 710 PHE Chi-restraints excluded: chain I residue 716 LYS Chi-restraints excluded: chain I residue 751 VAL Chi-restraints excluded: chain I residue 786 LEU Chi-restraints excluded: chain J residue 302 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 7.9990 chunk 317 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 362 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 chunk 319 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 122 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 268 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN I 206 HIS ** I 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 780 HIS ** J 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.119077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.090645 restraints weight = 88744.562| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.21 r_work: 0.3362 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 31626 Z= 0.200 Angle : 0.672 27.520 43048 Z= 0.330 Chirality : 0.044 0.336 4797 Planarity : 0.004 0.047 5272 Dihedral : 15.709 171.991 4795 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.48 % Allowed : 27.27 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3596 helix: 1.08 (0.13), residues: 1718 sheet: -1.03 (0.26), residues: 387 loop : -1.37 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 272 TYR 0.023 0.002 TYR A 534 PHE 0.029 0.002 PHE B 448 TRP 0.036 0.002 TRP C 539 HIS 0.007 0.001 HIS I 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (31600) covalent geometry : angle 0.63907 / 0.33 (43009) hydrogen bonds : bond 0.04489 / 2.99 ( 1424) hydrogen bonds : angle 4.49528 / 3.18 ( 4021) metal coordination : bond 0.01357 / 0.79 ( 24) metal coordination : angle 6.91939 / 4.28 ( 39) Misc. bond : bond 0.00020 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8239.18 seconds wall clock time: 141 minutes 40.51 seconds (8500.51 seconds total)