Starting phenix.real_space_refine on Thu Sep 18 08:52:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2k_47455/09_2025/9e2k_47455.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2k_47455/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9e2k_47455/09_2025/9e2k_47455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2k_47455/09_2025/9e2k_47455.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e2k_47455/09_2025/9e2k_47455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2k_47455/09_2025/9e2k_47455.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.58, per 1000 atoms: 0.30 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: 1.49 Conformation dependent library (CDL) restraints added in 754.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.54 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: 2.96 Time building geometry restraints manager: 1.93 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: 5.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.510 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:7.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.910 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (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 ARG 0.015 0.001 ARG F 661 TYR 0.019 0.002 TYR A 686 PHE 0.014 0.001 PHE F 607 TRP 0.021 0.002 TRP B 89 HIS 0.006 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00408 (15797) covalent geometry : angle 0.76971 (21332) hydrogen bonds : bond 0.18567 ( 1014) hydrogen bonds : angle 5.72755 ( 3003) *********************** 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 : 0.659 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: 0.7650 time to fit residues: 442.3302 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 : 0.668 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.143577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124065 restraints weight = 22099.319| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.81 r_work: 0.3496 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15797 Z= 0.155 Angle : 0.610 8.015 21332 Z= 0.311 Chirality : 0.038 0.144 2383 Planarity : 0.005 0.064 2773 Dihedral : 6.186 59.817 2158 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.63 % Allowed : 3.57 % Favored : 95.80 % Rotamer: Outliers : 5.91 % Allowed : 28.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.20), residues: 1907 helix: 1.83 (0.14), residues: 1441 sheet: None (None), residues: 0 loop : -2.09 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 611 TYR 0.017 0.002 TYR B 115 PHE 0.011 0.001 PHE B 221 TRP 0.010 0.001 TRP B 73 HIS 0.007 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00353 (15797) covalent geometry : angle 0.60972 (21332) hydrogen bonds : bond 0.05248 ( 1014) hydrogen bonds : angle 3.94482 ( 3003) *********************** 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 600 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 498 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 436 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7565 (mt-10) REVERT: A 444 LYS cc_start: 0.6634 (OUTLIER) cc_final: 0.5668 (mtmt) REVERT: A 487 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7485 (m-30) REVERT: A 520 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7332 (mp0) REVERT: A 563 TYR cc_start: 0.8641 (t80) cc_final: 0.8407 (t80) REVERT: A 581 MET cc_start: 0.8664 (mtt) cc_final: 0.8374 (mtt) REVERT: A 582 MET cc_start: 0.8740 (mtp) cc_final: 0.8516 (mtp) REVERT: A 591 LYS cc_start: 0.5368 (OUTLIER) cc_final: 0.4740 (mptt) REVERT: A 593 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7273 (pt) REVERT: A 670 LEU cc_start: 0.8453 (mt) cc_final: 0.8182 (mp) REVERT: A 672 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 675 LEU cc_start: 0.8565 (tp) cc_final: 0.8328 (tm) REVERT: B 63 ASN cc_start: 0.7206 (OUTLIER) cc_final: 0.6913 (m110) REVERT: B 75 GLN cc_start: 0.8307 (tp40) cc_final: 0.8063 (mm-40) REVERT: B 76 PHE cc_start: 0.8051 (m-10) cc_final: 0.7721 (m-10) REVERT: B 89 TRP cc_start: 0.7615 (m100) cc_final: 0.7218 (m100) REVERT: B 106 LEU cc_start: 0.8174 (pt) cc_final: 0.7866 (pp) REVERT: B 171 PRO cc_start: 0.7462 (Cg_endo) cc_final: 0.7197 (Cg_exo) REVERT: B 218 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7097 (mp) REVERT: B 470 SER cc_start: 0.8738 (t) cc_final: 0.8375 (m) REVERT: B 489 SER cc_start: 0.8604 (t) cc_final: 0.8303 (p) REVERT: B 493 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6453 (mmp-170) REVERT: B 536 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6642 (tm-30) REVERT: B 612 ASP cc_start: 0.7961 (m-30) cc_final: 0.7471 (p0) REVERT: B 696 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6972 (pp20) REVERT: C 428 ASP cc_start: 0.7009 (t0) cc_final: 0.6770 (t0) REVERT: C 483 ASP cc_start: 0.7551 (m-30) cc_final: 0.7301 (m-30) REVERT: C 487 ASP cc_start: 0.7504 (t70) cc_final: 0.7005 (t70) REVERT: C 576 ARG cc_start: 0.8357 (ttp80) cc_final: 0.8060 (mtm-85) REVERT: C 672 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7561 (mp0) REVERT: C 685 GLU cc_start: 0.7767 (mp0) cc_final: 0.7310 (mp0) REVERT: C 688 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: D 483 ASP cc_start: 0.7684 (m-30) cc_final: 0.7392 (m-30) REVERT: D 524 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7848 (mp10) REVERT: D 577 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8117 (tp) REVERT: D 611 ARG cc_start: 0.8600 (ttp80) cc_final: 0.8296 (ttt180) REVERT: D 662 SER cc_start: 0.8298 (t) cc_final: 0.8041 (p) REVERT: D 695 MET cc_start: 0.7018 (tpt) cc_final: 0.6735 (tpt) REVERT: E 444 LYS cc_start: 0.6134 (OUTLIER) cc_final: 0.5322 (mptt) REVERT: E 459 VAL cc_start: 0.8237 (t) cc_final: 0.7838 (p) REVERT: E 487 ASP cc_start: 0.8122 (m-30) cc_final: 0.7782 (m-30) REVERT: E 505 GLU cc_start: 0.7809 (mp0) cc_final: 0.7560 (mp0) REVERT: E 527 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7819 (t70) REVERT: E 612 ASP cc_start: 0.8155 (m-30) cc_final: 0.7915 (m-30) REVERT: E 633 GLU cc_start: 0.5070 (OUTLIER) cc_final: 0.4829 (tm-30) REVERT: E 672 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7351 (mt-10) REVERT: F 432 LEU cc_start: 0.8491 (mp) cc_final: 0.8234 (mm) REVERT: F 447 ARG cc_start: 0.8398 (mpp-170) cc_final: 0.8180 (mmt-90) REVERT: F 491 LEU cc_start: 0.8854 (mt) cc_final: 0.8628 (mm) REVERT: F 516 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8048 (mm) REVERT: F 608 PHE cc_start: 0.8655 (m-80) cc_final: 0.8146 (m-80) REVERT: F 632 ASP cc_start: 0.8273 (t0) cc_final: 0.7915 (t70) REVERT: F 633 GLU cc_start: 0.5737 (OUTLIER) cc_final: 0.5339 (tm-30) REVERT: F 666 LEU cc_start: 0.8354 (mt) cc_final: 0.7904 (mt) REVERT: F 684 ILE cc_start: 0.8570 (mm) cc_final: 0.8160 (mm) REVERT: F 693 GLU cc_start: 0.7456 (tp30) cc_final: 0.6921 (tp30) REVERT: F 696 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7393 (mp0) outliers start: 102 outliers final: 29 residues processed: 564 average time/residue: 0.7546 time to fit residues: 461.6655 Evaluate side-chains 532 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 487 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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 333 VAL 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 536 GLU Chi-restraints excluded: chain B residue 588 VAL 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 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 498 THR Chi-restraints excluded: chain F residue 516 ILE Chi-restraints excluded: chain F residue 578 LEU 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 91 optimal weight: 0.1980 chunk 146 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 1 optimal weight: 0.0040 chunk 172 optimal weight: 0.9980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 GLN B 63 ASN 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 C 609 GLN D 545 GLN E 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 = 0.3875 r_free = 0.3875 target = 0.143579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124013 restraints weight = 22298.299| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.81 r_work: 0.3485 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15797 Z= 0.147 Angle : 0.590 8.258 21332 Z= 0.297 Chirality : 0.038 0.147 2383 Planarity : 0.005 0.061 2773 Dihedral : 5.451 59.431 2132 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.63 % Allowed : 3.25 % Favored : 96.12 % Rotamer: Outliers : 5.68 % Allowed : 28.62 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.20), residues: 1907 helix: 1.96 (0.14), residues: 1442 sheet: None (None), residues: 0 loop : -1.95 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 661 TYR 0.019 0.001 TYR B 115 PHE 0.012 0.001 PHE B 221 TRP 0.012 0.001 TRP B 180 HIS 0.004 0.001 HIS E 642 Details of bonding type rmsd covalent geometry : bond 0.00336 (15797) covalent geometry : angle 0.59006 (21332) hydrogen bonds : bond 0.04932 ( 1014) hydrogen bonds : angle 3.73793 ( 3003) *********************** 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 601 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 503 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7364 (pp) REVERT: A 444 LYS cc_start: 0.6635 (OUTLIER) cc_final: 0.5671 (mtmt) REVERT: A 487 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: A 520 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7273 (mp0) REVERT: A 563 TYR cc_start: 0.8660 (t80) cc_final: 0.8445 (t80) REVERT: A 581 MET cc_start: 0.8683 (mtt) cc_final: 0.8233 (mtt) REVERT: A 593 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7342 (pt) REVERT: A 659 GLN cc_start: 0.8663 (tp40) cc_final: 0.8322 (tp-100) REVERT: A 670 LEU cc_start: 0.8479 (mt) cc_final: 0.8238 (mp) REVERT: A 672 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7449 (mt-10) REVERT: B 63 ASN cc_start: 0.7256 (OUTLIER) cc_final: 0.6997 (m110) REVERT: B 75 GLN cc_start: 0.8234 (tp40) cc_final: 0.8013 (mm-40) REVERT: B 76 PHE cc_start: 0.8022 (m-10) cc_final: 0.7649 (m-10) REVERT: B 218 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7098 (mp) REVERT: B 470 SER cc_start: 0.8733 (t) cc_final: 0.8371 (m) REVERT: B 493 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6451 (mmp-170) REVERT: B 536 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6810 (tm-30) REVERT: B 612 ASP cc_start: 0.7995 (m-30) cc_final: 0.7479 (p0) REVERT: B 645 THR cc_start: 0.8356 (t) cc_final: 0.8091 (m) REVERT: B 675 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8362 (mt) REVERT: B 679 ARG cc_start: 0.8321 (ttm-80) cc_final: 0.8062 (ttm170) REVERT: B 696 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6898 (pp20) REVERT: C 428 ASP cc_start: 0.7225 (t0) cc_final: 0.6895 (t0) REVERT: C 483 ASP cc_start: 0.7543 (m-30) cc_final: 0.7261 (m-30) REVERT: C 487 ASP cc_start: 0.7646 (t70) cc_final: 0.7128 (t70) REVERT: C 517 ASP cc_start: 0.7878 (t0) cc_final: 0.7672 (t0) REVERT: C 539 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.8110 (ttm-80) REVERT: C 576 ARG cc_start: 0.8360 (ttp80) cc_final: 0.8089 (mtm-85) REVERT: C 672 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7524 (mp0) REVERT: C 685 GLU cc_start: 0.7812 (mp0) cc_final: 0.7352 (mp0) REVERT: C 688 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: D 483 ASP cc_start: 0.7652 (m-30) cc_final: 0.7372 (m-30) REVERT: D 524 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7893 (mp10) REVERT: D 529 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7657 (mmm-85) REVERT: D 568 ARG cc_start: 0.7780 (ttm-80) cc_final: 0.7400 (ttp-170) REVERT: D 577 LEU cc_start: 0.8438 (tt) cc_final: 0.8094 (tp) REVERT: D 606 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7762 (mt-10) REVERT: D 611 ARG cc_start: 0.8663 (ttp80) cc_final: 0.8315 (ttt180) REVERT: D 647 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: D 695 MET cc_start: 0.7058 (tpt) cc_final: 0.6779 (tpt) REVERT: E 444 LYS cc_start: 0.5866 (OUTLIER) cc_final: 0.5340 (mptt) REVERT: E 459 VAL cc_start: 0.8195 (t) cc_final: 0.7801 (p) REVERT: E 487 ASP cc_start: 0.8152 (m-30) cc_final: 0.7808 (m-30) REVERT: E 505 GLU cc_start: 0.7824 (mp0) cc_final: 0.7610 (mp0) REVERT: E 527 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7791 (t70) REVERT: E 612 ASP cc_start: 0.8176 (m-30) cc_final: 0.7942 (m-30) REVERT: E 633 GLU cc_start: 0.5033 (OUTLIER) cc_final: 0.4814 (tm-30) REVERT: E 651 VAL cc_start: 0.8568 (m) cc_final: 0.8345 (t) REVERT: E 672 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7321 (mt-10) REVERT: F 432 LEU cc_start: 0.8540 (mp) cc_final: 0.8334 (mm) REVERT: F 447 ARG cc_start: 0.8367 (mpp-170) cc_final: 0.8140 (mmt-90) REVERT: F 491 LEU cc_start: 0.8867 (mt) cc_final: 0.8623 (mm) REVERT: F 516 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8105 (mm) REVERT: F 608 PHE cc_start: 0.8655 (m-80) cc_final: 0.8156 (m-80) REVERT: F 633 GLU cc_start: 0.5735 (OUTLIER) cc_final: 0.5319 (tm-30) REVERT: F 666 LEU cc_start: 0.8428 (mt) cc_final: 0.8062 (mt) REVERT: F 679 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7964 (ttp80) REVERT: F 693 GLU cc_start: 0.7468 (tp30) cc_final: 0.6954 (tp30) REVERT: F 696 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7415 (mp0) outliers start: 98 outliers final: 40 residues processed: 562 average time/residue: 0.7840 time to fit residues: 476.0451 Evaluate side-chains 538 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 480 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 462 ASP Chi-restraints excluded: chain A residue 487 ASP 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 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 516 ILE Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 556 GLU 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 604 LEU Chi-restraints excluded: chain C residue 617 LEU 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 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 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 465 VAL Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 516 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 113 optimal weight: 0.0000 chunk 126 optimal weight: 0.6980 chunk 1 optimal weight: 0.0020 chunk 153 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS A 473 GLN A 512 ASN A 524 GLN A 584 GLN A 658 GLN B 178 ASN B 232 GLN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 HIS B 463 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 554 ASN B 589 GLN C 609 GLN D 545 GLN E 545 GLN F 512 ASN F 562 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.143076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.123583 restraints weight = 22185.840| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.80 r_work: 0.3485 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1762 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= 0.152 Angle : 0.585 8.032 21332 Z= 0.293 Chirality : 0.038 0.162 2383 Planarity : 0.005 0.059 2773 Dihedral : 5.235 59.442 2126 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.30 % Favored : 96.12 % Rotamer: Outliers : 5.04 % Allowed : 29.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.20), residues: 1907 helix: 2.02 (0.14), residues: 1438 sheet: None (None), residues: 0 loop : -1.85 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 611 TYR 0.015 0.001 TYR A 686 PHE 0.015 0.001 PHE B 221 TRP 0.014 0.001 TRP B 180 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00353 (15797) covalent geometry : angle 0.58468 (21332) hydrogen bonds : bond 0.04843 ( 1014) hydrogen bonds : angle 3.63872 ( 3003) *********************** 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 577 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 490 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.5696 (mtmt) REVERT: A 452 ASP cc_start: 0.7509 (m-30) cc_final: 0.7228 (m-30) REVERT: A 487 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7396 (m-30) REVERT: A 520 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7297 (mp0) REVERT: A 563 TYR cc_start: 0.8689 (t80) cc_final: 0.8472 (t80) REVERT: A 581 MET cc_start: 0.8690 (mtt) cc_final: 0.8267 (mtt) REVERT: A 591 LYS cc_start: 0.5497 (OUTLIER) cc_final: 0.4749 (mptt) REVERT: A 593 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7400 (pt) REVERT: A 613 ASP cc_start: 0.8194 (m-30) cc_final: 0.7912 (m-30) REVERT: A 615 LYS cc_start: 0.8557 (ttpp) cc_final: 0.8308 (mtpp) REVERT: A 659 GLN cc_start: 0.8660 (tp40) cc_final: 0.8339 (tp40) REVERT: A 662 SER cc_start: 0.8075 (t) cc_final: 0.7753 (m) REVERT: A 672 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 675 LEU cc_start: 0.8602 (tp) cc_final: 0.8328 (tm) REVERT: A 715 VAL cc_start: 0.7803 (OUTLIER) cc_final: 0.7578 (t) REVERT: B 75 GLN cc_start: 0.8254 (tp40) cc_final: 0.8047 (mm-40) REVERT: B 76 PHE cc_start: 0.7903 (m-10) cc_final: 0.7555 (m-10) REVERT: B 223 MET cc_start: 0.6031 (mmp) cc_final: 0.5789 (pp-130) REVERT: B 294 GLN cc_start: 0.6046 (OUTLIER) cc_final: 0.5111 (tp-100) REVERT: B 303 GLN cc_start: 0.8164 (pp30) cc_final: 0.7924 (pp30) REVERT: B 444 LYS cc_start: 0.6734 (OUTLIER) cc_final: 0.4902 (mtmt) REVERT: B 470 SER cc_start: 0.8744 (t) cc_final: 0.8397 (m) REVERT: B 493 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6446 (mmp-170) REVERT: B 536 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6804 (tm-30) REVERT: B 612 ASP cc_start: 0.7950 (m-30) cc_final: 0.7454 (p0) REVERT: B 675 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8370 (mt) REVERT: B 679 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.8061 (ttm170) REVERT: B 696 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6873 (pp20) REVERT: C 428 ASP cc_start: 0.7336 (t0) cc_final: 0.6931 (t0) REVERT: C 429 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7936 (pm20) REVERT: C 483 ASP cc_start: 0.7619 (m-30) cc_final: 0.7327 (m-30) REVERT: C 487 ASP cc_start: 0.7682 (t70) cc_final: 0.7184 (t70) REVERT: C 493 ARG cc_start: 0.6417 (mtt180) cc_final: 0.6156 (mtt180) REVERT: C 515 LEU cc_start: 0.8556 (mp) cc_final: 0.8303 (mm) REVERT: C 576 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8100 (mtm-85) REVERT: C 672 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7565 (mp0) REVERT: C 685 GLU cc_start: 0.7833 (mp0) cc_final: 0.7475 (mp0) REVERT: C 688 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: D 483 ASP cc_start: 0.7651 (m-30) cc_final: 0.7371 (m-30) REVERT: D 524 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7873 (mp10) REVERT: D 568 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7371 (ttp-170) REVERT: D 577 LEU cc_start: 0.8452 (tt) cc_final: 0.8113 (tp) REVERT: D 606 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7501 (mt-10) REVERT: D 611 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8316 (ttt180) REVERT: D 617 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8196 (mp) REVERT: D 647 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: D 695 MET cc_start: 0.6938 (tpt) cc_final: 0.6666 (tpt) REVERT: E 444 LYS cc_start: 0.6172 (OUTLIER) cc_final: 0.5364 (mptt) REVERT: E 459 VAL cc_start: 0.8210 (t) cc_final: 0.7812 (p) REVERT: E 487 ASP cc_start: 0.8172 (m-30) cc_final: 0.7821 (m-30) REVERT: E 500 MET cc_start: 0.8663 (mmm) cc_final: 0.8451 (mmt) REVERT: E 519 MET cc_start: 0.7724 (ptp) cc_final: 0.7478 (mtp) REVERT: E 527 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7786 (t70) REVERT: E 612 ASP cc_start: 0.8175 (m-30) cc_final: 0.7957 (m-30) REVERT: E 672 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7347 (mt-10) REVERT: F 432 LEU cc_start: 0.8606 (mp) cc_final: 0.8395 (mm) REVERT: F 444 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6440 (mptt) REVERT: F 447 ARG cc_start: 0.8368 (mpp-170) cc_final: 0.8129 (mmt-90) REVERT: F 491 LEU cc_start: 0.8854 (mt) cc_final: 0.8613 (mm) REVERT: F 581 MET cc_start: 0.8681 (mtt) cc_final: 0.8416 (mtp) REVERT: F 608 PHE cc_start: 0.8647 (m-80) cc_final: 0.8145 (m-80) REVERT: F 633 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.5315 (tm-30) REVERT: F 666 LEU cc_start: 0.8427 (mt) cc_final: 0.8051 (mt) REVERT: F 679 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7978 (ttp80) REVERT: F 693 GLU cc_start: 0.7497 (tp30) cc_final: 0.6979 (tp30) REVERT: F 696 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7409 (mp0) outliers start: 87 outliers final: 42 residues processed: 536 average time/residue: 0.7429 time to fit residues: 431.6006 Evaluate side-chains 532 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 470 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 462 ASP 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 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 294 GLN Chi-restraints excluded: chain B residue 320 ILE 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 493 ARG 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 536 GLU 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 589 GLN 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 429 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 617 LEU Chi-restraints excluded: chain D residue 644 LEU 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 640 LEU Chi-restraints excluded: chain E residue 706 GLU 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 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 62 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 91 optimal weight: 0.0970 chunk 128 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 584 GLN A 658 GLN B 63 ASN B 178 ASN ** B 232 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 C 512 ASN C 609 GLN D 545 GLN E 545 GLN F 512 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.122807 restraints weight = 22221.660| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.80 r_work: 0.3472 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15797 Z= 0.172 Angle : 0.591 8.141 21332 Z= 0.297 Chirality : 0.039 0.145 2383 Planarity : 0.005 0.061 2773 Dihedral : 4.998 58.434 2123 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.67 % Favored : 95.75 % Rotamer: Outliers : 5.33 % Allowed : 28.79 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.20), residues: 1907 helix: 2.03 (0.14), residues: 1434 sheet: None (None), residues: 0 loop : -1.95 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 661 TYR 0.019 0.002 TYR B 115 PHE 0.015 0.001 PHE B 221 TRP 0.015 0.001 TRP B 180 HIS 0.004 0.001 HIS F 642 Details of bonding type rmsd covalent geometry : bond 0.00408 (15797) covalent geometry : angle 0.59068 (21332) hydrogen bonds : bond 0.05113 ( 1014) hydrogen bonds : angle 3.63242 ( 3003) *********************** 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 581 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 489 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.5721 (mtmt) REVERT: A 452 ASP cc_start: 0.7444 (m-30) cc_final: 0.7115 (m-30) REVERT: A 487 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7439 (m-30) REVERT: A 517 ASP cc_start: 0.7791 (t0) cc_final: 0.7538 (t0) REVERT: A 520 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7313 (mp0) REVERT: A 563 TYR cc_start: 0.8703 (t80) cc_final: 0.8460 (t80) REVERT: A 581 MET cc_start: 0.8701 (mtt) cc_final: 0.8300 (mtt) REVERT: A 582 MET cc_start: 0.8724 (mtp) cc_final: 0.8422 (mtm) REVERT: A 591 LYS cc_start: 0.5621 (OUTLIER) cc_final: 0.4781 (mptt) REVERT: A 593 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7470 (pt) REVERT: A 613 ASP cc_start: 0.8175 (m-30) cc_final: 0.7901 (m-30) REVERT: A 615 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8294 (mtpp) REVERT: A 659 GLN cc_start: 0.8653 (tp40) cc_final: 0.8332 (tp40) REVERT: A 662 SER cc_start: 0.8114 (t) cc_final: 0.7796 (m) REVERT: A 675 LEU cc_start: 0.8612 (tp) cc_final: 0.8318 (tm) REVERT: B 76 PHE cc_start: 0.7883 (m-10) cc_final: 0.7475 (m-10) REVERT: B 150 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8178 (p) REVERT: B 470 SER cc_start: 0.8728 (t) cc_final: 0.8380 (m) REVERT: B 612 ASP cc_start: 0.7983 (m-30) cc_final: 0.7480 (p0) REVERT: B 679 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.8074 (ttm170) REVERT: B 696 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6857 (pp20) REVERT: C 428 ASP cc_start: 0.7403 (t0) cc_final: 0.7047 (t0) REVERT: C 483 ASP cc_start: 0.7629 (m-30) cc_final: 0.7298 (m-30) REVERT: C 487 ASP cc_start: 0.7705 (t70) cc_final: 0.7224 (t70) REVERT: C 493 ARG cc_start: 0.6414 (mtt180) cc_final: 0.6149 (mtt180) REVERT: C 515 LEU cc_start: 0.8559 (mp) cc_final: 0.8281 (mm) REVERT: C 576 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8101 (mtm-85) REVERT: C 672 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7663 (mp0) REVERT: C 685 GLU cc_start: 0.7793 (mp0) cc_final: 0.7452 (mp0) REVERT: C 688 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: D 483 ASP cc_start: 0.7627 (m-30) cc_final: 0.7339 (m-30) REVERT: D 577 LEU cc_start: 0.8490 (tt) cc_final: 0.8176 (tp) REVERT: D 606 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7672 (mt-10) REVERT: D 611 ARG cc_start: 0.8656 (ttp80) cc_final: 0.8314 (ttt180) REVERT: D 647 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7622 (mt0) REVERT: D 675 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8614 (tt) REVERT: D 695 MET cc_start: 0.6961 (tpt) cc_final: 0.6682 (tpt) REVERT: E 444 LYS cc_start: 0.6133 (OUTLIER) cc_final: 0.5327 (mptt) REVERT: E 459 VAL cc_start: 0.8219 (t) cc_final: 0.7829 (p) REVERT: E 500 MET cc_start: 0.8657 (mmm) cc_final: 0.8447 (mmt) REVERT: E 519 MET cc_start: 0.7809 (ptp) cc_final: 0.7498 (mtm) REVERT: E 527 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7782 (t70) REVERT: E 612 ASP cc_start: 0.8213 (m-30) cc_final: 0.8007 (m-30) REVERT: E 672 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7396 (mt-10) REVERT: E 703 VAL cc_start: 0.8600 (p) cc_final: 0.8394 (t) REVERT: F 432 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8446 (mm) REVERT: F 444 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6420 (mptt) REVERT: F 447 ARG cc_start: 0.8408 (mpp-170) cc_final: 0.8145 (mmt-90) REVERT: F 448 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6904 (mm-30) REVERT: F 491 LEU cc_start: 0.8840 (mt) cc_final: 0.8614 (mm) REVERT: F 519 MET cc_start: 0.8040 (ttt) cc_final: 0.7831 (ttt) REVERT: F 581 MET cc_start: 0.8701 (mtt) cc_final: 0.8442 (mtp) REVERT: F 608 PHE cc_start: 0.8672 (m-80) cc_final: 0.8129 (m-80) REVERT: F 633 GLU cc_start: 0.5728 (OUTLIER) cc_final: 0.5306 (tm-30) REVERT: F 666 LEU cc_start: 0.8412 (mt) cc_final: 0.8030 (mt) REVERT: F 679 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7975 (ttp80) REVERT: F 693 GLU cc_start: 0.7504 (tp30) cc_final: 0.6998 (tp30) REVERT: F 696 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7441 (mp0) outliers start: 92 outliers final: 47 residues processed: 538 average time/residue: 0.7376 time to fit residues: 430.4422 Evaluate side-chains 540 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 477 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 117 PHE Chi-restraints excluded: chain B residue 150 SER 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 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 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 644 LEU 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 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 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 640 LEU 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 498 THR 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 84 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 158 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 58 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 584 GLN A 658 GLN B 63 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 658 GLN C 512 ASN C 609 GLN D 545 GLN E 545 GLN F 512 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.143124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.123690 restraints weight = 22051.103| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.78 r_work: 0.3488 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15797 Z= 0.142 Angle : 0.585 9.808 21332 Z= 0.290 Chirality : 0.038 0.156 2383 Planarity : 0.005 0.062 2773 Dihedral : 4.897 59.445 2121 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.36 % Favored : 96.07 % Rotamer: Outliers : 5.21 % Allowed : 29.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.20), residues: 1907 helix: 2.11 (0.14), residues: 1438 sheet: None (None), residues: 0 loop : -1.85 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 568 TYR 0.020 0.001 TYR B 115 PHE 0.014 0.001 PHE B 221 TRP 0.019 0.001 TRP B 180 HIS 0.003 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00331 (15797) covalent geometry : angle 0.58470 (21332) hydrogen bonds : bond 0.04655 ( 1014) hydrogen bonds : angle 3.54642 ( 3003) *********************** 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 581 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 491 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.5715 (mtmt) REVERT: A 448 GLU cc_start: 0.7848 (mp0) cc_final: 0.7603 (mp0) REVERT: A 452 ASP cc_start: 0.7441 (m-30) cc_final: 0.7106 (m-30) REVERT: A 487 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: A 517 ASP cc_start: 0.7776 (t0) cc_final: 0.7539 (t0) REVERT: A 520 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7302 (mp0) REVERT: A 581 MET cc_start: 0.8680 (mtt) cc_final: 0.8288 (mtt) REVERT: A 591 LYS cc_start: 0.5504 (OUTLIER) cc_final: 0.4681 (mptt) REVERT: A 593 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7473 (pt) REVERT: A 613 ASP cc_start: 0.8149 (m-30) cc_final: 0.7872 (m-30) REVERT: A 615 LYS cc_start: 0.8540 (ttpp) cc_final: 0.8274 (mtpp) REVERT: A 659 GLN cc_start: 0.8650 (tp40) cc_final: 0.8372 (tp40) REVERT: A 662 SER cc_start: 0.8145 (t) cc_final: 0.7818 (m) REVERT: A 670 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8258 (mp) REVERT: A 672 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7523 (mt-10) REVERT: A 675 LEU cc_start: 0.8633 (tp) cc_final: 0.8332 (tm) REVERT: B 76 PHE cc_start: 0.7806 (m-10) cc_final: 0.7547 (m-10) REVERT: B 117 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7005 (t80) REVERT: B 290 LYS cc_start: 0.8868 (pptt) cc_final: 0.8409 (pptt) REVERT: B 303 GLN cc_start: 0.8076 (pp30) cc_final: 0.7733 (pp30) REVERT: B 444 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6512 (mtmt) REVERT: B 470 SER cc_start: 0.8720 (t) cc_final: 0.8357 (m) REVERT: B 612 ASP cc_start: 0.7945 (m-30) cc_final: 0.7442 (p0) REVERT: B 675 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8470 (mt) REVERT: B 679 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.8064 (ttm170) REVERT: B 696 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6838 (pp20) REVERT: C 428 ASP cc_start: 0.7369 (t0) cc_final: 0.7029 (t0) REVERT: C 436 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7633 (mt-10) REVERT: C 483 ASP cc_start: 0.7642 (m-30) cc_final: 0.7285 (m-30) REVERT: C 487 ASP cc_start: 0.7691 (t70) cc_final: 0.7209 (t70) REVERT: C 493 ARG cc_start: 0.6429 (mtt180) cc_final: 0.6177 (mtt180) REVERT: C 505 GLU cc_start: 0.8143 (mp0) cc_final: 0.7826 (mp0) REVERT: C 576 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8097 (mtm-85) REVERT: C 672 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7675 (mp0) REVERT: C 685 GLU cc_start: 0.7782 (mp0) cc_final: 0.7446 (mp0) REVERT: C 688 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: D 483 ASP cc_start: 0.7651 (m-30) cc_final: 0.7378 (m-30) REVERT: D 519 MET cc_start: 0.8252 (tpp) cc_final: 0.7839 (tpt) REVERT: D 568 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7583 (ttp-170) REVERT: D 577 LEU cc_start: 0.8487 (tt) cc_final: 0.8159 (tp) REVERT: D 582 MET cc_start: 0.8585 (mtm) cc_final: 0.8360 (mtp) REVERT: D 611 ARG cc_start: 0.8665 (ttp80) cc_final: 0.8339 (ttt180) REVERT: D 647 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: D 675 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8606 (tt) REVERT: D 695 MET cc_start: 0.6936 (tpt) cc_final: 0.6640 (tpt) REVERT: E 444 LYS cc_start: 0.6067 (OUTLIER) cc_final: 0.5282 (mptt) REVERT: E 459 VAL cc_start: 0.8185 (t) cc_final: 0.7805 (p) REVERT: E 500 MET cc_start: 0.8631 (mmm) cc_final: 0.8424 (mmt) REVERT: E 519 MET cc_start: 0.7813 (ptp) cc_final: 0.7491 (mtm) REVERT: E 527 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7775 (t70) REVERT: E 612 ASP cc_start: 0.8215 (m-30) cc_final: 0.7991 (m-30) REVERT: E 651 VAL cc_start: 0.8570 (m) cc_final: 0.8310 (t) REVERT: E 672 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7388 (mt-10) REVERT: E 685 GLU cc_start: 0.7258 (mp0) cc_final: 0.6956 (mp0) REVERT: F 432 LEU cc_start: 0.8690 (mp) cc_final: 0.8474 (mm) REVERT: F 444 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.5003 (mptt) REVERT: F 447 ARG cc_start: 0.8368 (mpp-170) cc_final: 0.8135 (mmt-90) REVERT: F 469 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8570 (mttp) REVERT: F 491 LEU cc_start: 0.8831 (mt) cc_final: 0.8610 (mm) REVERT: F 519 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7792 (ttt) REVERT: F 581 MET cc_start: 0.8699 (mtt) cc_final: 0.8446 (mtp) REVERT: F 608 PHE cc_start: 0.8648 (m-80) cc_final: 0.8076 (m-80) REVERT: F 633 GLU cc_start: 0.5798 (OUTLIER) cc_final: 0.5373 (tm-30) REVERT: F 666 LEU cc_start: 0.8483 (mt) cc_final: 0.8178 (mt) REVERT: F 679 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7953 (ttp80) REVERT: F 693 GLU cc_start: 0.7498 (tp30) cc_final: 0.7000 (tp30) REVERT: F 696 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7467 (mp0) outliers start: 90 outliers final: 47 residues processed: 539 average time/residue: 0.7554 time to fit residues: 440.4359 Evaluate side-chains 548 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 482 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 670 LEU 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 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 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 604 LEU 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 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 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 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 465 VAL Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 519 MET 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 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 102 optimal weight: 0.9980 chunk 156 optimal weight: 0.8980 chunk 61 optimal weight: 0.0270 chunk 174 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 584 GLN A 658 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 C 512 ASN C 609 GLN D 545 GLN E 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 = 0.3870 r_free = 0.3870 target = 0.143298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.123870 restraints weight = 21958.481| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.80 r_work: 0.3490 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15797 Z= 0.141 Angle : 0.594 9.023 21332 Z= 0.294 Chirality : 0.038 0.167 2383 Planarity : 0.005 0.062 2773 Dihedral : 4.857 59.868 2121 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.36 % Favored : 96.07 % Rotamer: Outliers : 4.75 % Allowed : 30.30 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.20), residues: 1907 helix: 2.17 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -1.82 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 611 TYR 0.021 0.001 TYR B 115 PHE 0.013 0.001 PHE B 221 TRP 0.022 0.001 TRP B 180 HIS 0.003 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00330 (15797) covalent geometry : angle 0.59356 (21332) hydrogen bonds : bond 0.04553 ( 1014) hydrogen bonds : angle 3.49490 ( 3003) *********************** 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: 82 poor density : 494 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.5719 (mtmt) REVERT: A 448 GLU cc_start: 0.7850 (mp0) cc_final: 0.7593 (mp0) REVERT: A 452 ASP cc_start: 0.7475 (m-30) cc_final: 0.7087 (m-30) REVERT: A 487 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: A 517 ASP cc_start: 0.7772 (t0) cc_final: 0.7516 (t0) REVERT: A 520 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7295 (mp0) REVERT: A 581 MET cc_start: 0.8656 (mtt) cc_final: 0.8292 (mtt) REVERT: A 582 MET cc_start: 0.8670 (mtp) cc_final: 0.8389 (mtm) REVERT: A 591 LYS cc_start: 0.5492 (OUTLIER) cc_final: 0.4673 (mptt) REVERT: A 593 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7503 (pt) REVERT: A 613 ASP cc_start: 0.8123 (m-30) cc_final: 0.7836 (m-30) REVERT: A 615 LYS cc_start: 0.8512 (ttpp) cc_final: 0.8252 (mtpp) REVERT: A 659 GLN cc_start: 0.8644 (tp40) cc_final: 0.8363 (tp40) REVERT: A 662 SER cc_start: 0.8163 (t) cc_final: 0.7820 (m) REVERT: A 670 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8339 (mp) REVERT: A 672 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7507 (mt-10) REVERT: A 675 LEU cc_start: 0.8680 (tp) cc_final: 0.8333 (tm) REVERT: B 76 PHE cc_start: 0.7871 (m-10) cc_final: 0.7537 (m-10) REVERT: B 117 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.6959 (t80) REVERT: B 150 SER cc_start: 0.8419 (OUTLIER) cc_final: 0.8157 (p) REVERT: B 290 LYS cc_start: 0.8846 (pptt) cc_final: 0.8455 (pptt) REVERT: B 303 GLN cc_start: 0.8130 (pp30) cc_final: 0.7769 (pp30) REVERT: B 444 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6517 (mtmt) REVERT: B 470 SER cc_start: 0.8716 (t) cc_final: 0.8349 (m) REVERT: B 483 ASP cc_start: 0.7582 (m-30) cc_final: 0.7176 (t0) REVERT: B 612 ASP cc_start: 0.7964 (m-30) cc_final: 0.7442 (p0) REVERT: B 675 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8448 (mt) REVERT: B 679 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.8076 (ttm170) REVERT: B 696 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6817 (pp20) REVERT: C 428 ASP cc_start: 0.7368 (t0) cc_final: 0.7067 (t0) REVERT: C 483 ASP cc_start: 0.7606 (m-30) cc_final: 0.7269 (m-30) REVERT: C 487 ASP cc_start: 0.7664 (t70) cc_final: 0.7173 (t70) REVERT: C 493 ARG cc_start: 0.6445 (mtt180) cc_final: 0.6171 (mtt180) REVERT: C 505 GLU cc_start: 0.8083 (mp0) cc_final: 0.7775 (mp0) REVERT: C 515 LEU cc_start: 0.8553 (mp) cc_final: 0.8305 (mm) REVERT: C 576 ARG cc_start: 0.8337 (ttp80) cc_final: 0.8082 (mtm-85) REVERT: C 611 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8182 (ttt90) REVERT: C 672 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7694 (mp0) REVERT: C 685 GLU cc_start: 0.7769 (mp0) cc_final: 0.7425 (mp0) REVERT: C 688 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: D 483 ASP cc_start: 0.7637 (m-30) cc_final: 0.7381 (m-30) REVERT: D 519 MET cc_start: 0.8198 (tpp) cc_final: 0.7816 (tpt) REVERT: D 568 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7599 (ttp-110) REVERT: D 577 LEU cc_start: 0.8459 (tt) cc_final: 0.8126 (tp) REVERT: D 582 MET cc_start: 0.8588 (mtm) cc_final: 0.8363 (mtp) REVERT: D 611 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8341 (ttt180) REVERT: D 647 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7614 (mt0) REVERT: D 675 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8577 (tt) REVERT: D 695 MET cc_start: 0.6918 (tpt) cc_final: 0.6616 (tpt) REVERT: E 444 LYS cc_start: 0.5998 (OUTLIER) cc_final: 0.5202 (mptt) REVERT: E 459 VAL cc_start: 0.8191 (t) cc_final: 0.7810 (p) REVERT: E 500 MET cc_start: 0.8626 (mmm) cc_final: 0.8414 (mmt) REVERT: E 519 MET cc_start: 0.7805 (ptp) cc_final: 0.7511 (mtm) REVERT: E 527 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7796 (t70) REVERT: E 612 ASP cc_start: 0.8207 (m-30) cc_final: 0.7986 (m-30) REVERT: E 651 VAL cc_start: 0.8548 (m) cc_final: 0.8304 (t) REVERT: E 672 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7391 (mt-10) REVERT: F 432 LEU cc_start: 0.8721 (mp) cc_final: 0.8500 (mm) REVERT: F 444 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.4980 (mptt) REVERT: F 447 ARG cc_start: 0.8374 (mpp-170) cc_final: 0.8151 (mmt-90) REVERT: F 491 LEU cc_start: 0.8823 (mt) cc_final: 0.8601 (mm) REVERT: F 581 MET cc_start: 0.8674 (mtt) cc_final: 0.8411 (mtp) REVERT: F 608 PHE cc_start: 0.8624 (m-80) cc_final: 0.8087 (m-80) REVERT: F 633 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5374 (tm-30) REVERT: F 666 LEU cc_start: 0.8442 (mt) cc_final: 0.8124 (mt) REVERT: F 679 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7945 (ttp80) REVERT: F 693 GLU cc_start: 0.7475 (tp30) cc_final: 0.6997 (tp30) REVERT: F 696 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7526 (mp0) outliers start: 82 outliers final: 44 residues processed: 537 average time/residue: 0.7218 time to fit residues: 419.7552 Evaluate side-chains 546 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 484 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 670 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 256 ASP 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 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 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 548 ASP 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 706 GLU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 489 SER 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 667 ASP 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 80 optimal weight: 0.9980 chunk 185 optimal weight: 0.0010 chunk 139 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 0.0270 chunk 74 optimal weight: 0.1980 chunk 150 optimal weight: 0.0870 chunk 96 optimal weight: 0.6980 overall best weight: 0.2022 ------------------------------------------------------------------------------- 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 584 GLN A 658 GLN B 307 ASN B 463 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 554 ASN C 512 ASN C 609 GLN D 545 GLN E 477 ASN E 545 GLN F 512 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.145118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.125730 restraints weight = 22177.317| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.80 r_work: 0.3518 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15797 Z= 0.116 Angle : 0.580 8.989 21332 Z= 0.287 Chirality : 0.037 0.143 2383 Planarity : 0.005 0.063 2773 Dihedral : 4.785 59.889 2121 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.09 % Favored : 96.33 % Rotamer: Outliers : 4.23 % Allowed : 30.94 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.20), residues: 1907 helix: 2.19 (0.14), residues: 1465 sheet: None (None), residues: 0 loop : -1.83 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 611 TYR 0.020 0.001 TYR B 115 PHE 0.012 0.001 PHE B 221 TRP 0.029 0.001 TRP B 180 HIS 0.003 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00258 (15797) covalent geometry : angle 0.58025 (21332) hydrogen bonds : bond 0.03883 ( 1014) hydrogen bonds : angle 3.37207 ( 3003) *********************** 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 575 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 502 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6639 (OUTLIER) cc_final: 0.5678 (mtmt) REVERT: A 448 GLU cc_start: 0.7880 (mp0) cc_final: 0.7637 (mp0) REVERT: A 452 ASP cc_start: 0.7415 (m-30) cc_final: 0.7039 (m-30) REVERT: A 487 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: A 517 ASP cc_start: 0.7793 (t0) cc_final: 0.7530 (t0) REVERT: A 520 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7269 (mp0) REVERT: A 532 ASP cc_start: 0.8065 (m-30) cc_final: 0.7859 (m-30) REVERT: A 582 MET cc_start: 0.8652 (mtp) cc_final: 0.8367 (mtm) REVERT: A 591 LYS cc_start: 0.5426 (OUTLIER) cc_final: 0.4721 (mptt) REVERT: A 593 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7517 (pt) REVERT: A 613 ASP cc_start: 0.8080 (m-30) cc_final: 0.7707 (m-30) REVERT: A 615 LYS cc_start: 0.8474 (ttpp) cc_final: 0.8234 (mtpp) REVERT: A 659 GLN cc_start: 0.8645 (tp40) cc_final: 0.8368 (tp40) REVERT: A 662 SER cc_start: 0.8172 (t) cc_final: 0.7824 (m) REVERT: A 670 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8348 (mp) REVERT: A 672 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7468 (mt-10) REVERT: A 717 ARG cc_start: 0.8144 (mtp85) cc_final: 0.7893 (mtt180) REVERT: B 76 PHE cc_start: 0.7865 (m-10) cc_final: 0.7541 (m-10) REVERT: B 117 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.6880 (t80) REVERT: B 150 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8109 (p) REVERT: B 290 LYS cc_start: 0.8832 (pptt) cc_final: 0.8517 (pptt) REVERT: B 470 SER cc_start: 0.8676 (t) cc_final: 0.8277 (m) REVERT: B 483 ASP cc_start: 0.7512 (m-30) cc_final: 0.7117 (t0) REVERT: B 666 LEU cc_start: 0.7989 (mt) cc_final: 0.7662 (mt) REVERT: B 675 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8453 (mt) REVERT: B 679 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.8060 (ttm170) REVERT: B 696 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6788 (pp20) REVERT: C 428 ASP cc_start: 0.7354 (t0) cc_final: 0.7040 (t0) REVERT: C 436 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7651 (mt-10) REVERT: C 483 ASP cc_start: 0.7613 (m-30) cc_final: 0.7279 (m-30) REVERT: C 487 ASP cc_start: 0.7642 (t70) cc_final: 0.7152 (t70) REVERT: C 493 ARG cc_start: 0.6451 (mtt180) cc_final: 0.6168 (mtt180) REVERT: C 505 GLU cc_start: 0.8094 (mp0) cc_final: 0.7801 (mp0) REVERT: C 515 LEU cc_start: 0.8552 (mp) cc_final: 0.8313 (mm) REVERT: C 576 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7978 (mtm-85) REVERT: C 672 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7674 (mp0) REVERT: C 688 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: D 483 ASP cc_start: 0.7599 (m-30) cc_final: 0.7330 (m-30) REVERT: D 519 MET cc_start: 0.8220 (tpp) cc_final: 0.7840 (tpt) REVERT: D 529 ARG cc_start: 0.7774 (mmm-85) cc_final: 0.7458 (mmm-85) REVERT: D 541 LEU cc_start: 0.8272 (tt) cc_final: 0.7818 (mt) REVERT: D 568 ARG cc_start: 0.7805 (ttm-80) cc_final: 0.7294 (ttp-170) REVERT: D 577 LEU cc_start: 0.8438 (tt) cc_final: 0.8103 (tp) REVERT: D 582 MET cc_start: 0.8534 (mtm) cc_final: 0.8334 (mtp) REVERT: D 606 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7461 (mt-10) REVERT: D 608 PHE cc_start: 0.8556 (m-80) cc_final: 0.8350 (m-80) REVERT: D 611 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8228 (ttt90) REVERT: D 647 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7565 (mt0) REVERT: D 675 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8555 (tt) REVERT: D 695 MET cc_start: 0.6896 (tpt) cc_final: 0.6614 (tpt) REVERT: E 444 LYS cc_start: 0.5933 (OUTLIER) cc_final: 0.5155 (mptt) REVERT: E 459 VAL cc_start: 0.8144 (t) cc_final: 0.7757 (p) REVERT: E 500 MET cc_start: 0.8616 (mmm) cc_final: 0.8412 (mmt) REVERT: E 527 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7760 (t70) REVERT: E 651 VAL cc_start: 0.8525 (m) cc_final: 0.8304 (t) REVERT: E 672 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7446 (mt-10) REVERT: E 705 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7888 (mp) REVERT: F 432 LEU cc_start: 0.8692 (mp) cc_final: 0.8476 (mm) REVERT: F 444 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.4969 (mptt) REVERT: F 491 LEU cc_start: 0.8822 (mt) cc_final: 0.8596 (mm) REVERT: F 608 PHE cc_start: 0.8615 (m-80) cc_final: 0.8075 (m-80) REVERT: F 633 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.5389 (tm-30) REVERT: F 666 LEU cc_start: 0.8434 (mt) cc_final: 0.8097 (mt) REVERT: F 679 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7929 (ttp80) REVERT: F 693 GLU cc_start: 0.7495 (tp30) cc_final: 0.6974 (tp30) REVERT: F 696 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7555 (mp0) outliers start: 73 outliers final: 30 residues processed: 544 average time/residue: 0.7481 time to fit residues: 440.7337 Evaluate side-chains 532 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 484 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 670 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 175 VAL 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 475 LEU Chi-restraints excluded: chain B residue 516 ILE 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 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 505 GLU Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 588 VAL 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 444 LYS Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 489 SER 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 667 ASP 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 109 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 171 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 148 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 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 430 HIS A 473 GLN A 512 ASN A 524 GLN A 584 GLN A 658 GLN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 463 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 554 ASN C 512 ASN C 609 GLN D 545 GLN E 512 ASN E 545 GLN F 512 ASN F 569 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.142312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122767 restraints weight = 22223.249| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.81 r_work: 0.3473 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15797 Z= 0.178 Angle : 0.652 13.596 21332 Z= 0.320 Chirality : 0.039 0.165 2383 Planarity : 0.005 0.060 2773 Dihedral : 4.843 58.576 2121 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.30 % Favored : 96.12 % Rotamer: Outliers : 3.71 % Allowed : 31.87 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.20), residues: 1907 helix: 2.19 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -1.73 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 611 TYR 0.031 0.002 TYR A 614 PHE 0.013 0.002 PHE B 221 TRP 0.025 0.002 TRP B 180 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00425 (15797) covalent geometry : angle 0.65177 (21332) hydrogen bonds : bond 0.04967 ( 1014) hydrogen bonds : angle 3.51039 ( 3003) *********************** 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 547 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 483 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6675 (OUTLIER) cc_final: 0.5723 (mtmt) REVERT: A 487 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: A 517 ASP cc_start: 0.7820 (t0) cc_final: 0.7534 (t0) REVERT: A 520 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7299 (mp0) REVERT: A 584 GLN cc_start: 0.8367 (tp-100) cc_final: 0.8128 (tp-100) REVERT: A 591 LYS cc_start: 0.5511 (OUTLIER) cc_final: 0.4714 (mptt) REVERT: A 593 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7524 (pt) REVERT: A 613 ASP cc_start: 0.8079 (m-30) cc_final: 0.7772 (m-30) REVERT: A 615 LYS cc_start: 0.8515 (ttpp) cc_final: 0.8274 (mtpp) REVERT: A 659 GLN cc_start: 0.8646 (tp40) cc_final: 0.8359 (tp40) REVERT: A 662 SER cc_start: 0.8195 (t) cc_final: 0.7840 (m) REVERT: A 670 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8430 (mp) REVERT: A 672 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7530 (mt-10) REVERT: B 74 GLU cc_start: 0.7481 (pm20) cc_final: 0.7220 (pm20) REVERT: B 76 PHE cc_start: 0.7884 (m-10) cc_final: 0.7523 (m-10) REVERT: B 117 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7124 (t80) REVERT: B 256 ASP cc_start: 0.6390 (p0) cc_final: 0.5315 (p0) REVERT: B 290 LYS cc_start: 0.8900 (pptt) cc_final: 0.8554 (pptt) REVERT: B 303 GLN cc_start: 0.8162 (pp30) cc_final: 0.7904 (pp30) REVERT: B 470 SER cc_start: 0.8685 (t) cc_final: 0.8335 (m) REVERT: B 483 ASP cc_start: 0.7645 (m-30) cc_final: 0.7195 (t0) REVERT: B 560 GLU cc_start: 0.7471 (tp30) cc_final: 0.7232 (mm-30) REVERT: B 666 LEU cc_start: 0.8010 (mt) cc_final: 0.7715 (mt) REVERT: B 675 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8425 (mt) REVERT: B 679 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.8063 (ttm170) REVERT: B 696 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6826 (pp20) REVERT: C 428 ASP cc_start: 0.7419 (t0) cc_final: 0.7097 (t0) REVERT: C 436 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7630 (mt-10) REVERT: C 483 ASP cc_start: 0.7653 (m-30) cc_final: 0.7316 (m-30) REVERT: C 487 ASP cc_start: 0.7680 (t70) cc_final: 0.7201 (t70) REVERT: C 493 ARG cc_start: 0.6456 (mtt180) cc_final: 0.6180 (mtt180) REVERT: C 505 GLU cc_start: 0.8079 (mp0) cc_final: 0.7793 (mp0) REVERT: C 515 LEU cc_start: 0.8607 (mp) cc_final: 0.8341 (mm) REVERT: C 548 ASP cc_start: 0.8396 (t70) cc_final: 0.8186 (t0) REVERT: C 576 ARG cc_start: 0.8324 (ttp80) cc_final: 0.8079 (mtm-85) REVERT: C 672 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7699 (mt-10) REVERT: C 685 GLU cc_start: 0.7828 (mp0) cc_final: 0.7472 (mp0) REVERT: C 688 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: D 483 ASP cc_start: 0.7651 (m-30) cc_final: 0.7386 (m-30) REVERT: D 519 MET cc_start: 0.8284 (tpp) cc_final: 0.8032 (tpt) REVERT: D 529 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7505 (mmm-85) REVERT: D 568 ARG cc_start: 0.7827 (ttm-80) cc_final: 0.7319 (ttp-170) REVERT: D 577 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8183 (tp) REVERT: D 582 MET cc_start: 0.8561 (mtm) cc_final: 0.8347 (mtp) REVERT: D 606 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7685 (mt-10) REVERT: D 611 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8369 (ttt180) REVERT: D 647 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: D 675 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8570 (tt) REVERT: D 695 MET cc_start: 0.7002 (tpt) cc_final: 0.6704 (tpt) REVERT: E 444 LYS cc_start: 0.5980 (OUTLIER) cc_final: 0.5164 (mptt) REVERT: E 459 VAL cc_start: 0.8197 (t) cc_final: 0.7815 (p) REVERT: E 500 MET cc_start: 0.8632 (mmm) cc_final: 0.8407 (mmt) REVERT: E 527 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7795 (t70) REVERT: E 537 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7708 (mp0) REVERT: E 612 ASP cc_start: 0.8211 (m-30) cc_final: 0.7995 (m-30) REVERT: E 651 VAL cc_start: 0.8562 (m) cc_final: 0.8336 (t) REVERT: E 672 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7505 (mt-10) REVERT: E 685 GLU cc_start: 0.7307 (mp0) cc_final: 0.7003 (mp0) REVERT: F 432 LEU cc_start: 0.8776 (mp) cc_final: 0.8534 (mm) REVERT: F 444 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.4963 (mptt) REVERT: F 491 LEU cc_start: 0.8831 (mt) cc_final: 0.8606 (mm) REVERT: F 608 PHE cc_start: 0.8626 (m-80) cc_final: 0.8048 (m-80) REVERT: F 633 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.5405 (tm-30) REVERT: F 666 LEU cc_start: 0.8444 (mt) cc_final: 0.8093 (mt) REVERT: F 693 GLU cc_start: 0.7519 (tp30) cc_final: 0.7015 (tp30) REVERT: F 696 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7564 (mp0) outliers start: 64 outliers final: 36 residues processed: 519 average time/residue: 0.7694 time to fit residues: 432.0054 Evaluate side-chains 525 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 473 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 536 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 670 LEU Chi-restraints excluded: chain A residue 705 LEU 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 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 475 LEU 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 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 D residue 524 GLN 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 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 505 GLU 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 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 465 VAL 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 667 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 118 optimal weight: 0.6980 chunk 89 optimal weight: 0.0870 chunk 147 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.3980 chunk 126 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 C 512 ASN C 609 GLN D 545 GLN E 545 GLN F 512 ASN F 569 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.142867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123378 restraints weight = 22106.805| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.81 r_work: 0.3480 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: 0.7676 moved from start: 0.2417 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 : 0.648 10.456 21332 Z= 0.320 Chirality : 0.039 0.148 2383 Planarity : 0.005 0.087 2773 Dihedral : 4.781 58.339 2119 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.09 % Favored : 96.33 % Rotamer: Outliers : 3.48 % Allowed : 32.50 % Favored : 64.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.20), residues: 1907 helix: 2.19 (0.14), residues: 1444 sheet: None (None), residues: 0 loop : -1.71 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 661 TYR 0.028 0.002 TYR A 614 PHE 0.011 0.001 PHE B 221 TRP 0.029 0.001 TRP B 180 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00377 (15797) covalent geometry : angle 0.64812 (21332) hydrogen bonds : bond 0.04713 ( 1014) hydrogen bonds : angle 3.48893 ( 3003) ********************** 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 545 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 485 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.6657 (OUTLIER) cc_final: 0.5730 (mtmt) REVERT: A 517 ASP cc_start: 0.7758 (t0) cc_final: 0.7511 (t0) REVERT: A 520 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7300 (mp0) REVERT: A 582 MET cc_start: 0.8746 (mtp) cc_final: 0.8427 (mtm) REVERT: A 591 LYS cc_start: 0.5513 (OUTLIER) cc_final: 0.4681 (mptt) REVERT: A 593 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7548 (pt) REVERT: A 613 ASP cc_start: 0.8083 (m-30) cc_final: 0.7765 (m-30) REVERT: A 615 LYS cc_start: 0.8469 (ttpp) cc_final: 0.8243 (mtpp) REVERT: A 659 GLN cc_start: 0.8644 (tp40) cc_final: 0.8355 (tp40) REVERT: A 662 SER cc_start: 0.8211 (t) cc_final: 0.7859 (m) REVERT: A 670 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8441 (mp) REVERT: A 672 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7520 (mt-10) REVERT: B 74 GLU cc_start: 0.7498 (pm20) cc_final: 0.7237 (pm20) REVERT: B 76 PHE cc_start: 0.7850 (m-10) cc_final: 0.7538 (m-10) REVERT: B 117 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7123 (t80) REVERT: B 290 LYS cc_start: 0.8901 (pptt) cc_final: 0.8541 (pptt) REVERT: B 470 SER cc_start: 0.8670 (t) cc_final: 0.8314 (m) REVERT: B 483 ASP cc_start: 0.7657 (m-30) cc_final: 0.7203 (t0) REVERT: B 506 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: B 666 LEU cc_start: 0.7969 (mt) cc_final: 0.7479 (mt) REVERT: B 671 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8347 (mttm) REVERT: B 675 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8397 (mt) REVERT: B 679 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.8049 (ttm170) REVERT: B 696 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6853 (pp20) REVERT: C 428 ASP cc_start: 0.7429 (t0) cc_final: 0.7102 (t0) REVERT: C 436 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7635 (mt-10) REVERT: C 483 ASP cc_start: 0.7618 (m-30) cc_final: 0.7287 (m-30) REVERT: C 487 ASP cc_start: 0.7662 (t70) cc_final: 0.7180 (t70) REVERT: C 493 ARG cc_start: 0.6479 (mtt180) cc_final: 0.6230 (mtt180) REVERT: C 505 GLU cc_start: 0.8068 (mp0) cc_final: 0.7769 (mp0) REVERT: C 515 LEU cc_start: 0.8551 (mp) cc_final: 0.8295 (mm) REVERT: C 576 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7991 (mtm-85) REVERT: C 672 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7674 (mt-10) REVERT: C 685 GLU cc_start: 0.7837 (mp0) cc_final: 0.7474 (mp0) REVERT: C 688 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: D 483 ASP cc_start: 0.7649 (m-30) cc_final: 0.7375 (m-30) REVERT: D 519 MET cc_start: 0.8277 (tpp) cc_final: 0.8050 (tpt) REVERT: D 568 ARG cc_start: 0.7834 (ttm-80) cc_final: 0.7335 (ttp-170) REVERT: D 577 LEU cc_start: 0.8484 (tt) cc_final: 0.8173 (tp) REVERT: D 582 MET cc_start: 0.8563 (mtm) cc_final: 0.8351 (mtp) REVERT: D 606 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7491 (mt-10) REVERT: D 611 ARG cc_start: 0.8701 (ttp80) cc_final: 0.8365 (ttt180) REVERT: D 647 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: D 675 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8563 (tt) REVERT: D 695 MET cc_start: 0.6981 (tpt) cc_final: 0.6681 (tpt) REVERT: E 444 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5136 (mptt) REVERT: E 459 VAL cc_start: 0.8179 (t) cc_final: 0.7783 (p) REVERT: E 500 MET cc_start: 0.8638 (mmm) cc_final: 0.8411 (mmt) REVERT: E 527 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7808 (t70) REVERT: E 537 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7693 (mp0) REVERT: E 612 ASP cc_start: 0.8190 (m-30) cc_final: 0.7969 (m-30) REVERT: E 672 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7411 (mt-10) REVERT: E 685 GLU cc_start: 0.7293 (mp0) cc_final: 0.6983 (mp0) REVERT: F 432 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8546 (mm) REVERT: F 444 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.4991 (mptt) REVERT: F 491 LEU cc_start: 0.8829 (mt) cc_final: 0.8598 (mm) REVERT: F 608 PHE cc_start: 0.8611 (m-80) cc_final: 0.8036 (m-80) REVERT: F 633 GLU cc_start: 0.5819 (OUTLIER) cc_final: 0.5392 (tm-30) REVERT: F 666 LEU cc_start: 0.8443 (mt) cc_final: 0.8099 (mt) REVERT: F 679 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7934 (ttp80) REVERT: F 680 GLN cc_start: 0.8047 (tm130) cc_final: 0.7493 (tm130) REVERT: F 693 GLU cc_start: 0.7480 (tp30) cc_final: 0.6977 (tp30) REVERT: F 696 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7576 (mp0) outliers start: 60 outliers final: 34 residues processed: 518 average time/residue: 0.7489 time to fit residues: 419.3056 Evaluate side-chains 525 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 474 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 536 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 670 LEU Chi-restraints excluded: chain A residue 705 LEU 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 175 VAL 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 475 LEU 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 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 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 505 GLU Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 588 VAL 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 465 VAL 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 667 ASP 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 67 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 1 optimal weight: 0.0970 chunk 186 optimal weight: 0.2980 chunk 116 optimal weight: 0.2980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 B 463 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 554 ASN C 512 ASN C 609 GLN D 545 GLN E 545 GLN F 512 ASN F 569 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.143367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123958 restraints weight = 22140.210| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.81 r_work: 0.3489 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15797 Z= 0.145 Angle : 0.639 9.200 21332 Z= 0.318 Chirality : 0.038 0.182 2383 Planarity : 0.005 0.061 2773 Dihedral : 4.723 58.507 2117 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.09 % Favored : 96.33 % Rotamer: Outliers : 3.13 % Allowed : 33.26 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.20), residues: 1907 helix: 2.25 (0.14), residues: 1437 sheet: None (None), residues: 0 loop : -1.66 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 611 TYR 0.027 0.002 TYR A 614 PHE 0.013 0.001 PHE B 221 TRP 0.029 0.001 TRP B 180 HIS 0.005 0.001 HIS A 430 Details of bonding type rmsd covalent geometry : bond 0.00339 (15797) covalent geometry : angle 0.63915 (21332) hydrogen bonds : bond 0.04515 ( 1014) hydrogen bonds : angle 3.47967 ( 3003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8173.57 seconds wall clock time: 139 minutes 23.59 seconds (8363.59 seconds total)