Starting phenix.real_space_refine on Fri Jun 13 22:45:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2k_47455/06_2025/9e2k_47455.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2k_47455/06_2025/9e2k_47455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e2k_47455/06_2025/9e2k_47455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2k_47455/06_2025/9e2k_47455.map" model { file = "/net/cci-nas-00/data/ceres_data/9e2k_47455/06_2025/9e2k_47455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2k_47455/06_2025/9e2k_47455.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 94 5.16 5 C 9782 2.51 5 N 2677 2.21 5 O 2965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15520 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2301 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 4600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4600 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 23, 'TRANS': 544} Chain breaks: 4 Chain: "C" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2180 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 11, 'TRANS': 262} Chain breaks: 1 Chain: "D" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2074 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain breaks: 2 Chain: "E" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain breaks: 1 Chain: "F" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2184 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 11, 'TRANS': 263} Chain breaks: 1 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'POP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.49, per 1000 atoms: 0.68 Number of scatterers: 15520 At special positions: 0 Unit cell: (133.92, 127.44, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 P 2 15.00 O 2965 8.00 N 2677 7.00 C 9782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 2.1 seconds 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3634 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 7 sheets defined 79.7% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.903A pdb=" N VAL A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TRP A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 486 removed outlier: 3.606A pdb=" N ILE A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 503 through 522 removed outlier: 3.525A pdb=" N LEU A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 516 " --> pdb=" O ASN A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 removed outlier: 3.911A pdb=" N ASP A 526 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP A 527 " --> pdb=" O GLN A 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 527' Processing helix chain 'A' and resid 528 through 555 removed outlier: 4.211A pdb=" N ASP A 532 " --> pdb=" O PRO A 528 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.650A pdb=" N GLN A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.605A pdb=" N ARG A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 584 " --> pdb=" O ARG A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 619 removed outlier: 3.540A pdb=" N ASP A 612 " --> pdb=" O PHE A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 647 Processing helix chain 'A' and resid 652 through 662 removed outlier: 3.504A pdb=" N GLN A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 678 Processing helix chain 'A' and resid 682 through 708 Processing helix chain 'A' and resid 713 through 724 removed outlier: 3.534A pdb=" N ARG A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 718 " --> pdb=" O TRP A 714 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 724 " --> pdb=" O ILE A 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.905A pdb=" N GLY B 46 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 77 removed outlier: 3.528A pdb=" N ASN B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 67 " --> pdb=" O ASN B 63 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 106 through 120 removed outlier: 3.881A pdb=" N CYS B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 169 removed outlier: 3.803A pdb=" N SER B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU B 162 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 190 removed outlier: 4.362A pdb=" N VAL B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL B 176 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU B 182 " --> pdb=" O ASN B 178 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR B 187 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 4.415A pdb=" N ASP B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 228 through 265 removed outlier: 3.762A pdb=" N GLN B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Proline residue: B 237 - end of helix Proline residue: B 241 - end of helix removed outlier: 3.802A pdb=" N ASN B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASP B 256 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLU B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN B 263 " --> pdb=" O TRP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 282 removed outlier: 3.837A pdb=" N MET B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 280 " --> pdb=" O TRP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 removed outlier: 3.672A pdb=" N LYS B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 310 removed outlier: 3.610A pdb=" N TYR B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR B 304 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 314 Processing helix chain 'B' and resid 319 through 328 removed outlier: 3.563A pdb=" N THR B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR B 325 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS B 327 " --> pdb=" O GLN B 323 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 332 through 341 removed outlier: 3.676A pdb=" N ASN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 350 removed outlier: 4.378A pdb=" N LEU B 350 " --> pdb=" O HIS B 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 350' Processing helix chain 'B' and resid 351 through 358 removed outlier: 3.549A pdb=" N ALA B 355 " --> pdb=" O CYS B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.532A pdb=" N TYR B 437 " --> pdb=" O GLY B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 451 Processing helix chain 'B' and resid 461 through 486 removed outlier: 3.526A pdb=" N ILE B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 501 Processing helix chain 'B' and resid 503 through 523 removed outlier: 3.644A pdb=" N THR B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 526 No H-bonds generated for 'chain 'B' and resid 524 through 526' Processing helix chain 'B' and resid 527 through 529 No H-bonds generated for 'chain 'B' and resid 527 through 529' Processing helix chain 'B' and resid 530 through 554 removed outlier: 3.511A pdb=" N TYR B 534 " --> pdb=" O CYS B 530 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 535 " --> pdb=" O MET B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.701A pdb=" N GLN B 569 " --> pdb=" O ASP B 565 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 571 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 Processing helix chain 'B' and resid 594 through 619 removed outlier: 3.858A pdb=" N LEU B 617 " --> pdb=" O ASP B 613 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 619 " --> pdb=" O LYS B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 647 removed outlier: 3.503A pdb=" N HIS B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 664 removed outlier: 4.189A pdb=" N ARG B 654 " --> pdb=" O ASN B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 681 Processing helix chain 'B' and resid 682 through 698 removed outlier: 3.502A pdb=" N TYR B 686 " --> pdb=" O GLY B 682 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 697 " --> pdb=" O GLU B 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 439 removed outlier: 4.498A pdb=" N ALA C 435 " --> pdb=" O LEU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 458 removed outlier: 3.731A pdb=" N VAL C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TRP C 457 " --> pdb=" O GLY C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 486 removed outlier: 3.510A pdb=" N ASP C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 501 Processing helix chain 'C' and resid 503 through 523 removed outlier: 3.591A pdb=" N LEU C 515 " --> pdb=" O ALA C 511 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE C 516 " --> pdb=" O ASN C 512 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS C 521 " --> pdb=" O ASP C 517 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG C 523 " --> pdb=" O MET C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 526 No H-bonds generated for 'chain 'C' and resid 524 through 526' Processing helix chain 'C' and resid 527 through 554 removed outlier: 4.212A pdb=" N MET C 531 " --> pdb=" O ASP C 527 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP C 532 " --> pdb=" O PRO C 528 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 539 " --> pdb=" O LEU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 567 Processing helix chain 'C' and resid 571 through 583 removed outlier: 4.617A pdb=" N PHE C 575 " --> pdb=" O THR C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 619 removed outlier: 3.553A pdb=" N GLN C 609 " --> pdb=" O GLY C 605 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP C 612 " --> pdb=" O PHE C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 647 removed outlier: 3.553A pdb=" N HIS C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 664 removed outlier: 3.725A pdb=" N GLN C 658 " --> pdb=" O ARG C 654 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 681 removed outlier: 3.628A pdb=" N ALA C 681 " --> pdb=" O HIS C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 709 Processing helix chain 'D' and resid 432 through 441 removed outlier: 3.732A pdb=" N LEU D 441 " --> pdb=" O TYR D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 451 Processing helix chain 'D' and resid 461 through 486 removed outlier: 3.666A pdb=" N ILE D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 501 Processing helix chain 'D' and resid 503 through 524 removed outlier: 3.557A pdb=" N THR D 507 " --> pdb=" O GLY D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 555 removed outlier: 4.312A pdb=" N MET D 531 " --> pdb=" O ASP D 527 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP D 532 " --> pdb=" O PRO D 528 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D 533 " --> pdb=" O ARG D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 567 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 593 through 615 Processing helix chain 'D' and resid 637 through 647 Processing helix chain 'D' and resid 650 through 662 removed outlier: 4.061A pdb=" N ARG D 654 " --> pdb=" O ASN D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 682 Processing helix chain 'D' and resid 683 through 701 removed outlier: 3.505A pdb=" N LYS D 690 " --> pdb=" O TYR D 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 441 Processing helix chain 'E' and resid 445 through 459 removed outlier: 3.688A pdb=" N VAL E 456 " --> pdb=" O ASP E 452 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TRP E 457 " --> pdb=" O GLY E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 486 removed outlier: 3.526A pdb=" N ILE E 485 " --> pdb=" O MET E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 Processing helix chain 'E' and resid 503 through 523 removed outlier: 3.682A pdb=" N MET E 519 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU E 520 " --> pdb=" O ILE E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 527 removed outlier: 6.341A pdb=" N ASP E 527 " --> pdb=" O GLN E 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 524 through 527' Processing helix chain 'E' and resid 528 through 555 removed outlier: 4.101A pdb=" N ASP E 532 " --> pdb=" O PRO E 528 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE E 533 " --> pdb=" O ARG E 529 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR E 534 " --> pdb=" O CYS E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 571 removed outlier: 3.722A pdb=" N GLN E 569 " --> pdb=" O ASP E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 586 removed outlier: 3.543A pdb=" N ARG E 576 " --> pdb=" O GLY E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 619 Processing helix chain 'E' and resid 637 through 647 Processing helix chain 'E' and resid 650 through 664 removed outlier: 3.602A pdb=" N ARG E 654 " --> pdb=" O ASN E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 667 through 682 Processing helix chain 'E' and resid 682 through 709 Processing helix chain 'F' and resid 432 through 441 removed outlier: 3.733A pdb=" N SER F 439 " --> pdb=" O ALA F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 459 removed outlier: 3.943A pdb=" N VAL F 456 " --> pdb=" O ASP F 452 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TRP F 457 " --> pdb=" O GLY F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 486 removed outlier: 3.567A pdb=" N ILE F 485 " --> pdb=" O MET F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 501 Processing helix chain 'F' and resid 502 through 524 removed outlier: 4.305A pdb=" N GLN F 506 " --> pdb=" O PHE F 502 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 515 " --> pdb=" O ALA F 511 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE F 516 " --> pdb=" O ASN F 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG F 523 " --> pdb=" O MET F 519 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN F 524 " --> pdb=" O GLU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 555 removed outlier: 4.111A pdb=" N MET F 531 " --> pdb=" O ASP F 527 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP F 532 " --> pdb=" O PRO F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 570 Processing helix chain 'F' and resid 571 through 586 removed outlier: 4.684A pdb=" N PHE F 575 " --> pdb=" O THR F 571 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN F 584 " --> pdb=" O ARG F 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 619 Processing helix chain 'F' and resid 637 through 647 Processing helix chain 'F' and resid 650 through 664 removed outlier: 3.684A pdb=" N ARG F 654 " --> pdb=" O ASN F 650 " (cutoff:3.500A) Processing helix chain 'F' and resid 667 through 679 Processing helix chain 'F' and resid 685 through 705 removed outlier: 3.852A pdb=" N LYS F 690 " --> pdb=" O TYR F 686 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 491 through 492 Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AA3, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AA4, first strand: chain 'C' and resid 491 through 492 Processing sheet with id=AA5, first strand: chain 'D' and resid 491 through 492 Processing sheet with id=AA6, first strand: chain 'E' and resid 491 through 492 Processing sheet with id=AA7, first strand: chain 'F' and resid 491 through 492 1014 hydrogen bonds defined for protein. 3003 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.41 Time building geometry restraints manager: 4.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5216 1.34 - 1.46: 3250 1.46 - 1.58: 7167 1.58 - 1.70: 2 1.70 - 1.82: 162 Bond restraints: 15797 Sorted by residual: bond pdb=" O POP B 801 " pdb=" P2 POP B 801 " ideal model delta sigma weight residual 1.661 1.612 0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" N ASN B 250 " pdb=" CA ASN B 250 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.16e-02 7.43e+03 5.85e+00 bond pdb=" O POP B 801 " pdb=" P1 POP B 801 " ideal model delta sigma weight residual 1.660 1.612 0.048 2.00e-02 2.50e+03 5.69e+00 bond pdb=" N ASP B 120 " pdb=" CA ASP B 120 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.25e-02 6.40e+03 5.68e+00 bond pdb=" N SER B 340 " pdb=" CA SER B 340 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.35e-02 5.49e+03 4.26e+00 ... (remaining 15792 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 20698 1.91 - 3.81: 495 3.81 - 5.72: 110 5.72 - 7.63: 23 7.63 - 9.53: 6 Bond angle restraints: 21332 Sorted by residual: angle pdb=" N THR B 210 " pdb=" CA THR B 210 " pdb=" C THR B 210 " ideal model delta sigma weight residual 111.40 103.93 7.47 1.22e+00 6.72e-01 3.74e+01 angle pdb=" N CYS B 530 " pdb=" CA CYS B 530 " pdb=" C CYS B 530 " ideal model delta sigma weight residual 114.64 106.12 8.52 1.52e+00 4.33e-01 3.14e+01 angle pdb=" N ILE B 501 " pdb=" CA ILE B 501 " pdb=" C ILE B 501 " ideal model delta sigma weight residual 113.53 108.09 5.44 9.80e-01 1.04e+00 3.08e+01 angle pdb=" N ILE F 501 " pdb=" CA ILE F 501 " pdb=" C ILE F 501 " ideal model delta sigma weight residual 113.53 108.37 5.16 9.80e-01 1.04e+00 2.77e+01 angle pdb=" N ASN D 616 " pdb=" CA ASN D 616 " pdb=" C ASN D 616 " ideal model delta sigma weight residual 114.75 108.57 6.18 1.26e+00 6.30e-01 2.41e+01 ... (remaining 21327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 7989 18.07 - 36.14: 1170 36.14 - 54.21: 382 54.21 - 72.27: 80 72.27 - 90.34: 27 Dihedral angle restraints: 9648 sinusoidal: 4035 harmonic: 5613 Sorted by residual: dihedral pdb=" CA ASP E 667 " pdb=" C ASP E 667 " pdb=" N VAL E 668 " pdb=" CA VAL E 668 " ideal model delta harmonic sigma weight residual -180.00 -158.32 -21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ASP B 209 " pdb=" CB ASP B 209 " pdb=" CG ASP B 209 " pdb=" OD1 ASP B 209 " ideal model delta sinusoidal sigma weight residual -30.00 -89.51 59.51 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP B 310 " pdb=" C ASP B 310 " pdb=" N PHE B 311 " pdb=" CA PHE B 311 " ideal model delta harmonic sigma weight residual -180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 9645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1441 0.031 - 0.062: 665 0.062 - 0.093: 212 0.093 - 0.124: 59 0.124 - 0.155: 6 Chirality restraints: 2383 Sorted by residual: chirality pdb=" CB THR B 210 " pdb=" CA THR B 210 " pdb=" OG1 THR B 210 " pdb=" CG2 THR B 210 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CB THR D 673 " pdb=" CA THR D 673 " pdb=" OG1 THR D 673 " pdb=" CG2 THR D 673 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CG LEU F 666 " pdb=" CB LEU F 666 " pdb=" CD1 LEU F 666 " pdb=" CD2 LEU F 666 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 2380 not shown) Planarity restraints: 2773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN F 647 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.87e+00 pdb=" CD GLN F 647 " 0.048 2.00e-02 2.50e+03 pdb=" OE1 GLN F 647 " -0.018 2.00e-02 2.50e+03 pdb=" NE2 GLN F 647 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 428 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C ASP C 428 " 0.044 2.00e-02 2.50e+03 pdb=" O ASP C 428 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU C 429 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 433 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO B 434 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 434 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 434 " 0.035 5.00e-02 4.00e+02 ... (remaining 2770 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1313 2.74 - 3.28: 15770 3.28 - 3.82: 26316 3.82 - 4.36: 30166 4.36 - 4.90: 52330 Nonbonded interactions: 125895 Sorted by model distance: nonbonded pdb=" OE1 GLN F 589 " pdb=" NE2 GLN F 590 " model vdw 2.199 3.120 nonbonded pdb=" OH TYR F 437 " pdb=" O PRO F 496 " model vdw 2.207 3.040 nonbonded pdb=" O TYR C 614 " pdb=" OG1 THR C 618 " model vdw 2.225 3.040 nonbonded pdb=" N GLU E 448 " pdb=" OE1 GLU E 448 " model vdw 2.239 3.120 nonbonded pdb=" N GLU B 104 " pdb=" OE1 GLU B 104 " model vdw 2.261 3.120 ... (remaining 125890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 426 through 451 or resid 458 through 701)) selection = (chain 'C' and (resid 426 through 451 or resid 458 through 701)) selection = (chain 'D' and resid 426 through 701) selection = (chain 'E' and (resid 426 through 451 or resid 458 through 701)) selection = (chain 'F' and (resid 426 through 451 or resid 458 through 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.420 Find NCS groups from input model: 0.910 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: 0.000 Load rotamer database and sin/cos tables:19.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 : 0.004 0.049 15797 Z= 0.194 Angle : 0.770 9.531 21332 Z= 0.457 Chirality : 0.039 0.155 2383 Planarity : 0.005 0.063 2773 Dihedral : 19.330 90.343 6014 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.63 % Allowed : 3.72 % Favored : 95.65 % Rotamer: Outliers : 2.32 % Allowed : 35.63 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1907 helix: 1.65 (0.15), residues: 1386 sheet: None (None), residues: 0 loop : -2.07 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 89 HIS 0.006 0.001 HIS B 347 PHE 0.014 0.001 PHE F 607 TYR 0.019 0.002 TYR A 686 ARG 0.015 0.001 ARG F 661 Details of bonding type rmsd hydrogen bonds : bond 0.18567 ( 1014) hydrogen bonds : angle 5.72755 ( 3003) covalent geometry : bond 0.00408 (15797) covalent geometry : angle 0.76971 (21332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 508 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7620 (mt-10) REVERT: A 487 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: A 517 ASP cc_start: 0.7856 (t0) cc_final: 0.7590 (t0) REVERT: A 563 TYR cc_start: 0.8740 (t80) cc_final: 0.8328 (t80) REVERT: A 581 MET cc_start: 0.8646 (mtt) cc_final: 0.8319 (mtt) REVERT: A 584 GLN cc_start: 0.8402 (tp40) cc_final: 0.8159 (tp40) REVERT: A 593 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7194 (pt) REVERT: A 659 GLN cc_start: 0.8645 (tp40) cc_final: 0.8356 (tp40) REVERT: A 670 LEU cc_start: 0.8490 (mt) cc_final: 0.8206 (mp) REVERT: A 671 LYS cc_start: 0.8239 (tptp) cc_final: 0.7848 (tptp) REVERT: B 106 LEU cc_start: 0.8191 (pt) cc_final: 0.7861 (pp) REVERT: B 115 TYR cc_start: 0.7239 (t80) cc_final: 0.7006 (t80) REVERT: B 271 MET cc_start: 0.4747 (ptm) cc_final: 0.4531 (ppp) REVERT: B 290 LYS cc_start: 0.8442 (tmmt) cc_final: 0.7780 (tmmt) REVERT: B 470 SER cc_start: 0.8736 (t) cc_final: 0.8362 (m) REVERT: B 483 ASP cc_start: 0.7567 (m-30) cc_final: 0.7273 (t0) REVERT: B 489 SER cc_start: 0.8575 (t) cc_final: 0.8261 (p) REVERT: B 536 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6585 (tm-30) REVERT: B 671 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8444 (mmtm) REVERT: B 672 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7785 (mm-30) REVERT: B 675 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8312 (mt) REVERT: C 483 ASP cc_start: 0.7537 (m-30) cc_final: 0.7309 (m-30) REVERT: C 659 GLN cc_start: 0.8394 (tp40) cc_final: 0.7885 (tp40) REVERT: C 672 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7577 (mp0) REVERT: C 685 GLU cc_start: 0.7696 (mp0) cc_final: 0.7259 (mp0) REVERT: D 483 ASP cc_start: 0.7559 (m-30) cc_final: 0.7316 (m-30) REVERT: D 519 MET cc_start: 0.8259 (tpp) cc_final: 0.7884 (tpt) REVERT: D 528 PRO cc_start: 0.8772 (Cg_exo) cc_final: 0.8560 (Cg_endo) REVERT: D 579 THR cc_start: 0.8834 (t) cc_final: 0.8452 (p) REVERT: D 611 ARG cc_start: 0.8616 (ttp80) cc_final: 0.8263 (ttt180) REVERT: D 695 MET cc_start: 0.7020 (tpt) cc_final: 0.6813 (tpt) REVERT: E 459 VAL cc_start: 0.8227 (t) cc_final: 0.7952 (p) REVERT: E 487 ASP cc_start: 0.8017 (m-30) cc_final: 0.7589 (m-30) REVERT: E 505 GLU cc_start: 0.7823 (mp0) cc_final: 0.7567 (mp0) REVERT: E 527 ASP cc_start: 0.8018 (t0) cc_final: 0.7804 (t70) REVERT: E 672 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7419 (mt-10) REVERT: F 447 ARG cc_start: 0.8487 (mpp-170) cc_final: 0.8183 (mmt-90) REVERT: F 448 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7064 (mm-30) REVERT: F 561 GLU cc_start: 0.7352 (mp0) cc_final: 0.7001 (mp0) REVERT: F 608 PHE cc_start: 0.8679 (m-80) cc_final: 0.8244 (m-80) REVERT: F 611 ARG cc_start: 0.8556 (ttp80) cc_final: 0.8354 (tmm160) REVERT: F 632 ASP cc_start: 0.8208 (t0) cc_final: 0.8003 (t70) REVERT: F 666 LEU cc_start: 0.8135 (mt) cc_final: 0.7807 (mt) REVERT: F 684 ILE cc_start: 0.8730 (mm) cc_final: 0.8322 (mm) REVERT: F 688 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6921 (mt-10) REVERT: F 696 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7421 (mp0) outliers start: 40 outliers final: 23 residues processed: 534 average time/residue: 1.5542 time to fit residues: 901.1282 Evaluate side-chains 527 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 500 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 633 GLU Chi-restraints excluded: chain E residue 634 CYS Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 489 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.0170 chunk 77 optimal weight: 0.0970 chunk 149 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 173 optimal weight: 0.0980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN A 658 GLN B 178 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 554 ASN B 658 GLN ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN D 545 GLN E 545 GLN F 512 ASN F 589 GLN F 590 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.144657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.125153 restraints weight = 22098.020| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.81 r_work: 0.3513 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15797 Z= 0.134 Angle : 0.597 7.925 21332 Z= 0.305 Chirality : 0.037 0.144 2383 Planarity : 0.005 0.063 2773 Dihedral : 6.143 58.668 2158 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.63 % Allowed : 3.41 % Favored : 95.96 % Rotamer: Outliers : 5.79 % Allowed : 29.08 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.20), residues: 1907 helix: 1.92 (0.14), residues: 1444 sheet: None (None), residues: 0 loop : -2.15 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 73 HIS 0.006 0.001 HIS B 56 PHE 0.010 0.001 PHE B 221 TYR 0.017 0.001 TYR B 115 ARG 0.008 0.001 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.05020 ( 1014) hydrogen bonds : angle 3.94349 ( 3003) covalent geometry : bond 0.00293 (15797) covalent geometry : angle 0.59711 (21332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 498 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7422 (pp) REVERT: A 436 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7523 (mt-10) REVERT: A 444 LYS cc_start: 0.6611 (OUTLIER) cc_final: 0.5682 (mtmt) REVERT: A 456 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8472 (m) REVERT: A 487 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: A 520 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7195 (mp0) REVERT: A 563 TYR cc_start: 0.8625 (t80) cc_final: 0.8405 (t80) REVERT: A 581 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8320 (mtt) REVERT: A 582 MET cc_start: 0.8700 (mtp) cc_final: 0.8422 (mtp) REVERT: A 591 LYS cc_start: 0.5282 (OUTLIER) cc_final: 0.4706 (mptt) REVERT: A 593 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7240 (pt) REVERT: A 614 TYR cc_start: 0.8583 (t80) cc_final: 0.8373 (t80) REVERT: A 670 LEU cc_start: 0.8416 (mt) cc_final: 0.8094 (mp) REVERT: A 672 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7468 (mt-10) REVERT: A 675 LEU cc_start: 0.8562 (tp) cc_final: 0.8315 (tm) REVERT: B 63 ASN cc_start: 0.7187 (OUTLIER) cc_final: 0.6914 (m110) REVERT: B 76 PHE cc_start: 0.8038 (m-10) cc_final: 0.7674 (m-10) REVERT: B 89 TRP cc_start: 0.7573 (m100) cc_final: 0.7141 (m100) REVERT: B 106 LEU cc_start: 0.8161 (pt) cc_final: 0.7830 (pp) REVERT: B 218 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7069 (mp) REVERT: B 470 SER cc_start: 0.8724 (t) cc_final: 0.8350 (m) REVERT: B 489 SER cc_start: 0.8593 (t) cc_final: 0.8290 (p) REVERT: B 493 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6450 (mmp-170) REVERT: B 612 ASP cc_start: 0.7955 (m-30) cc_final: 0.7469 (p0) REVERT: B 675 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8287 (mt) REVERT: B 696 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6881 (pp20) REVERT: C 428 ASP cc_start: 0.6873 (t0) cc_final: 0.6600 (t0) REVERT: C 429 GLU cc_start: 0.7954 (pm20) cc_final: 0.7683 (pm20) REVERT: C 483 ASP cc_start: 0.7536 (m-30) cc_final: 0.7279 (m-30) REVERT: C 487 ASP cc_start: 0.7471 (t70) cc_final: 0.6964 (t70) REVERT: C 576 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8054 (mtm-85) REVERT: C 672 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7552 (mp0) REVERT: C 685 GLU cc_start: 0.7776 (mp0) cc_final: 0.7316 (mp0) REVERT: C 688 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: D 483 ASP cc_start: 0.7659 (m-30) cc_final: 0.7396 (m-30) REVERT: D 519 MET cc_start: 0.8206 (tpp) cc_final: 0.7629 (tpt) REVERT: D 524 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7829 (mp10) REVERT: D 577 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8086 (tp) REVERT: D 611 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8300 (ttt180) REVERT: D 662 SER cc_start: 0.8311 (t) cc_final: 0.8053 (p) REVERT: D 695 MET cc_start: 0.6985 (tpt) cc_final: 0.6722 (tpt) REVERT: E 444 LYS cc_start: 0.5850 (OUTLIER) cc_final: 0.5315 (mptt) REVERT: E 459 VAL cc_start: 0.8214 (t) cc_final: 0.7831 (p) REVERT: E 487 ASP cc_start: 0.8088 (m-30) cc_final: 0.7752 (m-30) REVERT: E 527 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7795 (t70) REVERT: E 612 ASP cc_start: 0.8129 (m-30) cc_final: 0.7879 (m-30) REVERT: E 633 GLU cc_start: 0.5080 (OUTLIER) cc_final: 0.4845 (tm-30) REVERT: E 672 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7347 (mt-10) REVERT: F 432 LEU cc_start: 0.8419 (mp) cc_final: 0.8155 (mm) REVERT: F 491 LEU cc_start: 0.8852 (mt) cc_final: 0.8623 (mm) REVERT: F 608 PHE cc_start: 0.8635 (m-80) cc_final: 0.8089 (m-80) REVERT: F 632 ASP cc_start: 0.8260 (t0) cc_final: 0.7892 (t70) REVERT: F 633 GLU cc_start: 0.5728 (OUTLIER) cc_final: 0.5337 (tm-30) REVERT: F 661 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7583 (ttp-110) REVERT: F 666 LEU cc_start: 0.8305 (mt) cc_final: 0.7830 (mt) REVERT: F 684 ILE cc_start: 0.8560 (mm) cc_final: 0.8155 (mm) REVERT: F 696 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7392 (mp0) outliers start: 100 outliers final: 26 residues processed: 561 average time/residue: 1.5305 time to fit residues: 931.5708 Evaluate side-chains 539 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 495 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain E residue 428 ASP Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 633 GLU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 578 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 667 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 137 optimal weight: 1.9990 chunk 34 optimal weight: 0.0670 chunk 134 optimal weight: 0.6980 chunk 165 optimal weight: 0.3980 chunk 116 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS A 658 GLN B 178 ASN B 197 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 554 ASN ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN D 545 GLN F 512 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.142600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.123178 restraints weight = 21934.121| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.77 r_work: 0.3478 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15797 Z= 0.182 Angle : 0.611 8.054 21332 Z= 0.309 Chirality : 0.039 0.152 2383 Planarity : 0.005 0.059 2773 Dihedral : 5.552 58.560 2134 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.63 % Allowed : 3.46 % Favored : 95.91 % Rotamer: Outliers : 5.10 % Allowed : 28.91 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.20), residues: 1907 helix: 1.89 (0.14), residues: 1446 sheet: None (None), residues: 0 loop : -1.99 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 180 HIS 0.005 0.001 HIS E 642 PHE 0.013 0.002 PHE B 221 TYR 0.019 0.002 TYR B 115 ARG 0.013 0.001 ARG B 661 Details of bonding type rmsd hydrogen bonds : bond 0.05403 ( 1014) hydrogen bonds : angle 3.82770 ( 3003) covalent geometry : bond 0.00424 (15797) covalent geometry : angle 0.61127 (21332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 491 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7404 (pp) REVERT: A 444 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.5708 (mtmt) REVERT: A 487 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: A 517 ASP cc_start: 0.7739 (t0) cc_final: 0.7487 (t0) REVERT: A 520 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7244 (mp0) REVERT: A 563 TYR cc_start: 0.8665 (t80) cc_final: 0.8412 (t80) REVERT: A 581 MET cc_start: 0.8710 (mtt) cc_final: 0.8375 (mtt) REVERT: A 591 LYS cc_start: 0.5396 (OUTLIER) cc_final: 0.4776 (mptt) REVERT: A 593 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7320 (pt) REVERT: A 662 SER cc_start: 0.8070 (t) cc_final: 0.7777 (m) REVERT: A 670 LEU cc_start: 0.8505 (mt) cc_final: 0.8231 (mp) REVERT: A 672 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7446 (mt-10) REVERT: B 63 ASN cc_start: 0.7193 (OUTLIER) cc_final: 0.6922 (m110) REVERT: B 75 GLN cc_start: 0.8255 (tp40) cc_final: 0.7996 (mm-40) REVERT: B 76 PHE cc_start: 0.8026 (m-10) cc_final: 0.7644 (m-10) REVERT: B 171 PRO cc_start: 0.7530 (Cg_endo) cc_final: 0.7315 (Cg_exo) REVERT: B 218 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7111 (mp) REVERT: B 470 SER cc_start: 0.8742 (t) cc_final: 0.8400 (m) REVERT: B 493 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6445 (mmp-170) REVERT: B 612 ASP cc_start: 0.7987 (m-30) cc_final: 0.7497 (p0) REVERT: B 696 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6909 (pp20) REVERT: C 428 ASP cc_start: 0.7297 (t0) cc_final: 0.6975 (t0) REVERT: C 483 ASP cc_start: 0.7570 (m-30) cc_final: 0.7288 (m-30) REVERT: C 487 ASP cc_start: 0.7734 (t70) cc_final: 0.7236 (t70) REVERT: C 517 ASP cc_start: 0.7868 (t0) cc_final: 0.7660 (t0) REVERT: C 576 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8083 (mtm-85) REVERT: C 672 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7543 (mp0) REVERT: C 685 GLU cc_start: 0.7804 (mp0) cc_final: 0.7349 (mp0) REVERT: C 688 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: D 483 ASP cc_start: 0.7682 (m-30) cc_final: 0.7374 (m-30) REVERT: D 524 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7942 (mp10) REVERT: D 529 ARG cc_start: 0.7930 (mmm-85) cc_final: 0.7682 (mmm-85) REVERT: D 568 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.7420 (ttp-170) REVERT: D 577 LEU cc_start: 0.8458 (tt) cc_final: 0.8125 (tp) REVERT: D 606 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7741 (mt-10) REVERT: D 611 ARG cc_start: 0.8661 (ttp80) cc_final: 0.8348 (ttt180) REVERT: D 647 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: D 695 MET cc_start: 0.7001 (tpt) cc_final: 0.6739 (tpt) REVERT: E 444 LYS cc_start: 0.6160 (OUTLIER) cc_final: 0.5355 (mptt) REVERT: E 459 VAL cc_start: 0.8234 (t) cc_final: 0.7838 (p) REVERT: E 487 ASP cc_start: 0.8145 (m-30) cc_final: 0.7790 (m-30) REVERT: E 527 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7790 (t70) REVERT: E 612 ASP cc_start: 0.8172 (m-30) cc_final: 0.7957 (m-30) REVERT: E 633 GLU cc_start: 0.5034 (OUTLIER) cc_final: 0.4823 (tm-30) REVERT: E 651 VAL cc_start: 0.8578 (m) cc_final: 0.8369 (t) REVERT: E 672 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7324 (mt-10) REVERT: F 432 LEU cc_start: 0.8605 (mp) cc_final: 0.8398 (mm) REVERT: F 491 LEU cc_start: 0.8874 (mt) cc_final: 0.8639 (mm) REVERT: F 608 PHE cc_start: 0.8659 (m-80) cc_final: 0.8135 (m-80) REVERT: F 632 ASP cc_start: 0.8279 (t0) cc_final: 0.7864 (t70) REVERT: F 633 GLU cc_start: 0.5746 (OUTLIER) cc_final: 0.5356 (tm-30) REVERT: F 666 LEU cc_start: 0.8449 (mt) cc_final: 0.8127 (mt) REVERT: F 693 GLU cc_start: 0.7480 (tp30) cc_final: 0.6953 (tp30) REVERT: F 696 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7428 (mp0) outliers start: 88 outliers final: 40 residues processed: 546 average time/residue: 1.6732 time to fit residues: 988.6695 Evaluate side-chains 532 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 477 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 647 GLN Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 633 GLU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 578 LEU Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 647 GLN Chi-restraints excluded: chain F residue 667 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 169 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 33 optimal weight: 0.0050 chunk 76 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 ASN A 658 GLN B 178 ASN B 232 GLN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 554 ASN ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 ASN C 609 GLN D 545 GLN F 512 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.141813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122451 restraints weight = 21982.144| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.76 r_work: 0.3466 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15797 Z= 0.186 Angle : 0.616 8.524 21332 Z= 0.307 Chirality : 0.039 0.179 2383 Planarity : 0.005 0.060 2773 Dihedral : 5.343 59.674 2128 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.51 % Favored : 95.91 % Rotamer: Outliers : 5.39 % Allowed : 29.32 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.20), residues: 1907 helix: 1.89 (0.14), residues: 1438 sheet: None (None), residues: 0 loop : -1.96 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 180 HIS 0.004 0.001 HIS D 499 PHE 0.016 0.002 PHE B 221 TYR 0.017 0.002 TYR A 686 ARG 0.009 0.001 ARG E 611 Details of bonding type rmsd hydrogen bonds : bond 0.05414 ( 1014) hydrogen bonds : angle 3.74862 ( 3003) covalent geometry : bond 0.00442 (15797) covalent geometry : angle 0.61564 (21332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 493 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.5705 (mtmt) REVERT: A 452 ASP cc_start: 0.7509 (m-30) cc_final: 0.7246 (m-30) REVERT: A 487 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: A 517 ASP cc_start: 0.7775 (t0) cc_final: 0.7531 (t0) REVERT: A 520 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7279 (mp0) REVERT: A 563 TYR cc_start: 0.8680 (t80) cc_final: 0.8441 (t80) REVERT: A 581 MET cc_start: 0.8711 (mtt) cc_final: 0.8300 (mtt) REVERT: A 582 MET cc_start: 0.8793 (mtp) cc_final: 0.8570 (mtp) REVERT: A 584 GLN cc_start: 0.8377 (tp40) cc_final: 0.8159 (tp40) REVERT: A 591 LYS cc_start: 0.5498 (OUTLIER) cc_final: 0.4713 (mptt) REVERT: A 593 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7425 (pt) REVERT: A 615 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8316 (mtpp) REVERT: A 659 GLN cc_start: 0.8676 (tp40) cc_final: 0.8380 (tp40) REVERT: A 662 SER cc_start: 0.8103 (t) cc_final: 0.7786 (m) REVERT: A 670 LEU cc_start: 0.8420 (mt) cc_final: 0.8144 (mp) REVERT: A 675 LEU cc_start: 0.8620 (tp) cc_final: 0.8339 (tm) REVERT: A 715 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7625 (t) REVERT: B 75 GLN cc_start: 0.8271 (tp40) cc_final: 0.8057 (tp-100) REVERT: B 76 PHE cc_start: 0.7954 (m-10) cc_final: 0.7634 (m-10) REVERT: B 223 MET cc_start: 0.6180 (mmp) cc_final: 0.5957 (pp-130) REVERT: B 470 SER cc_start: 0.8752 (t) cc_final: 0.8399 (m) REVERT: B 612 ASP cc_start: 0.7999 (m-30) cc_final: 0.7495 (p0) REVERT: B 675 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8319 (mt) REVERT: B 696 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6915 (pp20) REVERT: C 428 ASP cc_start: 0.7372 (t0) cc_final: 0.7017 (t0) REVERT: C 483 ASP cc_start: 0.7617 (m-30) cc_final: 0.7296 (m-30) REVERT: C 487 ASP cc_start: 0.7712 (t70) cc_final: 0.7227 (t70) REVERT: C 493 ARG cc_start: 0.6382 (mtt180) cc_final: 0.6126 (mtt180) REVERT: C 517 ASP cc_start: 0.7887 (t0) cc_final: 0.7672 (t0) REVERT: C 576 ARG cc_start: 0.8364 (ttp80) cc_final: 0.8098 (mtm-85) REVERT: C 672 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7564 (mp0) REVERT: C 685 GLU cc_start: 0.7810 (mp0) cc_final: 0.7470 (mp0) REVERT: C 688 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: D 483 ASP cc_start: 0.7654 (m-30) cc_final: 0.7381 (m-30) REVERT: D 524 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7965 (mp10) REVERT: D 568 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7360 (ttp-170) REVERT: D 577 LEU cc_start: 0.8486 (tt) cc_final: 0.8161 (tp) REVERT: D 606 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7478 (mt-10) REVERT: D 611 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8339 (ttt180) REVERT: D 647 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7671 (mt0) REVERT: D 695 MET cc_start: 0.7031 (tpt) cc_final: 0.6753 (tpt) REVERT: E 444 LYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5388 (mptt) REVERT: E 459 VAL cc_start: 0.8233 (t) cc_final: 0.7833 (p) REVERT: E 487 ASP cc_start: 0.8168 (m-30) cc_final: 0.7815 (m-30) REVERT: E 500 MET cc_start: 0.8643 (mmm) cc_final: 0.8415 (mmt) REVERT: E 527 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7785 (t70) REVERT: E 633 GLU cc_start: 0.4976 (OUTLIER) cc_final: 0.4771 (tm-30) REVERT: E 651 VAL cc_start: 0.8578 (m) cc_final: 0.8357 (t) REVERT: E 672 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7343 (mt-10) REVERT: F 432 LEU cc_start: 0.8668 (mp) cc_final: 0.8424 (mm) REVERT: F 444 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6410 (mptt) REVERT: F 448 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6869 (mm-30) REVERT: F 491 LEU cc_start: 0.8851 (mt) cc_final: 0.8624 (mm) REVERT: F 608 PHE cc_start: 0.8645 (m-80) cc_final: 0.8123 (m-80) REVERT: F 633 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.5321 (tm-30) REVERT: F 661 ARG cc_start: 0.7844 (ttm110) cc_final: 0.7612 (ttp-110) REVERT: F 666 LEU cc_start: 0.8432 (mt) cc_final: 0.8046 (mt) REVERT: F 679 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8007 (ttp80) REVERT: F 693 GLU cc_start: 0.7477 (tp30) cc_final: 0.6976 (tp30) REVERT: F 696 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7424 (mp0) outliers start: 93 outliers final: 46 residues processed: 542 average time/residue: 1.5179 time to fit residues: 893.9043 Evaluate side-chains 544 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 482 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 647 GLN Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain E residue 428 ASP Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 505 GLU Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 633 GLU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 578 LEU Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 647 GLN Chi-restraints excluded: chain F residue 679 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 106 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 184 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 512 ASN A 658 GLN B 178 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 554 ASN ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 ASN C 609 GLN D 545 GLN F 512 ASN F 569 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.142219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122648 restraints weight = 22314.782| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.81 r_work: 0.3468 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15797 Z= 0.173 Angle : 0.606 8.558 21332 Z= 0.302 Chirality : 0.039 0.151 2383 Planarity : 0.005 0.060 2773 Dihedral : 5.313 58.425 2128 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.57 % Favored : 95.86 % Rotamer: Outliers : 5.04 % Allowed : 29.14 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.20), residues: 1907 helix: 1.95 (0.14), residues: 1433 sheet: None (None), residues: 0 loop : -1.90 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 180 HIS 0.004 0.001 HIS F 642 PHE 0.013 0.001 PHE B 221 TYR 0.022 0.002 TYR B 115 ARG 0.008 0.001 ARG B 291 Details of bonding type rmsd hydrogen bonds : bond 0.05204 ( 1014) hydrogen bonds : angle 3.66846 ( 3003) covalent geometry : bond 0.00410 (15797) covalent geometry : angle 0.60588 (21332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 487 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.5722 (mtmt) REVERT: A 452 ASP cc_start: 0.7533 (m-30) cc_final: 0.7197 (m-30) REVERT: A 487 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7451 (m-30) REVERT: A 517 ASP cc_start: 0.7785 (t0) cc_final: 0.7522 (t0) REVERT: A 520 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7282 (mp0) REVERT: A 563 TYR cc_start: 0.8704 (t80) cc_final: 0.8449 (t80) REVERT: A 581 MET cc_start: 0.8713 (mtt) cc_final: 0.8310 (mtt) REVERT: A 582 MET cc_start: 0.8721 (mtp) cc_final: 0.8416 (mtp) REVERT: A 584 GLN cc_start: 0.8350 (tp40) cc_final: 0.8114 (tp40) REVERT: A 593 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7463 (pt) REVERT: A 615 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8309 (mtpp) REVERT: A 659 GLN cc_start: 0.8663 (tp40) cc_final: 0.8339 (tp40) REVERT: A 675 LEU cc_start: 0.8636 (tp) cc_final: 0.8320 (tm) REVERT: B 75 GLN cc_start: 0.8267 (tp40) cc_final: 0.8056 (tp-100) REVERT: B 76 PHE cc_start: 0.7905 (m-10) cc_final: 0.7508 (m-10) REVERT: B 290 LYS cc_start: 0.8872 (pptt) cc_final: 0.8416 (pptt) REVERT: B 444 LYS cc_start: 0.6767 (OUTLIER) cc_final: 0.5005 (mtmt) REVERT: B 470 SER cc_start: 0.8743 (t) cc_final: 0.8403 (m) REVERT: B 591 LYS cc_start: 0.6142 (OUTLIER) cc_final: 0.5876 (mttm) REVERT: B 612 ASP cc_start: 0.8000 (m-30) cc_final: 0.7479 (p0) REVERT: B 696 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6842 (pp20) REVERT: C 428 ASP cc_start: 0.7392 (t0) cc_final: 0.7068 (t0) REVERT: C 483 ASP cc_start: 0.7634 (m-30) cc_final: 0.7266 (m-30) REVERT: C 487 ASP cc_start: 0.7684 (t70) cc_final: 0.7204 (t70) REVERT: C 493 ARG cc_start: 0.6417 (mtt180) cc_final: 0.6151 (mtt180) REVERT: C 505 GLU cc_start: 0.8154 (mp0) cc_final: 0.7813 (mp0) REVERT: C 515 LEU cc_start: 0.8554 (mp) cc_final: 0.8278 (mm) REVERT: C 576 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8104 (mtm-85) REVERT: C 672 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7654 (mp0) REVERT: C 685 GLU cc_start: 0.7821 (mp0) cc_final: 0.7491 (mp0) REVERT: C 688 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: D 483 ASP cc_start: 0.7643 (m-30) cc_final: 0.7358 (m-30) REVERT: D 577 LEU cc_start: 0.8492 (tt) cc_final: 0.8164 (tp) REVERT: D 606 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7661 (mt-10) REVERT: D 611 ARG cc_start: 0.8665 (ttp80) cc_final: 0.8328 (ttt180) REVERT: D 647 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: D 695 MET cc_start: 0.7064 (tpt) cc_final: 0.6790 (tpt) REVERT: E 444 LYS cc_start: 0.6116 (OUTLIER) cc_final: 0.5307 (mptt) REVERT: E 459 VAL cc_start: 0.8221 (t) cc_final: 0.7820 (p) REVERT: E 487 ASP cc_start: 0.8182 (m-30) cc_final: 0.7825 (m-30) REVERT: E 500 MET cc_start: 0.8652 (mmm) cc_final: 0.8419 (mmt) REVERT: E 519 MET cc_start: 0.7706 (ptp) cc_final: 0.7437 (ptp) REVERT: E 527 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7814 (t70) REVERT: E 633 GLU cc_start: 0.4962 (OUTLIER) cc_final: 0.4731 (tm-30) REVERT: E 651 VAL cc_start: 0.8572 (m) cc_final: 0.8345 (t) REVERT: E 672 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7405 (mt-10) REVERT: F 432 LEU cc_start: 0.8598 (mp) cc_final: 0.8393 (mm) REVERT: F 444 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.5133 (mptt) REVERT: F 448 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6885 (mm-30) REVERT: F 469 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8572 (mttp) REVERT: F 491 LEU cc_start: 0.8840 (mt) cc_final: 0.8615 (mm) REVERT: F 519 MET cc_start: 0.7977 (ttt) cc_final: 0.7383 (ttt) REVERT: F 608 PHE cc_start: 0.8655 (m-80) cc_final: 0.8118 (m-80) REVERT: F 633 GLU cc_start: 0.5735 (OUTLIER) cc_final: 0.5333 (tm-30) REVERT: F 661 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7654 (ttp-110) REVERT: F 666 LEU cc_start: 0.8421 (mt) cc_final: 0.8042 (mt) REVERT: F 679 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8020 (ttp80) REVERT: F 680 GLN cc_start: 0.7977 (tm130) cc_final: 0.7500 (tm130) REVERT: F 693 GLU cc_start: 0.7491 (tp30) cc_final: 0.7010 (tp30) REVERT: F 696 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7435 (mp0) outliers start: 87 outliers final: 46 residues processed: 537 average time/residue: 1.5190 time to fit residues: 886.0528 Evaluate side-chains 536 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 474 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 647 GLN Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 505 GLU Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 633 GLU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 705 LEU Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 578 LEU Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 647 GLN Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 679 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 64 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 185 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 172 optimal weight: 0.5980 chunk 78 optimal weight: 0.0020 chunk 2 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 512 ASN A 658 GLN B 178 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 554 ASN B 658 GLN ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 ASN C 609 GLN D 545 GLN F 512 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122896 restraints weight = 22039.230| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.79 r_work: 0.3474 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15797 Z= 0.162 Angle : 0.603 9.820 21332 Z= 0.299 Chirality : 0.039 0.145 2383 Planarity : 0.005 0.061 2773 Dihedral : 5.285 59.747 2128 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.46 % Favored : 95.96 % Rotamer: Outliers : 5.10 % Allowed : 29.90 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.20), residues: 1907 helix: 2.00 (0.14), residues: 1442 sheet: None (None), residues: 0 loop : -1.86 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 180 HIS 0.004 0.001 HIS B 56 PHE 0.014 0.001 PHE B 221 TYR 0.021 0.001 TYR B 115 ARG 0.009 0.001 ARG D 568 Details of bonding type rmsd hydrogen bonds : bond 0.05013 ( 1014) hydrogen bonds : angle 3.60925 ( 3003) covalent geometry : bond 0.00381 (15797) covalent geometry : angle 0.60336 (21332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 489 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.5721 (mtmt) REVERT: A 487 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: A 517 ASP cc_start: 0.7788 (t0) cc_final: 0.7536 (t0) REVERT: A 520 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7328 (mp0) REVERT: A 563 TYR cc_start: 0.8685 (t80) cc_final: 0.8371 (t80) REVERT: A 581 MET cc_start: 0.8715 (mtt) cc_final: 0.8344 (mtt) REVERT: A 582 MET cc_start: 0.8729 (mtp) cc_final: 0.8465 (mtp) REVERT: A 584 GLN cc_start: 0.8346 (tp40) cc_final: 0.8115 (tp40) REVERT: A 591 LYS cc_start: 0.5585 (OUTLIER) cc_final: 0.4715 (mptt) REVERT: A 593 LEU cc_start: 0.7729 (pt) cc_final: 0.7494 (pt) REVERT: A 613 ASP cc_start: 0.8165 (m-30) cc_final: 0.7942 (m-30) REVERT: A 615 LYS cc_start: 0.8563 (ttpp) cc_final: 0.8323 (mtpp) REVERT: A 659 GLN cc_start: 0.8651 (tp40) cc_final: 0.8364 (tp40) REVERT: A 670 LEU cc_start: 0.8534 (mt) cc_final: 0.8184 (mp) REVERT: A 672 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7527 (mt-10) REVERT: A 675 LEU cc_start: 0.8640 (tp) cc_final: 0.8405 (tm) REVERT: B 75 GLN cc_start: 0.8274 (tp40) cc_final: 0.8061 (tp-100) REVERT: B 76 PHE cc_start: 0.7878 (m-10) cc_final: 0.7536 (m-10) REVERT: B 117 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.7107 (t80) REVERT: B 150 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.8117 (p) REVERT: B 290 LYS cc_start: 0.8866 (pptt) cc_final: 0.8481 (pptt) REVERT: B 470 SER cc_start: 0.8733 (t) cc_final: 0.8393 (m) REVERT: B 591 LYS cc_start: 0.6141 (OUTLIER) cc_final: 0.5859 (mttm) REVERT: B 612 ASP cc_start: 0.7969 (m-30) cc_final: 0.7471 (p0) REVERT: B 675 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8371 (mt) REVERT: B 696 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6843 (pp20) REVERT: C 428 ASP cc_start: 0.7414 (t0) cc_final: 0.7099 (t0) REVERT: C 483 ASP cc_start: 0.7625 (m-30) cc_final: 0.7288 (m-30) REVERT: C 487 ASP cc_start: 0.7669 (t70) cc_final: 0.7190 (t70) REVERT: C 493 ARG cc_start: 0.6518 (mtt180) cc_final: 0.6262 (mtt180) REVERT: C 505 GLU cc_start: 0.8153 (mp0) cc_final: 0.7817 (mp0) REVERT: C 576 ARG cc_start: 0.8352 (ttp80) cc_final: 0.8095 (mtm-85) REVERT: C 672 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7644 (mp0) REVERT: C 685 GLU cc_start: 0.7826 (mp0) cc_final: 0.7486 (mp0) REVERT: C 688 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: D 483 ASP cc_start: 0.7622 (m-30) cc_final: 0.7348 (m-30) REVERT: D 519 MET cc_start: 0.8270 (tpp) cc_final: 0.7847 (tpt) REVERT: D 568 ARG cc_start: 0.7886 (ttm-80) cc_final: 0.7527 (ttp-110) REVERT: D 577 LEU cc_start: 0.8473 (tt) cc_final: 0.8170 (tp) REVERT: D 582 MET cc_start: 0.8584 (mtm) cc_final: 0.8356 (mtp) REVERT: D 611 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8348 (ttt180) REVERT: D 647 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7630 (mt0) REVERT: D 695 MET cc_start: 0.6924 (tpt) cc_final: 0.6652 (tpt) REVERT: E 444 LYS cc_start: 0.6074 (OUTLIER) cc_final: 0.5271 (mptt) REVERT: E 459 VAL cc_start: 0.8205 (t) cc_final: 0.7823 (p) REVERT: E 487 ASP cc_start: 0.8181 (m-30) cc_final: 0.7827 (m-30) REVERT: E 500 MET cc_start: 0.8649 (mmm) cc_final: 0.8442 (mmt) REVERT: E 527 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7811 (t70) REVERT: E 633 GLU cc_start: 0.4949 (OUTLIER) cc_final: 0.4736 (tm-30) REVERT: E 651 VAL cc_start: 0.8564 (m) cc_final: 0.8345 (t) REVERT: E 672 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7396 (mt-10) REVERT: E 685 GLU cc_start: 0.7297 (mp0) cc_final: 0.6979 (mp0) REVERT: F 432 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8461 (mm) REVERT: F 444 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.5135 (mptt) REVERT: F 448 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6852 (mm-30) REVERT: F 469 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8564 (mttp) REVERT: F 491 LEU cc_start: 0.8842 (mt) cc_final: 0.8612 (mm) REVERT: F 608 PHE cc_start: 0.8649 (m-80) cc_final: 0.8110 (m-80) REVERT: F 633 GLU cc_start: 0.5768 (OUTLIER) cc_final: 0.5349 (tm-30) REVERT: F 666 LEU cc_start: 0.8471 (mt) cc_final: 0.8187 (mt) REVERT: F 679 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8005 (ttp80) REVERT: F 680 GLN cc_start: 0.7989 (tm130) cc_final: 0.7468 (tm130) REVERT: F 693 GLU cc_start: 0.7479 (tp30) cc_final: 0.6986 (tp30) REVERT: F 696 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7487 (mp0) outliers start: 88 outliers final: 46 residues processed: 541 average time/residue: 1.4600 time to fit residues: 861.0630 Evaluate side-chains 543 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 478 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 647 GLN Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 505 GLU Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 633 GLU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 697 LYS Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 578 LEU Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 647 GLN Chi-restraints excluded: chain F residue 667 ASP Chi-restraints excluded: chain F residue 670 LEU Chi-restraints excluded: chain F residue 679 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 40 optimal weight: 0.2980 chunk 182 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 19 optimal weight: 0.0070 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 140 optimal weight: 0.0370 chunk 131 optimal weight: 0.6980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 512 ASN A 658 GLN B 307 ASN B 463 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 554 ASN ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 ASN C 609 GLN D 545 GLN F 512 ASN F 569 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.143764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124261 restraints weight = 22315.900| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.82 r_work: 0.3488 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15797 Z= 0.130 Angle : 0.611 13.882 21332 Z= 0.300 Chirality : 0.037 0.141 2383 Planarity : 0.005 0.062 2773 Dihedral : 5.192 59.599 2126 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.36 % Favored : 96.07 % Rotamer: Outliers : 4.69 % Allowed : 30.42 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.20), residues: 1907 helix: 2.07 (0.14), residues: 1462 sheet: None (None), residues: 0 loop : -1.85 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 180 HIS 0.003 0.001 HIS B 56 PHE 0.012 0.001 PHE B 221 TYR 0.022 0.001 TYR B 115 ARG 0.008 0.001 ARG E 611 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 1014) hydrogen bonds : angle 3.47757 ( 3003) covalent geometry : bond 0.00299 (15797) covalent geometry : angle 0.61132 (21332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 495 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6646 (OUTLIER) cc_final: 0.5691 (mtmt) REVERT: A 487 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: A 517 ASP cc_start: 0.7842 (t0) cc_final: 0.7529 (t0) REVERT: A 520 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7407 (mp0) REVERT: A 563 TYR cc_start: 0.8671 (t80) cc_final: 0.8406 (t80) REVERT: A 581 MET cc_start: 0.8669 (mtt) cc_final: 0.8306 (mtt) REVERT: A 582 MET cc_start: 0.8733 (mtp) cc_final: 0.8380 (mtp) REVERT: A 584 GLN cc_start: 0.8329 (tp40) cc_final: 0.8114 (tp40) REVERT: A 591 LYS cc_start: 0.5456 (OUTLIER) cc_final: 0.4655 (mptt) REVERT: A 593 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7517 (pt) REVERT: A 613 ASP cc_start: 0.8126 (m-30) cc_final: 0.7896 (m-30) REVERT: A 659 GLN cc_start: 0.8651 (tp40) cc_final: 0.8350 (tp40) REVERT: A 670 LEU cc_start: 0.8502 (mt) cc_final: 0.8180 (mp) REVERT: A 672 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7512 (mt-10) REVERT: A 716 VAL cc_start: 0.8109 (m) cc_final: 0.7834 (t) REVERT: B 74 GLU cc_start: 0.7445 (pm20) cc_final: 0.7240 (pm20) REVERT: B 75 GLN cc_start: 0.8229 (tp40) cc_final: 0.7977 (tp-100) REVERT: B 76 PHE cc_start: 0.7889 (m-10) cc_final: 0.7511 (m-10) REVERT: B 117 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6965 (t80) REVERT: B 150 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.8073 (p) REVERT: B 290 LYS cc_start: 0.8824 (pptt) cc_final: 0.8516 (pptt) REVERT: B 470 SER cc_start: 0.8698 (t) cc_final: 0.8359 (m) REVERT: B 483 ASP cc_start: 0.7577 (m-30) cc_final: 0.7120 (t0) REVERT: B 591 LYS cc_start: 0.6097 (OUTLIER) cc_final: 0.5783 (mttm) REVERT: B 675 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8380 (mt) REVERT: B 696 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6834 (pp20) REVERT: C 428 ASP cc_start: 0.7388 (t0) cc_final: 0.7073 (t0) REVERT: C 483 ASP cc_start: 0.7621 (m-30) cc_final: 0.7273 (m-30) REVERT: C 487 ASP cc_start: 0.7635 (t70) cc_final: 0.7149 (t70) REVERT: C 493 ARG cc_start: 0.6347 (mtt180) cc_final: 0.6096 (mtt180) REVERT: C 505 GLU cc_start: 0.8097 (mp0) cc_final: 0.7792 (mp0) REVERT: C 515 LEU cc_start: 0.8523 (mp) cc_final: 0.8277 (mm) REVERT: C 576 ARG cc_start: 0.8266 (ttp80) cc_final: 0.8002 (mtm-85) REVERT: C 672 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7685 (mp0) REVERT: C 685 GLU cc_start: 0.7827 (mp0) cc_final: 0.7489 (mp0) REVERT: C 688 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: D 432 LEU cc_start: 0.8582 (mt) cc_final: 0.8364 (mp) REVERT: D 483 ASP cc_start: 0.7619 (m-30) cc_final: 0.7357 (m-30) REVERT: D 519 MET cc_start: 0.8207 (tpp) cc_final: 0.7823 (tpt) REVERT: D 554 ASN cc_start: 0.8515 (m-40) cc_final: 0.8276 (m-40) REVERT: D 568 ARG cc_start: 0.7842 (ttm-80) cc_final: 0.7574 (ttp-110) REVERT: D 577 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8139 (tp) REVERT: D 582 MET cc_start: 0.8552 (mtm) cc_final: 0.8339 (mtp) REVERT: D 608 PHE cc_start: 0.8543 (m-80) cc_final: 0.8256 (m-80) REVERT: D 611 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8366 (ttt180) REVERT: D 647 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: D 695 MET cc_start: 0.6890 (tpt) cc_final: 0.6619 (tpt) REVERT: E 444 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5171 (mptt) REVERT: E 459 VAL cc_start: 0.8182 (t) cc_final: 0.7803 (p) REVERT: E 487 ASP cc_start: 0.8164 (m-30) cc_final: 0.7664 (m-30) REVERT: E 500 MET cc_start: 0.8648 (mmm) cc_final: 0.8417 (mmt) REVERT: E 527 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7794 (t70) REVERT: E 651 VAL cc_start: 0.8538 (m) cc_final: 0.8320 (t) REVERT: E 672 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7414 (mt-10) REVERT: E 705 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7920 (mp) REVERT: F 432 LEU cc_start: 0.8676 (mp) cc_final: 0.8465 (mm) REVERT: F 444 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.5074 (mptt) REVERT: F 448 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6859 (mm-30) REVERT: F 491 LEU cc_start: 0.8823 (mt) cc_final: 0.8601 (mm) REVERT: F 608 PHE cc_start: 0.8626 (m-80) cc_final: 0.8058 (m-80) REVERT: F 633 GLU cc_start: 0.5804 (OUTLIER) cc_final: 0.5386 (tm-30) REVERT: F 666 LEU cc_start: 0.8446 (mt) cc_final: 0.8126 (mt) REVERT: F 679 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8000 (ttp80) REVERT: F 693 GLU cc_start: 0.7481 (tp30) cc_final: 0.6983 (tp30) REVERT: F 696 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7507 (mp0) outliers start: 81 outliers final: 38 residues processed: 537 average time/residue: 1.5230 time to fit residues: 891.5991 Evaluate side-chains 542 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 485 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 647 GLN Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 505 GLU Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 697 LYS Chi-restraints excluded: chain E residue 705 LEU Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 647 GLN Chi-restraints excluded: chain F residue 679 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 101 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 130 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 158 optimal weight: 0.4980 chunk 96 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 512 ASN A 658 GLN B 463 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 554 ASN ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 ASN C 609 GLN D 545 GLN E 477 ASN F 512 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.142794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.123298 restraints weight = 22008.455| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.77 r_work: 0.3478 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15797 Z= 0.164 Angle : 0.638 17.159 21332 Z= 0.313 Chirality : 0.039 0.150 2383 Planarity : 0.005 0.062 2773 Dihedral : 4.974 59.931 2123 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.25 % Favored : 96.17 % Rotamer: Outliers : 4.35 % Allowed : 30.76 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.20), residues: 1907 helix: 2.07 (0.14), residues: 1451 sheet: None (None), residues: 0 loop : -1.81 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 180 HIS 0.004 0.001 HIS B 56 PHE 0.013 0.001 PHE B 221 TYR 0.026 0.002 TYR A 614 ARG 0.008 0.001 ARG E 611 Details of bonding type rmsd hydrogen bonds : bond 0.04858 ( 1014) hydrogen bonds : angle 3.52318 ( 3003) covalent geometry : bond 0.00389 (15797) covalent geometry : angle 0.63787 (21332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 489 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.5697 (mtmt) REVERT: A 452 ASP cc_start: 0.7497 (m-30) cc_final: 0.7085 (m-30) REVERT: A 487 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: A 517 ASP cc_start: 0.7809 (t0) cc_final: 0.7539 (t0) REVERT: A 520 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7399 (mp0) REVERT: A 563 TYR cc_start: 0.8686 (t80) cc_final: 0.8406 (t80) REVERT: A 581 MET cc_start: 0.8702 (mtt) cc_final: 0.8356 (mtt) REVERT: A 584 GLN cc_start: 0.8367 (tp40) cc_final: 0.8164 (tp40) REVERT: A 591 LYS cc_start: 0.5630 (OUTLIER) cc_final: 0.4807 (mptt) REVERT: A 593 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7520 (pt) REVERT: A 613 ASP cc_start: 0.8130 (m-30) cc_final: 0.7904 (m-30) REVERT: A 615 LYS cc_start: 0.8520 (ttpp) cc_final: 0.8288 (mtpp) REVERT: A 659 GLN cc_start: 0.8649 (tp40) cc_final: 0.8349 (tp40) REVERT: A 672 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7528 (mt-10) REVERT: A 716 VAL cc_start: 0.8172 (m) cc_final: 0.7903 (t) REVERT: B 75 GLN cc_start: 0.8194 (tp40) cc_final: 0.7969 (tp-100) REVERT: B 76 PHE cc_start: 0.7845 (m-10) cc_final: 0.7474 (m-10) REVERT: B 117 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.6989 (t80) REVERT: B 149 ARG cc_start: 0.6677 (tmm-80) cc_final: 0.6449 (tmm-80) REVERT: B 290 LYS cc_start: 0.8843 (pptt) cc_final: 0.8536 (pptt) REVERT: B 303 GLN cc_start: 0.8088 (pp30) cc_final: 0.7608 (pp30) REVERT: B 332 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7214 (mt0) REVERT: B 470 SER cc_start: 0.8720 (t) cc_final: 0.8366 (m) REVERT: B 483 ASP cc_start: 0.7641 (m-30) cc_final: 0.7185 (t0) REVERT: B 591 LYS cc_start: 0.6069 (OUTLIER) cc_final: 0.5785 (mttm) REVERT: B 666 LEU cc_start: 0.8039 (mt) cc_final: 0.7794 (mt) REVERT: B 675 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8326 (mt) REVERT: B 696 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6801 (pp20) REVERT: C 428 ASP cc_start: 0.7448 (t0) cc_final: 0.7126 (t0) REVERT: C 436 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7629 (mt-10) REVERT: C 483 ASP cc_start: 0.7629 (m-30) cc_final: 0.7259 (m-30) REVERT: C 487 ASP cc_start: 0.7669 (t70) cc_final: 0.7187 (t70) REVERT: C 493 ARG cc_start: 0.6456 (mtt180) cc_final: 0.6202 (mtt180) REVERT: C 505 GLU cc_start: 0.8081 (mp0) cc_final: 0.7781 (mp0) REVERT: C 515 LEU cc_start: 0.8569 (mp) cc_final: 0.8318 (mm) REVERT: C 548 ASP cc_start: 0.8360 (t70) cc_final: 0.8159 (t0) REVERT: C 576 ARG cc_start: 0.8334 (ttp80) cc_final: 0.8072 (mtm-85) REVERT: C 672 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7673 (mp0) REVERT: C 685 GLU cc_start: 0.7830 (mp0) cc_final: 0.7489 (mp0) REVERT: C 688 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: D 432 LEU cc_start: 0.8603 (mt) cc_final: 0.8368 (mp) REVERT: D 483 ASP cc_start: 0.7620 (m-30) cc_final: 0.7353 (m-30) REVERT: D 519 MET cc_start: 0.8258 (tpp) cc_final: 0.7798 (tpt) REVERT: D 568 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.7304 (ttp-170) REVERT: D 577 LEU cc_start: 0.8488 (tt) cc_final: 0.8188 (tp) REVERT: D 606 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: D 611 ARG cc_start: 0.8701 (ttp80) cc_final: 0.8389 (ttt180) REVERT: D 647 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7587 (mt0) REVERT: D 675 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8618 (tt) REVERT: D 695 MET cc_start: 0.6902 (tpt) cc_final: 0.6634 (tpt) REVERT: E 444 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5204 (mptt) REVERT: E 459 VAL cc_start: 0.8198 (t) cc_final: 0.7816 (p) REVERT: E 487 ASP cc_start: 0.8144 (m-30) cc_final: 0.7686 (m-30) REVERT: E 500 MET cc_start: 0.8629 (mmm) cc_final: 0.8403 (mmt) REVERT: E 527 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7805 (t70) REVERT: E 537 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7634 (mp0) REVERT: E 651 VAL cc_start: 0.8556 (m) cc_final: 0.8343 (t) REVERT: E 672 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7417 (mt-10) REVERT: E 685 GLU cc_start: 0.7269 (mp0) cc_final: 0.6963 (mp0) REVERT: F 432 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8502 (mm) REVERT: F 444 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.5005 (mptt) REVERT: F 448 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6851 (mm-30) REVERT: F 491 LEU cc_start: 0.8832 (mt) cc_final: 0.8606 (mm) REVERT: F 608 PHE cc_start: 0.8631 (m-80) cc_final: 0.8064 (m-80) REVERT: F 633 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.5376 (tm-30) REVERT: F 666 LEU cc_start: 0.8457 (mt) cc_final: 0.8128 (mt) REVERT: F 679 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7983 (ttp80) REVERT: F 693 GLU cc_start: 0.7488 (tp30) cc_final: 0.7004 (tp30) REVERT: F 696 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7535 (mp0) outliers start: 75 outliers final: 40 residues processed: 531 average time/residue: 1.8687 time to fit residues: 1081.8352 Evaluate side-chains 537 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 477 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 606 GLU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 647 GLN Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 505 GLU Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 705 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 489 SER Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 647 GLN Chi-restraints excluded: chain F residue 679 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 87 optimal weight: 0.9980 chunk 107 optimal weight: 0.0470 chunk 170 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 94 optimal weight: 0.0770 chunk 100 optimal weight: 1.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 512 ASN A 524 GLN A 658 GLN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 554 ASN ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 ASN C 609 GLN D 545 GLN F 512 ASN F 569 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.142931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123386 restraints weight = 22107.489| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.81 r_work: 0.3482 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15797 Z= 0.159 Angle : 0.654 17.936 21332 Z= 0.319 Chirality : 0.039 0.151 2383 Planarity : 0.005 0.062 2773 Dihedral : 4.964 59.590 2123 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.09 % Favored : 96.33 % Rotamer: Outliers : 4.00 % Allowed : 31.34 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.20), residues: 1907 helix: 2.08 (0.14), residues: 1450 sheet: None (None), residues: 0 loop : -1.81 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 180 HIS 0.004 0.001 HIS B 56 PHE 0.012 0.001 PHE B 221 TYR 0.023 0.001 TYR A 614 ARG 0.013 0.001 ARG B 661 Details of bonding type rmsd hydrogen bonds : bond 0.04831 ( 1014) hydrogen bonds : angle 3.53035 ( 3003) covalent geometry : bond 0.00376 (15797) covalent geometry : angle 0.65424 (21332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 484 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6629 (OUTLIER) cc_final: 0.5685 (mtmt) REVERT: A 452 ASP cc_start: 0.7541 (m-30) cc_final: 0.7095 (m-30) REVERT: A 517 ASP cc_start: 0.7752 (t0) cc_final: 0.7469 (t0) REVERT: A 520 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7352 (mp0) REVERT: A 563 TYR cc_start: 0.8657 (t80) cc_final: 0.8380 (t80) REVERT: A 581 MET cc_start: 0.8624 (mtt) cc_final: 0.8274 (mtt) REVERT: A 582 MET cc_start: 0.8705 (mtp) cc_final: 0.8428 (mtm) REVERT: A 584 GLN cc_start: 0.8334 (tp40) cc_final: 0.8088 (tp40) REVERT: A 591 LYS cc_start: 0.5666 (OUTLIER) cc_final: 0.4830 (mptt) REVERT: A 593 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7522 (pt) REVERT: A 613 ASP cc_start: 0.8070 (m-30) cc_final: 0.7823 (m-30) REVERT: A 615 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8257 (mtpp) REVERT: A 659 GLN cc_start: 0.8603 (tp40) cc_final: 0.8302 (tp40) REVERT: A 672 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7486 (mt-10) REVERT: A 716 VAL cc_start: 0.8184 (m) cc_final: 0.7897 (t) REVERT: B 75 GLN cc_start: 0.8248 (tp40) cc_final: 0.8025 (tp-100) REVERT: B 76 PHE cc_start: 0.7934 (m-10) cc_final: 0.7595 (m-10) REVERT: B 117 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7110 (t80) REVERT: B 149 ARG cc_start: 0.6724 (tmm-80) cc_final: 0.6447 (tmm-80) REVERT: B 290 LYS cc_start: 0.8866 (pptt) cc_final: 0.8529 (pptt) REVERT: B 303 GLN cc_start: 0.8162 (pp30) cc_final: 0.7725 (pp30) REVERT: B 332 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7233 (mt0) REVERT: B 444 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.5213 (mtmt) REVERT: B 470 SER cc_start: 0.8693 (t) cc_final: 0.8332 (m) REVERT: B 483 ASP cc_start: 0.7585 (m-30) cc_final: 0.7106 (t0) REVERT: B 591 LYS cc_start: 0.6146 (OUTLIER) cc_final: 0.5830 (mttm) REVERT: B 612 ASP cc_start: 0.8003 (m-30) cc_final: 0.7438 (p0) REVERT: B 666 LEU cc_start: 0.7974 (mt) cc_final: 0.7677 (mt) REVERT: B 675 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8273 (mt) REVERT: B 696 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6842 (pp20) REVERT: C 428 ASP cc_start: 0.7479 (t0) cc_final: 0.7134 (t0) REVERT: C 436 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7603 (mt-10) REVERT: C 483 ASP cc_start: 0.7602 (m-30) cc_final: 0.7236 (m-30) REVERT: C 487 ASP cc_start: 0.7630 (t70) cc_final: 0.7138 (t70) REVERT: C 493 ARG cc_start: 0.6446 (mtt180) cc_final: 0.6199 (mtt180) REVERT: C 505 GLU cc_start: 0.8066 (mp0) cc_final: 0.7755 (mp0) REVERT: C 515 LEU cc_start: 0.8504 (mp) cc_final: 0.8229 (mm) REVERT: C 548 ASP cc_start: 0.8340 (t70) cc_final: 0.8138 (t0) REVERT: C 576 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7975 (mtm-85) REVERT: C 672 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7643 (mt-10) REVERT: C 685 GLU cc_start: 0.7868 (mp0) cc_final: 0.7489 (mp0) REVERT: C 688 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: D 432 LEU cc_start: 0.8576 (mt) cc_final: 0.8343 (mp) REVERT: D 483 ASP cc_start: 0.7596 (m-30) cc_final: 0.7322 (m-30) REVERT: D 519 MET cc_start: 0.8252 (tpp) cc_final: 0.8033 (tpt) REVERT: D 568 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7315 (ttp-170) REVERT: D 577 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8161 (tp) REVERT: D 606 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: D 611 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8344 (ttt180) REVERT: D 647 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: D 675 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8577 (tt) REVERT: D 695 MET cc_start: 0.6913 (tpt) cc_final: 0.6631 (tpt) REVERT: E 444 LYS cc_start: 0.5916 (OUTLIER) cc_final: 0.5103 (mptt) REVERT: E 448 GLU cc_start: 0.7645 (mp0) cc_final: 0.7136 (mp0) REVERT: E 459 VAL cc_start: 0.8187 (t) cc_final: 0.7793 (p) REVERT: E 487 ASP cc_start: 0.8125 (m-30) cc_final: 0.7677 (m-30) REVERT: E 500 MET cc_start: 0.8645 (mmm) cc_final: 0.8409 (mmt) REVERT: E 527 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7867 (t70) REVERT: E 537 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7681 (mp0) REVERT: E 651 VAL cc_start: 0.8517 (m) cc_final: 0.8300 (t) REVERT: E 672 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7382 (mt-10) REVERT: E 685 GLU cc_start: 0.7304 (mp0) cc_final: 0.6985 (mp0) REVERT: F 432 LEU cc_start: 0.8710 (mp) cc_final: 0.8478 (mm) REVERT: F 444 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.4997 (mptt) REVERT: F 448 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6815 (mm-30) REVERT: F 491 LEU cc_start: 0.8808 (mt) cc_final: 0.8569 (mm) REVERT: F 608 PHE cc_start: 0.8603 (m-80) cc_final: 0.8021 (m-80) REVERT: F 633 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5394 (tm-30) REVERT: F 666 LEU cc_start: 0.8405 (mt) cc_final: 0.8092 (mt) REVERT: F 679 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7970 (ttp80) REVERT: F 680 GLN cc_start: 0.8037 (tm130) cc_final: 0.7463 (tm130) REVERT: F 693 GLU cc_start: 0.7466 (tp30) cc_final: 0.6944 (tp30) REVERT: F 696 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7494 (mp0) outliers start: 69 outliers final: 41 residues processed: 521 average time/residue: 1.6005 time to fit residues: 905.6853 Evaluate side-chains 531 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 470 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 606 GLU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 647 GLN Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 505 GLU Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 697 LYS Chi-restraints excluded: chain E residue 705 LEU Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 489 SER Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 647 GLN Chi-restraints excluded: chain F residue 679 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 186 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 chunk 122 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.0470 chunk 118 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 512 ASN A 524 GLN A 658 GLN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 554 ASN ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 ASN C 609 GLN D 545 GLN F 512 ASN F 569 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.142946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123421 restraints weight = 22165.504| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.81 r_work: 0.3481 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15797 Z= 0.158 Angle : 0.658 19.165 21332 Z= 0.322 Chirality : 0.039 0.163 2383 Planarity : 0.005 0.061 2773 Dihedral : 4.931 59.512 2121 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.09 % Favored : 96.33 % Rotamer: Outliers : 3.71 % Allowed : 31.98 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.20), residues: 1907 helix: 2.09 (0.14), residues: 1452 sheet: None (None), residues: 0 loop : -1.77 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 180 HIS 0.004 0.001 HIS B 56 PHE 0.012 0.001 PHE B 255 TYR 0.023 0.002 TYR B 115 ARG 0.011 0.001 ARG B 661 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 1014) hydrogen bonds : angle 3.52522 ( 3003) covalent geometry : bond 0.00374 (15797) covalent geometry : angle 0.65766 (21332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 486 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.5626 (mtmt) REVERT: A 452 ASP cc_start: 0.7514 (m-30) cc_final: 0.7070 (m-30) REVERT: A 517 ASP cc_start: 0.7746 (t0) cc_final: 0.7464 (t0) REVERT: A 520 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7345 (mp0) REVERT: A 563 TYR cc_start: 0.8667 (t80) cc_final: 0.8394 (t80) REVERT: A 581 MET cc_start: 0.8628 (mtt) cc_final: 0.8282 (mtt) REVERT: A 582 MET cc_start: 0.8690 (mtp) cc_final: 0.8409 (mtm) REVERT: A 584 GLN cc_start: 0.8351 (tp40) cc_final: 0.8098 (tp40) REVERT: A 591 LYS cc_start: 0.5662 (OUTLIER) cc_final: 0.4789 (mptt) REVERT: A 593 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7532 (pt) REVERT: A 613 ASP cc_start: 0.8038 (m-30) cc_final: 0.7804 (m-30) REVERT: A 615 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8249 (mtpp) REVERT: A 659 GLN cc_start: 0.8606 (tp40) cc_final: 0.8321 (tp40) REVERT: A 662 SER cc_start: 0.8211 (t) cc_final: 0.7812 (m) REVERT: A 672 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7464 (mt-10) REVERT: A 716 VAL cc_start: 0.8186 (m) cc_final: 0.7902 (t) REVERT: B 75 GLN cc_start: 0.8237 (tp40) cc_final: 0.7964 (tp-100) REVERT: B 76 PHE cc_start: 0.7876 (m-10) cc_final: 0.7518 (m-10) REVERT: B 117 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7118 (t80) REVERT: B 256 ASP cc_start: 0.6423 (p0) cc_final: 0.5318 (p0) REVERT: B 290 LYS cc_start: 0.8878 (pptt) cc_final: 0.8541 (pptt) REVERT: B 303 GLN cc_start: 0.8151 (pp30) cc_final: 0.7708 (pp30) REVERT: B 332 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7231 (mt0) REVERT: B 470 SER cc_start: 0.8697 (t) cc_final: 0.8335 (m) REVERT: B 483 ASP cc_start: 0.7580 (m-30) cc_final: 0.7103 (t0) REVERT: B 591 LYS cc_start: 0.6135 (OUTLIER) cc_final: 0.5825 (mttm) REVERT: B 666 LEU cc_start: 0.7938 (mt) cc_final: 0.7511 (mt) REVERT: B 671 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8339 (mttm) REVERT: B 696 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6816 (pp20) REVERT: C 428 ASP cc_start: 0.7472 (t0) cc_final: 0.7143 (t0) REVERT: C 483 ASP cc_start: 0.7621 (m-30) cc_final: 0.7255 (m-30) REVERT: C 487 ASP cc_start: 0.7636 (t70) cc_final: 0.7149 (t70) REVERT: C 493 ARG cc_start: 0.6458 (mtt180) cc_final: 0.6211 (mtt180) REVERT: C 505 GLU cc_start: 0.8062 (mp0) cc_final: 0.7739 (mp0) REVERT: C 515 LEU cc_start: 0.8496 (mp) cc_final: 0.8221 (mm) REVERT: C 548 ASP cc_start: 0.8347 (t70) cc_final: 0.8145 (t0) REVERT: C 576 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7973 (mtm-85) REVERT: C 672 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7623 (mt-10) REVERT: C 685 GLU cc_start: 0.7875 (mp0) cc_final: 0.7497 (mp0) REVERT: C 688 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: D 432 LEU cc_start: 0.8577 (mt) cc_final: 0.8348 (mp) REVERT: D 483 ASP cc_start: 0.7602 (m-30) cc_final: 0.7334 (m-30) REVERT: D 568 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7323 (ttp-170) REVERT: D 577 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8143 (tp) REVERT: D 606 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: D 611 ARG cc_start: 0.8681 (ttp80) cc_final: 0.8334 (ttt180) REVERT: D 647 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: D 675 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8570 (tt) REVERT: D 695 MET cc_start: 0.7005 (tpt) cc_final: 0.6725 (tpt) REVERT: E 444 LYS cc_start: 0.5915 (OUTLIER) cc_final: 0.5088 (mptt) REVERT: E 448 GLU cc_start: 0.7641 (mp0) cc_final: 0.7132 (mp0) REVERT: E 459 VAL cc_start: 0.8179 (t) cc_final: 0.7789 (p) REVERT: E 500 MET cc_start: 0.8634 (mmm) cc_final: 0.8395 (mmt) REVERT: E 527 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7868 (t70) REVERT: E 537 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7679 (mp0) REVERT: E 651 VAL cc_start: 0.8530 (m) cc_final: 0.8310 (t) REVERT: E 672 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7379 (mt-10) REVERT: E 685 GLU cc_start: 0.7310 (mp0) cc_final: 0.6988 (mp0) REVERT: F 444 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.5013 (mptt) REVERT: F 448 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6799 (mm-30) REVERT: F 491 LEU cc_start: 0.8811 (mt) cc_final: 0.8569 (mm) REVERT: F 608 PHE cc_start: 0.8605 (m-80) cc_final: 0.8023 (m-80) REVERT: F 633 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.5405 (tm-30) REVERT: F 666 LEU cc_start: 0.8399 (mt) cc_final: 0.8058 (mt) REVERT: F 679 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7971 (ttp80) REVERT: F 680 GLN cc_start: 0.8055 (tm130) cc_final: 0.7480 (tm130) REVERT: F 693 GLU cc_start: 0.7475 (tp30) cc_final: 0.6953 (tp30) REVERT: F 696 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7520 (mp0) outliers start: 64 outliers final: 40 residues processed: 520 average time/residue: 1.8159 time to fit residues: 1023.5936 Evaluate side-chains 533 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 475 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 180 TRP Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 606 GLU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 647 GLN Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 505 GLU Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 697 LYS Chi-restraints excluded: chain E residue 705 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 647 GLN Chi-restraints excluded: chain F residue 679 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 121 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 138 optimal weight: 0.0030 chunk 28 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 176 optimal weight: 0.9980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 512 ASN A 524 GLN A 658 GLN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 554 ASN ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 ASN C 609 GLN D 545 GLN F 512 ASN F 569 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.142708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123417 restraints weight = 22129.629| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.77 r_work: 0.3486 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15797 Z= 0.166 Angle : 0.656 14.606 21332 Z= 0.322 Chirality : 0.039 0.152 2383 Planarity : 0.005 0.062 2773 Dihedral : 4.925 58.546 2121 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.04 % Favored : 96.38 % Rotamer: Outliers : 3.59 % Allowed : 32.10 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.20), residues: 1907 helix: 2.08 (0.14), residues: 1451 sheet: None (None), residues: 0 loop : -1.73 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 180 HIS 0.004 0.001 HIS B 56 PHE 0.014 0.001 PHE B 255 TYR 0.024 0.002 TYR B 115 ARG 0.011 0.001 ARG D 529 Details of bonding type rmsd hydrogen bonds : bond 0.04892 ( 1014) hydrogen bonds : angle 3.53537 ( 3003) covalent geometry : bond 0.00392 (15797) covalent geometry : angle 0.65592 (21332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17110.83 seconds wall clock time: 298 minutes 14.48 seconds (17894.48 seconds total)