Starting phenix.real_space_refine on Sun Aug 9 01:22:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28jv_56566/08_2026/28jv_56566.cif Found real_map, /net/cci-nas-00/data/ceres_data/28jv_56566/08_2026/28jv_56566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28jv_56566/08_2026/28jv_56566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28jv_56566/08_2026/28jv_56566.map" model { file = "/net/cci-nas-00/data/ceres_data/28jv_56566/08_2026/28jv_56566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28jv_56566/08_2026/28jv_56566.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6074 SG CYS B 116 95.521 29.215 114.115 1.00100.03 S ATOM 6383 SG CYS B 155 94.138 22.481 115.614 1.00109.88 S ATOM 6214 SG CYS B 134 99.109 26.011 117.858 1.00 92.94 S ATOM 6672 SG CYS B 190 98.263 24.327 111.466 1.00 84.52 S ATOM 20331 SG CYS E 345 101.545 81.670 44.368 1.00 49.82 S ATOM 20353 SG CYS E 348 100.342 85.606 44.930 1.00 38.75 S ATOM 20510 SG CYS E 368 102.271 83.316 48.314 1.00 45.48 S ATOM 20531 SG CYS E 371 98.839 82.136 46.818 1.00 42.55 S ATOM 20451 SG CYS E 360 99.366 69.120 44.123 1.00 75.50 S ATOM 20469 SG CYS E 363 99.609 70.928 40.516 1.00 78.45 S ATOM 20618 SG CYS E 382 96.955 72.656 43.167 1.00 42.50 S ATOM 20635 SG CYS E 385 96.083 69.049 41.524 1.00 37.83 S ATOM 19895 SG CYS E 291 56.151 67.061 51.402 1.00 61.92 S ATOM 19917 SG CYS E 294 52.716 66.724 53.381 1.00 61.58 S ATOM 20006 SG CYS E 305 55.731 68.493 55.114 1.00 49.68 S ATOM 20029 SG CYS E 308 56.025 64.657 54.129 1.00 50.81 S ATOM 22523 SG CYS F 268 75.846 55.281 51.094 1.00 28.32 S ATOM 22542 SG CYS F 271 78.775 56.236 48.379 1.00 39.14 S ATOM 22627 SG CYS F 282 76.505 52.984 48.288 1.00 84.17 S ATOM 22647 SG CYS F 285 79.529 53.786 51.020 1.00 64.64 S ATOM 22415 SG CYS F 255 68.817 59.294 38.061 1.00 63.62 S ATOM 22432 SG CYS F 257 70.475 55.931 39.183 1.00 52.99 S ATOM 22581 SG CYS F 276 66.597 56.278 39.593 1.00 62.93 S Time building chain proxies: 6.13, per 1000 atoms: 0.20 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: 2.78 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " 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 382 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb=" ZN E 403 " 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 308 " 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 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " 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: 161 helices and 27 sheets defined 52.2% alpha, 8.7% beta 31 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.732A 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 162 removed outlier: 3.856A pdb=" N VAL A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.683A pdb=" N ARG A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 198' 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: 4.016A pdb=" N VAL A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.981A 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: 4.437A pdb=" N ARG A 425 " --> pdb=" O TRP A 421 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 492 through 498 Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.501A pdb=" N ALA A 524 " --> pdb=" O ARG A 520 " (cutoff:3.500A) removed outlier: 4.230A 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: 3.634A pdb=" N ARG A 554 " --> pdb=" O PHE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 632 through 642 Processing helix chain 'A' and resid 667 through 672 removed outlier: 4.143A 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 Processing helix chain 'B' and resid 48 through 63 removed outlier: 3.582A pdb=" N LEU B 52 " --> pdb=" O LYS B 48 " (cutoff:3.500A) 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: 3.897A pdb=" N GLU B 159 " --> pdb=" O CYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 3.607A pdb=" N LEU B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.628A pdb=" N LEU B 194 " --> pdb=" O CYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 214 through 219 removed outlier: 4.578A pdb=" N ASP B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.692A pdb=" N VAL B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 274 Processing helix chain 'B' and resid 278 through 291 Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.775A pdb=" N ARG B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 345 Processing helix chain 'B' and resid 353 through 365 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.908A pdb=" N LEU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 386 removed outlier: 3.853A pdb=" N LEU B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 408 removed outlier: 3.781A pdb=" N ASN B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 450 removed outlier: 3.972A pdb=" N ILE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Proline residue: B 446 - end of helix Processing helix chain 'B' and resid 465 through 472 removed outlier: 4.042A 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: 3.517A pdb=" N ILE B 517 " --> pdb=" O ASP B 513 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 556 removed outlier: 3.593A pdb=" N GLU B 546 " --> pdb=" O TYR B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.658A pdb=" N ASN B 560 " --> pdb=" O GLY B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 591 removed outlier: 3.788A pdb=" N SER B 578 " --> pdb=" O GLY B 574 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ALA B 580 " --> pdb=" O GLU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 608 removed outlier: 3.707A pdb=" N ILE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 3.666A pdb=" N TYR B 614 " --> pdb=" O VAL B 611 " (cutoff:3.500A) 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 691 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 Processing helix chain 'B' and resid 740 through 745 removed outlier: 3.561A 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 189 through 200 removed outlier: 3.717A pdb=" N SER C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 215 removed outlier: 3.583A pdb=" N LYS C 204 " --> pdb=" O TYR C 200 " (cutoff:3.500A) Proline residue: C 212 - end of helix removed outlier: 3.969A pdb=" N MET C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 226 Processing helix chain 'C' and resid 241 through 261 removed outlier: 4.284A pdb=" N GLU C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 3.990A 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: 3.673A pdb=" N ILE C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 413 " --> pdb=" O GLN C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 457 through 478 removed outlier: 3.979A pdb=" N CYS C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) 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: 3.616A pdb=" N GLU C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET C 545 " --> pdb=" O SER C 541 " (cutoff:3.500A) removed outlier: 3.581A 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: 3.837A 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: 4.024A pdb=" N GLN D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 4.823A 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: 3.737A pdb=" N PHE D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 222 removed outlier: 3.620A 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: 3.988A pdb=" N PHE D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 4.059A 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: 3.548A pdb=" N ILE D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 4.191A 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: 3.679A pdb=" N ILE D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 357 removed outlier: 3.558A pdb=" N GLN D 353 " --> pdb=" O GLU D 349 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER D 357 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 removed outlier: 3.742A 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 397 removed outlier: 3.642A pdb=" N THR D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 397 " --> pdb=" O LEU D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 429 removed outlier: 3.514A pdb=" N PHE D 418 " --> pdb=" O SER D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 462 removed outlier: 3.717A pdb=" N ASP D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS D 452 " --> pdb=" O HIS D 448 " (cutoff:3.500A) removed outlier: 3.911A 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 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 Processing helix chain 'E' and resid 181 through 193 removed outlier: 3.868A pdb=" N LEU E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 215 removed outlier: 3.898A pdb=" N THR E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 237 removed outlier: 3.503A pdb=" N HIS E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 319 removed outlier: 3.820A pdb=" N LEU E 318 " --> pdb=" O SER E 314 " (cutoff:3.500A) removed outlier: 3.716A 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 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 368 through 378 Processing helix chain 'E' and resid 382 through 387 removed outlier: 3.747A pdb=" N ILE E 386 " --> pdb=" O CYS E 382 " (cutoff:3.500A) removed outlier: 4.006A 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: 4.437A pdb=" N ASN F 52 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 121 removed outlier: 3.724A pdb=" N VAL F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE F 111 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 4.353A 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 222 through 230 removed outlier: 4.113A pdb=" N TYR F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 240 removed outlier: 3.840A pdb=" N GLN F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 27 removed outlier: 3.554A pdb=" N ASN G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) 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: 3.684A pdb=" N ASN H 112 " --> pdb=" O ASN H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 129 removed outlier: 3.783A pdb=" N ASN H 129 " --> pdb=" O TYR H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 140 removed outlier: 3.865A pdb=" N LYS H 135 " --> pdb=" O ASP H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 225 removed outlier: 4.314A pdb=" N ALA I 173 " --> pdb=" O THR I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 237 removed outlier: 3.534A 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 290 Processing helix chain 'I' and resid 294 through 307 Processing helix chain 'I' and resid 554 through 562 Processing helix chain 'I' and resid 581 through 586 removed outlier: 4.114A pdb=" N TYR I 585 " --> pdb=" O VAL I 581 " (cutoff:3.500A) Processing helix chain 'I' and resid 599 through 606 removed outlier: 3.806A pdb=" N TRP I 603 " --> pdb=" O ASP I 599 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR I 606 " --> pdb=" O TRP I 602 " (cutoff:3.500A) Processing helix chain 'I' and resid 614 through 631 removed outlier: 4.434A 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 651 through 653 No H-bonds generated for 'chain 'I' and resid 651 through 653' 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: 4.064A pdb=" N GLU I 726 " --> pdb=" O PRO I 722 " (cutoff:3.500A) removed outlier: 3.839A 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 787 removed outlier: 4.321A 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 914 removed outlier: 4.490A pdb=" N ARG I 908 " --> pdb=" O TRP I 904 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU I 909 " --> pdb=" O PRO I 905 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN I 914 " --> pdb=" O ASP I 910 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 281 removed outlier: 3.841A pdb=" N ARG J 280 " --> pdb=" O LEU J 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 295 removed outlier: 3.523A pdb=" N GLN J 286 " --> pdb=" O GLN J 282 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN J 295 " --> pdb=" O ILE J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 307 removed outlier: 3.777A pdb=" N GLN J 305 " --> pdb=" O ALA J 301 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 318 removed outlier: 3.561A pdb=" N LEU J 314 " --> pdb=" O ASN J 310 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER J 318 " --> pdb=" O LEU J 314 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 330 removed outlier: 3.626A pdb=" N PHE J 324 " --> pdb=" O HIS J 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 114 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 59 through 60 removed outlier: 6.335A pdb=" N VAL D 343 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87 removed outlier: 5.235A pdb=" N LYS A 117 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 171 removed outlier: 4.183A pdb=" N TYR A 175 " --> pdb=" O VAL A 272 " (cutoff:3.500A) 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: 3.500A pdb=" N ALA A 406 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 362 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASP A 441 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A 364 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY A 436 " --> pdb=" O CYS A 462 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU A 464 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N MET A 438 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU A 466 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU A 440 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL A 337 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU A 490 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 7.128A 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: 6.496A pdb=" N ILE A 558 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE A 607 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 623 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU A 662 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN A 625 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N SER A 664 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLN A 506 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N SER A 661 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA A 508 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL A 663 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL A 510 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 688 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 690 " --> pdb=" O GLU A 509 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 174 through 175 removed outlier: 6.476A pdb=" N GLY B 106 " --> pdb=" O TYR B 175 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY B 38 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N SER B 458 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU B 40 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 249 through 252 Processing sheet with id=AA9, first strand: chain 'B' and resid 491 through 494 removed outlier: 6.844A pdb=" N CYS B 491 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N PHE B 679 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N MET B 493 " --> pdb=" O PHE B 679 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL B 618 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 535 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N SER B 598 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA B 537 " --> pdb=" O SER B 598 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 186 through 188 removed outlier: 3.797A 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 249 through 250 removed outlier: 3.861A pdb=" N TYR D 281 " --> pdb=" O TYR D 249 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 431 through 433 Processing sheet with id=AB5, first strand: chain 'E' and resid 113 through 121 removed outlier: 3.715A pdb=" N LEU E 117 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLU E 119 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE E 104 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU E 61 " --> pdb=" O GLY E 105 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE E 107 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL E 63 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR E 109 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL E 65 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N HIS E 60 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU E 168 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR E 62 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE E 170 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL E 64 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL E 167 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE E 199 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE E 169 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS E 220 " --> pdb=" O VAL E 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 303 through 304 removed outlier: 4.298A pdb=" N THR E 311 " --> pdb=" O ARG E 251 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY F 265 " --> pdb=" O MET E 252 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 289 through 290 Processing sheet with id=AB8, first strand: chain 'E' and resid 332 through 334 Processing sheet with id=AB9, first strand: chain 'F' and resid 67 through 71 removed outlier: 6.634A pdb=" N VAL F 59 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN F 9 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA F 58 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU F 11 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE F 60 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE F 13 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER F 62 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL F 15 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP F 16 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU F 190 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU F 215 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA F 193 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 266 through 267 removed outlier: 6.028A pdb=" N THR I 266 " --> pdb=" O ALA I 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 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 649 removed outlier: 3.728A pdb=" N TYR I 676 " --> pdb=" O ALA I 648 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL I 675 " --> pdb=" O LEU I 667 " (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: 3.653A 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: 3.684A 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: 6.503A 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 Processing sheet with id=AC9, first strand: chain 'I' and resid 797 through 798 1328 hydrogen bonds defined for protein. 3825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 6.79 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 13302 1.43 - 1.64: 18040 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 7.39e+01 bond pdb=" C26 VM6 L 24 " pdb=" N2 VM6 L 24 " ideal model delta sigma weight residual 1.381 1.540 -0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" C10 VM6 L 24 " pdb=" C20 VM6 L 24 " ideal model delta sigma weight residual 1.534 1.394 0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" C7 VM6 L 24 " pdb=" C8 VM6 L 24 " ideal model delta sigma weight residual 1.502 1.396 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C8 VM6 L 24 " pdb=" C9 VM6 L 24 " ideal model delta sigma weight residual 1.504 1.400 0.104 2.00e-02 2.50e+03 2.73e+01 ... (remaining 31595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 42620 2.96 - 5.91: 327 5.91 - 8.87: 45 8.87 - 11.82: 13 11.82 - 14.78: 4 Bond angle restraints: 43009 Sorted by residual: angle pdb=" CA MET H 122 " pdb=" CB MET H 122 " pdb=" CG MET H 122 " ideal model delta sigma weight residual 114.10 128.88 -14.78 2.00e+00 2.50e-01 5.46e+01 angle pdb=" C HIS D 302 " pdb=" CA HIS D 302 " pdb=" CB HIS D 302 " ideal model delta sigma weight residual 116.54 110.29 6.25 1.15e+00 7.56e-01 2.95e+01 angle pdb=" CA MET K 145 " pdb=" CB MET K 145 " pdb=" CG MET K 145 " ideal model delta sigma weight residual 114.10 104.75 9.35 2.00e+00 2.50e-01 2.18e+01 angle pdb=" O4' DA M 20 " pdb=" C4' DA M 20 " pdb=" C3' DA M 20 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.17e+01 angle pdb=" O4' DA L 28 " pdb=" C4' DA L 28 " pdb=" C3' DA L 28 " ideal model delta sigma weight residual 106.00 103.32 2.68 6.00e-01 2.78e+00 2.00e+01 ... (remaining 43004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 18049 35.37 - 70.75: 912 70.75 - 106.12: 58 106.12 - 141.50: 9 141.50 - 176.87: 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 -153.88 -26.12 0 5.00e+00 4.00e-02 2.73e+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 34.27 146.82 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 246.92 115.90 131.02 1 3.00e+01 1.11e-03 1.77e+01 ... (remaining 19030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4084 0.063 - 0.127: 650 0.127 - 0.190: 56 0.190 - 0.254: 5 0.254 - 0.317: 2 Chirality restraints: 4797 Sorted by residual: chirality pdb=" CG LEU B 461 " pdb=" CB LEU B 461 " pdb=" CD1 LEU B 461 " pdb=" CD2 LEU B 461 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA ASP K 114 " pdb=" N ASP K 114 " pdb=" C ASP K 114 " pdb=" CB ASP K 114 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB VAL H 106 " pdb=" CA VAL H 106 " pdb=" CG1 VAL H 106 " pdb=" CG2 VAL H 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 4794 not shown) Planarity restraints: 5272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP K 114 " -0.037 2.00e-02 2.50e+03 7.50e-02 5.62e+01 pdb=" CG ASP K 114 " 0.130 2.00e-02 2.50e+03 pdb=" OD1 ASP K 114 " -0.046 2.00e-02 2.50e+03 pdb=" OD2 ASP K 114 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 77 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C LYS H 77 " 0.063 2.00e-02 2.50e+03 pdb=" O LYS H 77 " -0.023 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=" CB TYR H 95 " 0.019 2.00e-02 2.50e+03 1.68e-02 5.64e+00 pdb=" CG TYR H 95 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR H 95 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR H 95 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR H 95 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 95 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR H 95 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 95 " -0.001 2.00e-02 2.50e+03 ... (remaining 5269 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 8202 2.81 - 3.33: 30760 3.33 - 3.85: 51219 3.85 - 4.38: 57446 4.38 - 4.90: 94915 Nonbonded interactions: 242542 Sorted by model distance: nonbonded pdb=" OD1 ASN K 125 " pdb="CA CA K1002 " model vdw 2.287 2.510 nonbonded pdb=" OD1 ASP K 150 " pdb="CA CA K1001 " model vdw 2.303 2.510 nonbonded pdb=" OD1 ASP K 152 " pdb="CA CA K1001 " model vdw 2.387 2.510 nonbonded pdb=" OD1 ASP K 154 " pdb="CA CA K1001 " model vdw 2.400 2.510 nonbonded pdb=" O LYS K 120 " pdb="CA CA K1002 " model vdw 2.405 2.510 ... (remaining 242537 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 37.890 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 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 : 0.007 0.561 31626 Z= 0.319 Angle : 0.772 15.382 43048 Z= 0.433 Chirality : 0.046 0.317 4797 Planarity : 0.005 0.075 5272 Dihedral : 19.456 176.869 12095 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.98 % Allowed : 24.73 % Favored : 73.29 % 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: -0.58 (0.14), residues: 3596 helix: 0.55 (0.13), residues: 1723 sheet: -0.93 (0.26), residues: 384 loop : -1.30 (0.16), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 125 TYR 0.042 0.002 TYR H 95 PHE 0.032 0.002 PHE K 113 TRP 0.014 0.001 TRP B 552 HIS 0.010 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.27 (31600) covalent geometry : angle 0.74570 / 0.43 (43009) hydrogen bonds : bond 0.14038 / 9.43 ( 1405) hydrogen bonds : angle 5.76075 / 4.00 ( 3979) metal coordination : bond 0.18152 / 13.17 ( 24) metal coordination : angle 6.68264 / 4.11 ( 39) Misc. bond : bond 0.04349 / 2.19 ( 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 299 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 235 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 TRP cc_start: 0.8020 (m100) cc_final: 0.7716 (m100) REVERT: A 380 MET cc_start: 0.8463 (tmm) cc_final: 0.7983 (tmm) REVERT: A 623 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9106 (tt) REVERT: A 693 LEU cc_start: 0.7262 (mp) cc_final: 0.6994 (mm) REVERT: B 101 LYS cc_start: 0.8775 (mttp) cc_final: 0.8261 (tptp) REVERT: B 637 LEU cc_start: 0.7760 (mt) cc_final: 0.7059 (pp) REVERT: B 748 GLU cc_start: 0.8142 (tp30) cc_final: 0.7534 (tm-30) REVERT: C 351 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7219 (mtt90) REVERT: C 354 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7360 (tt) REVERT: C 380 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7148 (p0) REVERT: C 384 HIS cc_start: 0.6479 (p-80) cc_final: 0.5734 (p90) REVERT: C 478 CYS cc_start: 0.8224 (m) cc_final: 0.7713 (t) REVERT: E 153 MET cc_start: 0.6980 (tpt) cc_final: 0.6748 (tpt) REVERT: E 256 GLN cc_start: 0.6967 (tp-100) cc_final: 0.6526 (pm20) REVERT: G 32 LYS cc_start: 0.4454 (OUTLIER) cc_final: 0.4054 (pptt) REVERT: G 40 ASP cc_start: 0.7335 (m-30) cc_final: 0.6768 (t70) REVERT: I 706 MET cc_start: 0.5069 (mmm) cc_final: 0.3827 (tpt) REVERT: I 766 MET cc_start: 0.3407 (ppp) cc_final: 0.2515 (ppp) REVERT: I 855 LEU cc_start: 0.6876 (mt) cc_final: 0.6664 (mt) outliers start: 64 outliers final: 54 residues processed: 287 average time/residue: 0.1845 time to fit residues: 89.5786 Evaluate side-chains 278 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 220 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 696 VAL Chi-restraints excluded: chain I residue 702 VAL Chi-restraints excluded: chain I residue 724 LEU Chi-restraints excluded: chain I residue 819 ASP Chi-restraints excluded: chain K residue 113 PHE Chi-restraints excluded: chain K residue 137 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 187 HIS A 286 HIS A 433 GLN A 539 ASN ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN A 586 GLN A 594 GLN A 665 GLN A 710 GLN B 92 ASN B 97 GLN B 176 ASN B 187 GLN B 203 ASN B 210 HIS B 241 ASN B 260 GLN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN B 543 GLN B 612 HIS ** B 662 GLN ** 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 455 ASN C 496 ASN C 534 ASN D 410 ASN D 424 HIS E 60 HIS E 220 HIS E 275 HIS ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN F 176 ASN F 205 GLN F 240 GLN ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 554 GLN I 644 HIS I 737 GLN ** I 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 758 ASN ** I 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 906 GLN I 907 ASN J 294 GLN J 316 GLN J 329 ASN K 143 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.132004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.112715 restraints weight = 103696.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.109539 restraints weight = 144554.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.107691 restraints weight = 105665.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.107695 restraints weight = 98211.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.107767 restraints weight = 84378.578| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 31626 Z= 0.267 Angle : 0.748 24.171 43048 Z= 0.371 Chirality : 0.046 0.285 4797 Planarity : 0.005 0.063 5272 Dihedral : 16.011 174.889 4869 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.33 % Allowed : 24.14 % Favored : 71.53 % 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: -0.79 (0.14), residues: 3596 helix: 0.52 (0.13), residues: 1730 sheet: -1.29 (0.26), residues: 371 loop : -1.52 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 75 TYR 0.026 0.002 TYR B 584 PHE 0.033 0.002 PHE F 50 TRP 0.038 0.002 TRP I 848 HIS 0.008 0.001 HIS F 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.27 (31600) covalent geometry : angle 0.70696 / 0.37 (43009) hydrogen bonds : bond 0.05271 / 3.52 ( 1405) hydrogen bonds : angle 5.06851 / 3.52 ( 3979) metal coordination : bond 0.01210 / 0.79 ( 24) metal coordination : angle 8.09889 / 5.24 ( 39) Misc. bond : bond 0.00078 / 0.04 ( 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 363 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 223 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.2243 (OUTLIER) cc_final: 0.1275 (mm-30) REVERT: A 380 MET cc_start: 0.8495 (tmm) cc_final: 0.7984 (tmm) REVERT: A 437 LEU cc_start: 0.4978 (OUTLIER) cc_final: 0.4652 (tp) REVERT: A 589 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7021 (mtm180) REVERT: A 623 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9156 (tt) REVERT: B 12 PHE cc_start: 0.6257 (OUTLIER) cc_final: 0.5674 (t80) REVERT: B 101 LYS cc_start: 0.8756 (mttp) cc_final: 0.8416 (tptp) REVERT: B 114 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7314 (m-40) REVERT: B 637 LEU cc_start: 0.7794 (mt) cc_final: 0.7192 (pp) REVERT: B 669 ARG cc_start: 0.5840 (OUTLIER) cc_final: 0.4877 (ttm-80) REVERT: B 699 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.5966 (pp20) REVERT: B 724 MET cc_start: 0.9208 (tpp) cc_final: 0.8921 (tpp) REVERT: B 748 GLU cc_start: 0.8083 (tp30) cc_final: 0.7333 (tm-30) REVERT: C 351 ARG cc_start: 0.8104 (mtt180) cc_final: 0.6674 (ptp90) REVERT: D 435 ASN cc_start: 0.6596 (t0) cc_final: 0.6294 (t0) REVERT: E 85 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8766 (mm) REVERT: E 256 GLN cc_start: 0.7113 (tp-100) cc_final: 0.6585 (pm20) REVERT: G 40 ASP cc_start: 0.7337 (m-30) cc_final: 0.6528 (t70) REVERT: I 706 MET cc_start: 0.5047 (mmm) cc_final: 0.4037 (tpp) REVERT: I 766 MET cc_start: 0.3431 (OUTLIER) cc_final: 0.2671 (ppp) outliers start: 140 outliers final: 81 residues processed: 337 average time/residue: 0.1811 time to fit residues: 103.0438 Evaluate side-chains 306 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 215 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 669 ARG Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 257 MET Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 702 VAL Chi-restraints excluded: chain I residue 766 MET Chi-restraints excluded: chain I residue 807 VAL Chi-restraints excluded: chain I residue 819 ASP Chi-restraints excluded: chain J residue 288 MET Chi-restraints excluded: chain K residue 113 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 242 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 321 optimal weight: 0.9990 chunk 290 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 333 optimal weight: 0.0770 chunk 296 optimal weight: 0.9980 chunk 310 optimal weight: 50.0000 chunk 170 optimal weight: 3.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 GLN B 267 GLN ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** 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 496 ASN E 275 HIS ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 800 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 = 0.4273 r_free = 0.4273 target = 0.134371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.110868 restraints weight = 104176.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.107941 restraints weight = 94562.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.108355 restraints weight = 97184.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.108675 restraints weight = 81621.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.108765 restraints weight = 73062.791| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31626 Z= 0.128 Angle : 0.639 22.409 43048 Z= 0.308 Chirality : 0.042 0.291 4797 Planarity : 0.004 0.059 5272 Dihedral : 15.762 174.203 4824 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.25 % Allowed : 25.41 % Favored : 71.34 % 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: -0.49 (0.14), residues: 3596 helix: 0.74 (0.13), residues: 1737 sheet: -1.08 (0.26), residues: 370 loop : -1.37 (0.16), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 112 TYR 0.025 0.001 TYR A 534 PHE 0.027 0.001 PHE F 50 TRP 0.032 0.001 TRP D 156 HIS 0.008 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (31600) covalent geometry : angle 0.59607 / 0.31 (43009) hydrogen bonds : bond 0.04196 / 2.83 ( 1405) hydrogen bonds : angle 4.60301 / 3.20 ( 3979) metal coordination : bond 0.00845 / 0.55 ( 24) metal coordination : angle 7.64771 / 4.84 ( 39) Misc. bond : bond 0.00213 / 0.10 ( 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 339 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 234 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7774 (tp) REVERT: A 380 MET cc_start: 0.8541 (tmm) cc_final: 0.8075 (tmm) REVERT: A 589 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.6844 (mtm180) REVERT: B 12 PHE cc_start: 0.5700 (OUTLIER) cc_final: 0.5322 (t80) REVERT: B 101 LYS cc_start: 0.8842 (mttp) cc_final: 0.8469 (tptp) REVERT: B 637 LEU cc_start: 0.7783 (mt) cc_final: 0.7193 (pp) REVERT: B 699 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.5945 (pp20) REVERT: B 748 GLU cc_start: 0.8288 (tp30) cc_final: 0.7576 (tm-30) REVERT: C 351 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7363 (mtt90) REVERT: D 435 ASN cc_start: 0.6433 (t0) cc_final: 0.6051 (t0) REVERT: E 256 GLN cc_start: 0.7018 (tp-100) cc_final: 0.6603 (pm20) REVERT: G 40 ASP cc_start: 0.7356 (m-30) cc_final: 0.6692 (t70) REVERT: I 706 MET cc_start: 0.5407 (mmm) cc_final: 0.4244 (tpp) REVERT: I 908 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8089 (mtm-85) REVERT: J 314 LEU cc_start: 0.2294 (OUTLIER) cc_final: 0.1506 (mp) outliers start: 105 outliers final: 59 residues processed: 321 average time/residue: 0.1866 time to fit residues: 100.1218 Evaluate side-chains 281 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 216 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 177 PHE Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 PHE Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 696 VAL Chi-restraints excluded: chain I residue 702 VAL Chi-restraints excluded: chain I residue 807 VAL Chi-restraints excluded: chain I residue 819 ASP Chi-restraints excluded: chain I residue 908 ARG Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain K residue 113 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 123 optimal weight: 0.0470 chunk 66 optimal weight: 8.9990 chunk 276 optimal weight: 0.8980 chunk 263 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 chunk 176 optimal weight: 8.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 549 HIS ** I 742 GLN ** 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 = 0.4276 r_free = 0.4276 target = 0.134549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.111104 restraints weight = 103888.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.107876 restraints weight = 96131.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.108378 restraints weight = 96042.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.108581 restraints weight = 83032.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.108729 restraints weight = 74425.098| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31626 Z= 0.122 Angle : 0.626 23.219 43048 Z= 0.299 Chirality : 0.042 0.444 4797 Planarity : 0.004 0.044 5272 Dihedral : 15.712 174.420 4806 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.65 % Allowed : 25.41 % Favored : 70.94 % 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: -0.35 (0.14), residues: 3596 helix: 0.85 (0.13), residues: 1736 sheet: -0.98 (0.26), residues: 370 loop : -1.30 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 348 TYR 0.024 0.001 TYR A 534 PHE 0.023 0.001 PHE F 50 TRP 0.021 0.001 TRP D 156 HIS 0.019 0.001 HIS E 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (31600) covalent geometry : angle 0.58448 / 0.30 (43009) hydrogen bonds : bond 0.03877 / 2.60 ( 1405) hydrogen bonds : angle 4.42843 / 3.09 ( 3979) metal coordination : bond 0.00755 / 0.49 ( 24) metal coordination : angle 7.48218 / 4.78 ( 39) Misc. bond : bond 0.00031 / 0.02 ( 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 346 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 228 time to evaluate : 1.207 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 189 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7630 (tp) REVERT: A 203 GLU cc_start: 0.2592 (OUTLIER) cc_final: 0.1481 (mm-30) REVERT: A 276 MET cc_start: 0.6776 (mpp) cc_final: 0.6487 (mpp) REVERT: B 12 PHE cc_start: 0.5920 (OUTLIER) cc_final: 0.5513 (t80) REVERT: B 101 LYS cc_start: 0.8831 (mttp) cc_final: 0.8486 (tptp) REVERT: B 114 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7259 (m-40) REVERT: B 545 MET cc_start: 0.7466 (mpp) cc_final: 0.7231 (mpp) REVERT: B 637 LEU cc_start: 0.7813 (mt) cc_final: 0.7262 (pp) REVERT: B 699 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6101 (pp20) REVERT: B 724 MET cc_start: 0.9121 (tpp) cc_final: 0.8857 (tpp) REVERT: B 748 GLU cc_start: 0.8286 (tp30) cc_final: 0.7575 (tm-30) REVERT: C 121 ASP cc_start: 0.7887 (m-30) cc_final: 0.7353 (m-30) REVERT: C 351 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7304 (mtt90) REVERT: D 435 ASN cc_start: 0.6611 (t0) cc_final: 0.6195 (t0) REVERT: E 85 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8729 (mm) REVERT: E 136 ASP cc_start: 0.7614 (p0) cc_final: 0.6983 (p0) REVERT: E 256 GLN cc_start: 0.7060 (tp-100) cc_final: 0.6651 (pm20) REVERT: G 40 ASP cc_start: 0.7367 (m-30) cc_final: 0.6698 (t70) REVERT: I 274 SER cc_start: 0.1755 (OUTLIER) cc_final: 0.1345 (p) REVERT: I 706 MET cc_start: 0.5433 (mmm) cc_final: 0.4220 (tpp) REVERT: I 766 MET cc_start: 0.3492 (ppp) cc_final: 0.3077 (ppp) REVERT: J 314 LEU cc_start: 0.2409 (OUTLIER) cc_final: 0.1752 (mp) outliers start: 118 outliers final: 71 residues processed: 327 average time/residue: 0.1832 time to fit residues: 100.2629 Evaluate side-chains 297 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 218 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 14 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 175 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 PHE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 696 VAL Chi-restraints excluded: chain I residue 702 VAL Chi-restraints excluded: chain I residue 819 ASP Chi-restraints excluded: chain I residue 900 LEU Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain K residue 113 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 249 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 321 optimal weight: 0.0980 chunk 348 optimal weight: 0.6980 chunk 296 optimal weight: 0.9980 chunk 142 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 326 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.134892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.114155 restraints weight = 103686.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.111650 restraints weight = 133710.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.112641 restraints weight = 120453.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.113417 restraints weight = 79448.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.113623 restraints weight = 74307.732| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31626 Z= 0.115 Angle : 0.612 23.027 43048 Z= 0.292 Chirality : 0.042 0.303 4797 Planarity : 0.004 0.043 5272 Dihedral : 15.657 174.633 4804 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.13 % Allowed : 25.81 % Favored : 71.06 % 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: -0.25 (0.14), residues: 3596 helix: 0.93 (0.13), residues: 1738 sheet: -0.88 (0.26), residues: 370 loop : -1.27 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 348 TYR 0.023 0.001 TYR A 534 PHE 0.023 0.001 PHE G 33 TRP 0.014 0.001 TRP D 156 HIS 0.011 0.001 HIS I 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (31600) covalent geometry : angle 0.57056 / 0.29 (43009) hydrogen bonds : bond 0.03688 / 2.47 ( 1405) hydrogen bonds : angle 4.30733 / 3.01 ( 3979) metal coordination : bond 0.00732 / 0.48 ( 24) metal coordination : angle 7.35740 / 4.69 ( 39) Misc. bond : bond 0.00016 / 0.01 ( 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 336 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 235 time to evaluate : 1.193 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 189 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7363 (tp) REVERT: A 276 MET cc_start: 0.6667 (mpp) cc_final: 0.6297 (mpp) REVERT: A 380 MET cc_start: 0.8433 (tmm) cc_final: 0.8163 (tmm) REVERT: B 12 PHE cc_start: 0.6072 (OUTLIER) cc_final: 0.5577 (t80) REVERT: B 101 LYS cc_start: 0.8711 (mttp) cc_final: 0.8458 (tptp) REVERT: B 748 GLU cc_start: 0.8125 (tp30) cc_final: 0.7454 (tm-30) REVERT: C 121 ASP cc_start: 0.7686 (m-30) cc_final: 0.7176 (m-30) REVERT: C 351 ARG cc_start: 0.7790 (mtt180) cc_final: 0.6393 (ptp90) REVERT: C 434 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7670 (tp) REVERT: D 435 ASN cc_start: 0.6374 (t0) cc_final: 0.5980 (t0) REVERT: E 85 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8757 (mm) REVERT: E 256 GLN cc_start: 0.6951 (tp-100) cc_final: 0.6698 (pm20) REVERT: E 268 LYS cc_start: 0.7644 (pttp) cc_final: 0.7351 (pttp) REVERT: G 33 PHE cc_start: 0.6566 (m-10) cc_final: 0.6323 (m-10) REVERT: G 40 ASP cc_start: 0.7010 (m-30) cc_final: 0.6399 (t70) REVERT: I 274 SER cc_start: 0.1647 (OUTLIER) cc_final: 0.1211 (p) REVERT: I 706 MET cc_start: 0.4941 (mmm) cc_final: 0.3998 (tpp) REVERT: I 766 MET cc_start: 0.3758 (ppp) cc_final: 0.3132 (ppp) REVERT: J 314 LEU cc_start: 0.2313 (OUTLIER) cc_final: 0.1438 (mp) outliers start: 101 outliers final: 68 residues processed: 322 average time/residue: 0.1754 time to fit residues: 95.5555 Evaluate side-chains 295 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 221 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 696 VAL Chi-restraints excluded: chain I residue 819 ASP Chi-restraints excluded: chain I residue 848 TRP Chi-restraints excluded: chain I residue 900 LEU Chi-restraints excluded: chain J residue 314 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 38 optimal weight: 0.5980 chunk 202 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 179 optimal weight: 0.0060 chunk 222 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 overall best weight: 3.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.132886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.109555 restraints weight = 103312.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.106295 restraints weight = 96072.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.106718 restraints weight = 99936.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.106920 restraints weight = 84015.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.107130 restraints weight = 74816.032| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31626 Z= 0.189 Angle : 0.677 26.187 43048 Z= 0.323 Chirality : 0.044 0.408 4797 Planarity : 0.004 0.043 5272 Dihedral : 15.707 175.853 4794 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.46 % Allowed : 25.26 % Favored : 70.29 % 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: -0.48 (0.14), residues: 3596 helix: 0.80 (0.13), residues: 1743 sheet: -1.12 (0.26), residues: 377 loop : -1.44 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 348 TYR 0.020 0.002 TYR B 584 PHE 0.030 0.002 PHE F 50 TRP 0.011 0.001 TRP D 55 HIS 0.008 0.001 HIS E 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (31600) covalent geometry : angle 0.63335 / 0.32 (43009) hydrogen bonds : bond 0.04136 / 2.75 ( 1405) hydrogen bonds : angle 4.46038 / 3.11 ( 3979) metal coordination : bond 0.00891 / 0.55 ( 24) metal coordination : angle 7.92832 / 5.18 ( 39) Misc. bond : bond 0.00018 / 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 375 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 231 time to evaluate : 1.007 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 189 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7368 (tp) REVERT: A 203 GLU cc_start: 0.2568 (OUTLIER) cc_final: 0.1526 (mm-30) REVERT: A 276 MET cc_start: 0.6996 (mpp) cc_final: 0.6496 (mpp) REVERT: A 380 MET cc_start: 0.8546 (tmm) cc_final: 0.8198 (tmm) REVERT: A 623 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9113 (tt) REVERT: B 12 PHE cc_start: 0.5956 (OUTLIER) cc_final: 0.5670 (t80) REVERT: B 25 MET cc_start: 0.5905 (mtp) cc_final: 0.5686 (mtt) REVERT: B 101 LYS cc_start: 0.8768 (mttp) cc_final: 0.8455 (tptp) REVERT: B 114 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7344 (m-40) REVERT: B 438 MET cc_start: 0.5240 (mmt) cc_final: 0.4864 (mmm) REVERT: B 616 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.6682 (tpp-160) REVERT: B 637 LEU cc_start: 0.7785 (mt) cc_final: 0.7114 (pp) REVERT: B 748 GLU cc_start: 0.8284 (tp30) cc_final: 0.7565 (tm-30) REVERT: C 121 ASP cc_start: 0.7884 (m-30) cc_final: 0.7315 (m-30) REVERT: C 351 ARG cc_start: 0.7927 (mtt180) cc_final: 0.6575 (ptp90) REVERT: C 354 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7341 (tt) REVERT: C 380 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7089 (p0) REVERT: D 286 LEU cc_start: 0.8699 (mt) cc_final: 0.8259 (tt) REVERT: D 435 ASN cc_start: 0.6408 (t0) cc_final: 0.5956 (t0) REVERT: D 441 MET cc_start: 0.4325 (pmm) cc_final: 0.4086 (pmm) REVERT: E 17 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7038 (mmt-90) REVERT: E 85 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8802 (mm) REVERT: E 136 ASP cc_start: 0.7741 (p0) cc_final: 0.7173 (p0) REVERT: E 256 GLN cc_start: 0.7064 (tp-100) cc_final: 0.6619 (pm20) REVERT: E 268 LYS cc_start: 0.7631 (pttp) cc_final: 0.7283 (pttp) REVERT: G 24 ASP cc_start: 0.4927 (t0) cc_final: 0.3985 (t0) REVERT: G 32 LYS cc_start: 0.4473 (OUTLIER) cc_final: 0.3941 (pptt) REVERT: G 40 ASP cc_start: 0.7394 (m-30) cc_final: 0.6684 (t70) REVERT: I 274 SER cc_start: 0.1956 (OUTLIER) cc_final: 0.1477 (p) REVERT: I 537 GLU cc_start: 0.5644 (mt-10) cc_final: 0.4255 (tp30) REVERT: I 706 MET cc_start: 0.5452 (mmm) cc_final: 0.4201 (tpp) REVERT: J 278 PHE cc_start: 0.4239 (OUTLIER) cc_final: 0.3932 (m-10) REVERT: J 314 LEU cc_start: 0.2213 (OUTLIER) cc_final: 0.1401 (mp) REVERT: K 139 ASP cc_start: 0.8733 (p0) cc_final: 0.8416 (p0) REVERT: K 140 GLU cc_start: 0.8060 (pt0) cc_final: 0.7784 (mp0) outliers start: 144 outliers final: 92 residues processed: 353 average time/residue: 0.1800 time to fit residues: 106.5040 Evaluate side-chains 332 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 226 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 616 ARG Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 PHE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 643 ASN Chi-restraints excluded: chain I residue 696 VAL Chi-restraints excluded: chain I residue 702 VAL Chi-restraints excluded: chain I residue 819 ASP Chi-restraints excluded: chain I residue 848 TRP Chi-restraints excluded: chain I residue 900 LEU Chi-restraints excluded: chain I residue 937 PHE Chi-restraints excluded: chain J residue 278 PHE Chi-restraints excluded: chain J residue 314 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: 30.0000 chunk 204 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 327 optimal weight: 20.0000 chunk 202 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 239 optimal weight: 4.9990 chunk 262 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.134319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.115250 restraints weight = 103730.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.110917 restraints weight = 146521.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.109577 restraints weight = 114091.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.109805 restraints weight = 90362.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.109857 restraints weight = 80081.515| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31626 Z= 0.119 Angle : 0.635 25.264 43048 Z= 0.300 Chirality : 0.042 0.303 4797 Planarity : 0.004 0.044 5272 Dihedral : 15.633 174.668 4792 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.74 % Allowed : 26.12 % Favored : 70.13 % 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: -0.35 (0.14), residues: 3596 helix: 0.87 (0.13), residues: 1739 sheet: -0.97 (0.27), residues: 366 loop : -1.33 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 348 TYR 0.024 0.001 TYR A 534 PHE 0.037 0.001 PHE I 197 TRP 0.011 0.001 TRP D 156 HIS 0.011 0.001 HIS E 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (31600) covalent geometry : angle 0.58883 / 0.30 (43009) hydrogen bonds : bond 0.03702 / 2.48 ( 1405) hydrogen bonds : angle 4.29756 / 3.00 ( 3979) metal coordination : bond 0.00812 / 0.51 ( 24) metal coordination : angle 7.89261 / 5.09 ( 39) Misc. bond : bond 0.00011 / 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 355 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 234 time to evaluate : 1.141 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 189 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7215 (tp) REVERT: A 203 GLU cc_start: 0.2185 (OUTLIER) cc_final: 0.1269 (mm-30) REVERT: A 276 MET cc_start: 0.6677 (mpp) cc_final: 0.6195 (mpp) REVERT: A 380 MET cc_start: 0.8556 (tmm) cc_final: 0.8195 (tmm) REVERT: A 590 MET cc_start: 0.7198 (mpp) cc_final: 0.6893 (mpp) REVERT: A 623 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9153 (tt) REVERT: B 12 PHE cc_start: 0.6031 (OUTLIER) cc_final: 0.5796 (t80) REVERT: B 25 MET cc_start: 0.5824 (mtp) cc_final: 0.5594 (mtt) REVERT: B 101 LYS cc_start: 0.8648 (mttp) cc_final: 0.8398 (tptp) REVERT: B 114 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7302 (m-40) REVERT: B 438 MET cc_start: 0.5164 (mmt) cc_final: 0.4903 (mmm) REVERT: B 616 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.6529 (tpp-160) REVERT: B 637 LEU cc_start: 0.7643 (mt) cc_final: 0.6942 (pp) REVERT: B 662 GLN cc_start: 0.6955 (mt0) cc_final: 0.6484 (mt0) REVERT: B 748 GLU cc_start: 0.8139 (tp30) cc_final: 0.7474 (tm-30) REVERT: C 121 ASP cc_start: 0.7732 (m-30) cc_final: 0.7205 (m-30) REVERT: C 351 ARG cc_start: 0.7931 (mtt180) cc_final: 0.6466 (ptp90) REVERT: C 354 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7335 (tt) REVERT: C 380 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.7056 (p0) REVERT: D 286 LEU cc_start: 0.8644 (mt) cc_final: 0.8427 (tt) REVERT: D 371 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6853 (mtm180) REVERT: D 435 ASN cc_start: 0.6417 (t0) cc_final: 0.6107 (t0) REVERT: E 17 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7133 (mmt-90) REVERT: E 85 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8715 (mm) REVERT: E 256 GLN cc_start: 0.7125 (tp-100) cc_final: 0.6718 (pm20) REVERT: E 356 HIS cc_start: 0.5438 (m-70) cc_final: 0.4851 (m-70) REVERT: G 32 LYS cc_start: 0.4011 (OUTLIER) cc_final: 0.3639 (pptt) REVERT: G 40 ASP cc_start: 0.7198 (m-30) cc_final: 0.6530 (t70) REVERT: I 274 SER cc_start: 0.1817 (OUTLIER) cc_final: 0.1328 (p) REVERT: I 537 GLU cc_start: 0.5747 (mt-10) cc_final: 0.4299 (tp30) REVERT: I 706 MET cc_start: 0.5173 (mmm) cc_final: 0.3888 (tpt) REVERT: I 766 MET cc_start: 0.2898 (ppp) cc_final: 0.2629 (ppp) REVERT: J 314 LEU cc_start: 0.2268 (OUTLIER) cc_final: 0.1434 (mp) outliers start: 121 outliers final: 82 residues processed: 341 average time/residue: 0.1792 time to fit residues: 101.9019 Evaluate side-chains 325 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 229 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 616 ARG Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 PHE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 696 VAL Chi-restraints excluded: chain I residue 790 CYS Chi-restraints excluded: chain I residue 819 ASP Chi-restraints excluded: chain I residue 848 TRP Chi-restraints excluded: chain I residue 900 LEU Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 267 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 354 optimal weight: 0.4980 chunk 316 optimal weight: 50.0000 chunk 141 optimal weight: 0.0970 chunk 255 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN ** C 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS E 340 ASN ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 742 GLN ** 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 = 0.4277 r_free = 0.4277 target = 0.134762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.114096 restraints weight = 104072.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.112115 restraints weight = 145339.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.113123 restraints weight = 124622.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.114132 restraints weight = 80682.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.114201 restraints weight = 75688.919| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31626 Z= 0.112 Angle : 0.628 25.402 43048 Z= 0.295 Chirality : 0.042 0.307 4797 Planarity : 0.004 0.045 5272 Dihedral : 15.584 174.607 4792 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.19 % Allowed : 26.28 % Favored : 70.54 % 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: 0.98 (0.13), residues: 1723 sheet: -0.88 (0.27), residues: 370 loop : -1.23 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 348 TYR 0.024 0.001 TYR A 534 PHE 0.054 0.001 PHE I 197 TRP 0.012 0.001 TRP D 156 HIS 0.027 0.001 HIS E 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (31600) covalent geometry : angle 0.58373 / 0.29 (43009) hydrogen bonds : bond 0.03539 / 2.37 ( 1405) hydrogen bonds : angle 4.20059 / 2.94 ( 3979) metal coordination : bond 0.00747 / 0.49 ( 24) metal coordination : angle 7.74663 / 5.01 ( 39) Misc. bond : bond 0.00010 / 0.00 ( 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 341 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 238 time to evaluate : 1.137 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: symmetry clash REVERT: A 276 MET cc_start: 0.6598 (mpp) cc_final: 0.6155 (mpp) REVERT: A 623 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9090 (tt) REVERT: B 12 PHE cc_start: 0.5961 (OUTLIER) cc_final: 0.5564 (t80) REVERT: B 114 ASN cc_start: 0.7285 (OUTLIER) cc_final: 0.6957 (m-40) REVERT: B 610 PHE cc_start: 0.7173 (m-80) cc_final: 0.6818 (m-80) REVERT: B 616 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6173 (tpp-160) REVERT: B 637 LEU cc_start: 0.7431 (mt) cc_final: 0.6831 (pp) REVERT: B 748 GLU cc_start: 0.7986 (tp30) cc_final: 0.7358 (tm-30) REVERT: C 121 ASP cc_start: 0.7614 (m-30) cc_final: 0.7117 (m-30) REVERT: C 351 ARG cc_start: 0.7793 (mtt180) cc_final: 0.6389 (ptp90) REVERT: C 354 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7106 (tt) REVERT: D 435 ASN cc_start: 0.6237 (t0) cc_final: 0.6028 (t0) REVERT: D 441 MET cc_start: 0.4275 (pmm) cc_final: 0.3970 (pmm) REVERT: E 17 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7051 (mmt-90) REVERT: E 85 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8653 (mm) REVERT: E 136 ASP cc_start: 0.7456 (p0) cc_final: 0.6875 (p0) REVERT: E 256 GLN cc_start: 0.7041 (tp-100) cc_final: 0.6743 (pm20) REVERT: G 24 ASP cc_start: 0.4405 (t0) cc_final: 0.3548 (t0) REVERT: G 32 LYS cc_start: 0.3983 (OUTLIER) cc_final: 0.3498 (pptt) REVERT: G 40 ASP cc_start: 0.6938 (m-30) cc_final: 0.6443 (t70) REVERT: I 194 MET cc_start: 0.2736 (tpp) cc_final: 0.2457 (tpt) REVERT: I 274 SER cc_start: 0.1715 (OUTLIER) cc_final: 0.1250 (p) REVERT: I 537 GLU cc_start: 0.5758 (mt-10) cc_final: 0.4304 (tp30) REVERT: I 706 MET cc_start: 0.4744 (mmm) cc_final: 0.3873 (tpp) REVERT: I 766 MET cc_start: 0.3027 (ppp) cc_final: 0.2658 (ppp) REVERT: J 314 LEU cc_start: 0.2347 (OUTLIER) cc_final: 0.1509 (mp) outliers start: 103 outliers final: 83 residues processed: 327 average time/residue: 0.1787 time to fit residues: 97.7428 Evaluate side-chains 324 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 231 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 616 ARG Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 PHE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 643 ASN Chi-restraints excluded: chain I residue 696 VAL Chi-restraints excluded: chain I residue 702 VAL Chi-restraints excluded: chain I residue 751 VAL Chi-restraints excluded: chain I residue 790 CYS Chi-restraints excluded: chain I residue 819 ASP Chi-restraints excluded: chain I residue 848 TRP Chi-restraints excluded: chain I residue 900 LEU Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 311 optimal weight: 20.0000 chunk 309 optimal weight: 20.0000 chunk 340 optimal weight: 8.9990 chunk 262 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 85 optimal weight: 0.0070 chunk 149 optimal weight: 6.9990 chunk 337 optimal weight: 0.0370 chunk 79 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.135061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.114521 restraints weight = 104089.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.112645 restraints weight = 142986.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.113644 restraints weight = 121202.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.114640 restraints weight = 78377.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.114747 restraints weight = 72636.721| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 31626 Z= 0.113 Angle : 0.640 24.998 43048 Z= 0.299 Chirality : 0.041 0.311 4797 Planarity : 0.004 0.044 5272 Dihedral : 15.557 174.758 4792 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.88 % Allowed : 26.56 % Favored : 70.57 % 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: 1.01 (0.13), residues: 1727 sheet: -0.81 (0.27), residues: 371 loop : -1.21 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 348 TYR 0.024 0.001 TYR A 534 PHE 0.056 0.001 PHE I 197 TRP 0.019 0.001 TRP D 156 HIS 0.012 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (31600) covalent geometry : angle 0.59742 / 0.30 (43009) hydrogen bonds : bond 0.03447 / 2.31 ( 1405) hydrogen bonds : angle 4.14736 / 2.90 ( 3979) metal coordination : bond 0.00736 / 0.48 ( 24) metal coordination : angle 7.63893 / 4.93 ( 39) Misc. bond : bond 0.00011 / 0.01 ( 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 334 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 241 time to evaluate : 0.939 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: symmetry clash REVERT: A 276 MET cc_start: 0.6593 (mpp) cc_final: 0.6157 (mpp) REVERT: A 623 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9087 (tt) REVERT: B 12 PHE cc_start: 0.5984 (OUTLIER) cc_final: 0.5528 (t80) REVERT: B 114 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.7095 (m-40) REVERT: B 610 PHE cc_start: 0.7163 (m-80) cc_final: 0.6824 (m-80) REVERT: B 616 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6083 (tpp-160) REVERT: B 637 LEU cc_start: 0.7373 (mt) cc_final: 0.6804 (pp) REVERT: B 748 GLU cc_start: 0.7979 (tp30) cc_final: 0.7349 (tm-30) REVERT: C 351 ARG cc_start: 0.7775 (mtt180) cc_final: 0.6392 (ptp90) REVERT: C 354 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7074 (tt) REVERT: D 441 MET cc_start: 0.4242 (pmm) cc_final: 0.3983 (pmm) REVERT: E 17 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7040 (mmt-90) REVERT: E 85 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8599 (mm) REVERT: G 32 LYS cc_start: 0.3770 (OUTLIER) cc_final: 0.3300 (pptt) REVERT: G 40 ASP cc_start: 0.7004 (m-30) cc_final: 0.6597 (t70) REVERT: I 194 MET cc_start: 0.2720 (tpp) cc_final: 0.2429 (tpt) REVERT: I 274 SER cc_start: 0.1667 (OUTLIER) cc_final: 0.1200 (p) REVERT: I 537 GLU cc_start: 0.5762 (mt-10) cc_final: 0.4311 (tp30) REVERT: I 701 GLU cc_start: 0.4916 (OUTLIER) cc_final: 0.4609 (pm20) REVERT: I 706 MET cc_start: 0.4719 (mmm) cc_final: 0.3864 (tpp) REVERT: I 766 MET cc_start: 0.3099 (ppp) cc_final: 0.2677 (ppp) REVERT: J 314 LEU cc_start: 0.2345 (OUTLIER) cc_final: 0.1510 (mp) outliers start: 93 outliers final: 76 residues processed: 322 average time/residue: 0.1788 time to fit residues: 96.9150 Evaluate side-chains 320 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 233 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 616 ARG Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 256 PHE Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 643 ASN Chi-restraints excluded: chain I residue 696 VAL Chi-restraints excluded: chain I residue 701 GLU Chi-restraints excluded: chain I residue 702 VAL Chi-restraints excluded: chain I residue 790 CYS Chi-restraints excluded: chain I residue 819 ASP Chi-restraints excluded: chain I residue 848 TRP Chi-restraints excluded: chain I residue 900 LEU Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 237 optimal weight: 0.0970 chunk 352 optimal weight: 20.0000 chunk 140 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 349 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 662 GLN E 340 ASN ** I 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.134174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.113862 restraints weight = 103432.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.112931 restraints weight = 144961.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.113635 restraints weight = 122089.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.114488 restraints weight = 78388.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.114624 restraints weight = 71223.326| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31626 Z= 0.136 Angle : 0.653 26.293 43048 Z= 0.307 Chirality : 0.042 0.310 4797 Planarity : 0.004 0.048 5272 Dihedral : 15.590 175.501 4791 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.94 % Allowed : 26.62 % 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: -0.21 (0.14), residues: 3596 helix: 0.96 (0.13), residues: 1733 sheet: -0.82 (0.27), residues: 373 loop : -1.26 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 348 TYR 0.028 0.001 TYR I 741 PHE 0.056 0.001 PHE I 197 TRP 0.013 0.001 TRP C 539 HIS 0.011 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (31600) covalent geometry : angle 0.60937 / 0.31 (43009) hydrogen bonds : bond 0.03616 / 2.43 ( 1405) hydrogen bonds : angle 4.20408 / 2.94 ( 3979) metal coordination : bond 0.00746 / 0.48 ( 24) metal coordination : angle 7.83203 / 5.10 ( 39) Misc. bond : bond 0.00008 / 0.00 ( 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 332 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 237 time to evaluate : 1.191 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 276 MET cc_start: 0.6869 (mpp) cc_final: 0.6377 (mpp) REVERT: A 380 MET cc_start: 0.8336 (tmm) cc_final: 0.7976 (tmm) REVERT: A 623 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9095 (tt) REVERT: B 12 PHE cc_start: 0.5872 (OUTLIER) cc_final: 0.5458 (t80) REVERT: B 114 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.7174 (m-40) REVERT: B 616 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.5868 (tpp-160) REVERT: B 637 LEU cc_start: 0.7486 (mt) cc_final: 0.6865 (pp) REVERT: B 748 GLU cc_start: 0.7999 (tp30) cc_final: 0.7358 (tm-30) REVERT: C 351 ARG cc_start: 0.7866 (mtt180) cc_final: 0.6451 (ptp90) REVERT: C 354 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7068 (tt) REVERT: D 228 MET cc_start: 0.6398 (mmm) cc_final: 0.5993 (mmt) REVERT: D 441 MET cc_start: 0.4314 (pmm) cc_final: 0.4040 (pmm) REVERT: E 17 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7007 (mmt-90) REVERT: E 85 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8785 (mm) REVERT: E 136 ASP cc_start: 0.7596 (p0) cc_final: 0.7040 (p0) REVERT: G 32 LYS cc_start: 0.4062 (OUTLIER) cc_final: 0.3749 (pptt) REVERT: G 40 ASP cc_start: 0.7077 (m-30) cc_final: 0.6531 (t70) REVERT: I 194 MET cc_start: 0.3015 (tpp) cc_final: 0.2734 (tpt) REVERT: I 274 SER cc_start: 0.1757 (OUTLIER) cc_final: 0.1266 (p) REVERT: I 537 GLU cc_start: 0.5829 (mt-10) cc_final: 0.4341 (tp30) REVERT: I 706 MET cc_start: 0.4796 (mmm) cc_final: 0.3888 (tpp) REVERT: I 766 MET cc_start: 0.3193 (ppp) cc_final: 0.2750 (ppp) REVERT: J 278 PHE cc_start: 0.4180 (OUTLIER) cc_final: 0.3929 (m-10) REVERT: J 314 LEU cc_start: 0.2374 (OUTLIER) cc_final: 0.1530 (mp) outliers start: 95 outliers final: 77 residues processed: 321 average time/residue: 0.1796 time to fit residues: 97.1044 Evaluate side-chains 321 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 233 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 616 ARG Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 256 PHE Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 643 ASN Chi-restraints excluded: chain I residue 696 VAL Chi-restraints excluded: chain I residue 702 VAL Chi-restraints excluded: chain I residue 751 VAL Chi-restraints excluded: chain I residue 790 CYS Chi-restraints excluded: chain I residue 819 ASP Chi-restraints excluded: chain I residue 848 TRP Chi-restraints excluded: chain I residue 900 LEU Chi-restraints excluded: chain I residue 937 PHE Chi-restraints excluded: chain J residue 278 PHE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 6.9990 chunk 317 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 362 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 319 optimal weight: 2.9990 chunk 305 optimal weight: 40.0000 chunk 188 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 268 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 HIS ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 286 GLN J 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.131582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.112298 restraints weight = 103803.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.109085 restraints weight = 151533.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.107368 restraints weight = 108718.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.107316 restraints weight = 101537.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.107545 restraints weight = 82255.236| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1950 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= 0.246 Angle : 0.771 30.671 43048 Z= 0.369 Chirality : 0.046 0.356 4797 Planarity : 0.005 0.063 5272 Dihedral : 15.812 176.735 4791 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.31 % Allowed : 26.49 % Favored : 70.19 % 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: -0.69 (0.14), residues: 3596 helix: 0.63 (0.13), residues: 1733 sheet: -1.28 (0.27), residues: 364 loop : -1.50 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 348 TYR 0.031 0.002 TYR E 298 PHE 0.055 0.002 PHE I 197 TRP 0.017 0.002 TRP D 55 HIS 0.009 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 (31600) covalent geometry : angle 0.72398 / 0.37 (43009) hydrogen bonds : bond 0.04531 / 3.01 ( 1405) hydrogen bonds : angle 4.59228 / 3.20 ( 3979) metal coordination : bond 0.01233 / 0.80 ( 24) metal coordination : angle 8.85424 / 5.91 ( 39) Misc. bond : bond 0.00006 / 0.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4918.62 seconds wall clock time: 86 minutes 8.43 seconds (5168.43 seconds total)