Starting phenix.real_space_refine on Sat Jul 4 04:51:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9upg_64395/07_2026/9upg_64395.cif Found real_map, /net/cci-nas-00/data/ceres_data/9upg_64395/07_2026/9upg_64395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9upg_64395/07_2026/9upg_64395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9upg_64395/07_2026/9upg_64395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9upg_64395/07_2026/9upg_64395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9upg_64395/07_2026/9upg_64395.map" } resolution = 2.87 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= 0.004 sd= 0.092 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 Ca 6 9.91 5 S 104 5.16 5 C 11577 2.51 5 N 2969 2.21 5 O 3256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17912 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4173 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 14, 'TRANS': 497} Chain breaks: 1 Chain: "D" Number of atoms: 4245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4245 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 21, 'TRANS': 498} Chain: "C" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4185 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 14, 'TRANS': 499} Chain breaks: 1 Chain: "B" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4129 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 20, 'TRANS': 486} Chain breaks: 2 Chain: "H" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1174 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 146} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Time building chain proxies: 3.15, per 1000 atoms: 0.18 Number of scatterers: 17912 At special positions: 0 Unit cell: (109.56, 108.73, 179.28, 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) Ca 6 19.99 S 104 16.00 O 3256 8.00 N 2969 7.00 C 11577 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: 1.51 Conformation dependent library (CDL) restraints added in 701.4 milliseconds 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4162 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 13 sheets defined 70.5% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 137 through 164 removed outlier: 3.820A pdb=" N TYR A 141 " --> pdb=" O GLY A 137 " (cutoff:3.500A) Proline residue: A 150 - end of helix removed outlier: 4.988A pdb=" N VAL A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 171 through 194 removed outlier: 3.511A pdb=" N TYR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.936A pdb=" N HIS A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.943A pdb=" N LYS A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 252 removed outlier: 3.677A pdb=" N VAL A 245 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN A 248 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N HIS A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.724A pdb=" N THR A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 301 removed outlier: 3.527A pdb=" N PHE A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 336 Processing helix chain 'A' and resid 346 through 399 removed outlier: 4.553A pdb=" N THR A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG A 382 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 419 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 433 through 450 removed outlier: 3.653A pdb=" N ASN A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR A 448 " --> pdb=" O VAL A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 470 removed outlier: 3.518A pdb=" N LYS A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.819A pdb=" N ILE A 524 " --> pdb=" O GLY A 520 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 525' Processing helix chain 'A' and resid 553 through 560 Processing helix chain 'A' and resid 563 through 582 Processing helix chain 'A' and resid 596 through 648 removed outlier: 3.578A pdb=" N GLN A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 619 " --> pdb=" O PHE A 615 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 631 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 636 " --> pdb=" O ARG A 632 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 645 " --> pdb=" O LYS A 641 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A 646 " --> pdb=" O GLN A 642 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 648 " --> pdb=" O ASN A 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 41 Processing helix chain 'D' and resid 41 through 58 removed outlier: 3.574A pdb=" N VAL D 45 " --> pdb=" O MET D 41 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 52 " --> pdb=" O ASN D 48 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.576A pdb=" N TYR D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 88 removed outlier: 3.532A pdb=" N MET D 84 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 removed outlier: 4.183A pdb=" N ARG D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 122 removed outlier: 3.753A pdb=" N PHE D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 133 removed outlier: 4.008A pdb=" N LEU D 132 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 145 removed outlier: 3.531A pdb=" N LEU D 139 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN D 142 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.762A pdb=" N LEU D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 195 Processing helix chain 'D' and resid 213 through 230 Processing helix chain 'D' and resid 240 through 280 removed outlier: 3.511A pdb=" N PHE D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 280 " --> pdb=" O ASP D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 296 through 314 Processing helix chain 'D' and resid 318 through 324 Processing helix chain 'D' and resid 327 through 345 removed outlier: 5.736A pdb=" N SER D 341 " --> pdb=" O SER D 337 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N THR D 342 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG D 345 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.678A pdb=" N LEU D 362 " --> pdb=" O GLU D 358 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS D 363 " --> pdb=" O GLU D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 455 Processing helix chain 'D' and resid 457 through 475 removed outlier: 3.608A pdb=" N GLN D 461 " --> pdb=" O TYR D 457 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR D 462 " --> pdb=" O PRO D 458 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE D 463 " --> pdb=" O GLN D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 539 removed outlier: 4.044A pdb=" N ARG D 513 " --> pdb=" O THR D 509 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 519 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP D 534 " --> pdb=" O GLU D 530 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLN D 535 " --> pdb=" O ARG D 531 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 538 " --> pdb=" O TRP D 534 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP D 539 " --> pdb=" O GLN D 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 164 removed outlier: 3.629A pdb=" N TYR C 141 " --> pdb=" O GLY C 137 " (cutoff:3.500A) Proline residue: C 150 - end of helix removed outlier: 5.188A pdb=" N VAL C 159 " --> pdb=" O TRP C 155 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 171 removed outlier: 3.583A pdb=" N GLN C 168 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 195 removed outlier: 3.685A pdb=" N VAL C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 190 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 217 removed outlier: 4.030A pdb=" N HIS C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 229 removed outlier: 3.914A pdb=" N LYS C 222 " --> pdb=" O THR C 218 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 252 removed outlier: 3.639A pdb=" N VAL C 245 " --> pdb=" O SER C 242 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN C 248 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 267 removed outlier: 3.787A pdb=" N THR C 265 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 301 Processing helix chain 'C' and resid 314 through 319 removed outlier: 4.451A pdb=" N TYR C 319 " --> pdb=" O PRO C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 336 Processing helix chain 'C' and resid 346 through 379 removed outlier: 3.829A pdb=" N LEU C 362 " --> pdb=" O LEU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 399 Processing helix chain 'C' and resid 402 through 419 Processing helix chain 'C' and resid 424 through 430 Processing helix chain 'C' and resid 433 through 451 removed outlier: 3.532A pdb=" N VAL C 444 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N SER C 447 " --> pdb=" O ASN C 443 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N THR C 448 " --> pdb=" O VAL C 444 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 470 removed outlier: 3.549A pdb=" N GLU C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.611A pdb=" N ILE C 524 " --> pdb=" O GLY C 520 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 553 through 560 Processing helix chain 'C' and resid 563 through 582 removed outlier: 3.520A pdb=" N LYS C 567 " --> pdb=" O TYR C 563 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 568 " --> pdb=" O PRO C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 593 removed outlier: 3.609A pdb=" N THR C 591 " --> pdb=" O ASN C 587 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 647 removed outlier: 3.508A pdb=" N THR C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU C 609 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 628 " --> pdb=" O GLY C 624 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 632 " --> pdb=" O LYS C 628 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR C 634 " --> pdb=" O LYS C 630 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 636 " --> pdb=" O ARG C 632 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C 640 " --> pdb=" O LEU C 636 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN C 642 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN C 643 " --> pdb=" O LYS C 639 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN C 644 " --> pdb=" O MET C 640 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU C 645 " --> pdb=" O LYS C 641 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP C 646 " --> pdb=" O GLN C 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 588 removed outlier: 3.542A pdb=" N ILE B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 565 " --> pdb=" O SER B 561 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B 570 " --> pdb=" O ASP B 566 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 571 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 573 " --> pdb=" O GLN B 569 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 581 " --> pdb=" O GLU B 577 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 582 " --> pdb=" O ARG B 578 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 596 Processing helix chain 'B' and resid 653 through 680 Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 684 through 708 removed outlier: 3.670A pdb=" N HIS B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 693 " --> pdb=" O HIS B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 734 Processing helix chain 'B' and resid 735 through 745 Processing helix chain 'B' and resid 758 through 767 removed outlier: 3.760A pdb=" N ARG B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Proline residue: B 764 - end of helix Processing helix chain 'B' and resid 768 through 783 removed outlier: 4.042A pdb=" N PHE B 772 " --> pdb=" O LYS B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 817 Processing helix chain 'B' and resid 830 through 844 Processing helix chain 'B' and resid 854 through 907 removed outlier: 5.302A pdb=" N GLY B 889 " --> pdb=" O ALA B 885 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLN B 890 " --> pdb=" O ALA B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 929 Processing helix chain 'B' and resid 933 through 938 Processing helix chain 'B' and resid 941 through 959 removed outlier: 5.936A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 964 removed outlier: 3.812A pdb=" N GLN B 964 " --> pdb=" O ALA B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 978 Processing helix chain 'B' and resid 1029 through 1034 Processing helix chain 'B' and resid 1059 through 1067 removed outlier: 3.715A pdb=" N VAL B1067 " --> pdb=" O ASN B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1088 Processing helix chain 'B' and resid 1106 through 1119 removed outlier: 4.256A pdb=" N GLY B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS B1118 " --> pdb=" O ALA B1114 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 21 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 66 through 94 removed outlier: 3.676A pdb=" N MET H 73 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 114 removed outlier: 3.638A pdb=" N HIS H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR H 111 " --> pdb=" O ARG H 107 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN H 112 " --> pdb=" O HIS H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 130 removed outlier: 3.612A pdb=" N VAL H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 148 removed outlier: 3.522A pdb=" N GLN H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 475 removed outlier: 6.515A pdb=" N ASP A 547 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 480 through 482 removed outlier: 6.511A pdb=" N TYR A 480 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER A 542 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS A 482 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 539 " --> pdb=" O VAL A 502 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 92 through 94 removed outlier: 3.743A pdb=" N PHE D 92 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 365 through 369 removed outlier: 4.342A pdb=" N ASN D 433 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN D 392 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR D 439 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU D 390 " --> pdb=" O TYR D 439 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP D 441 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE D 388 " --> pdb=" O ASP D 441 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE D 443 " --> pdb=" O TYR D 386 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR D 386 " --> pdb=" O PHE D 443 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 445 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 384 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA D 405 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 374 through 376 removed outlier: 6.248A pdb=" N TYR D 374 " --> pdb=" O SER D 436 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER D 436 " --> pdb=" O TYR D 374 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN D 433 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN D 392 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR D 439 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU D 390 " --> pdb=" O TYR D 439 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP D 441 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE D 388 " --> pdb=" O ASP D 441 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE D 443 " --> pdb=" O TYR D 386 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR D 386 " --> pdb=" O PHE D 443 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 445 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU D 384 " --> pdb=" O LEU D 445 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 199 through 200 Processing sheet with id=AA8, first strand: chain 'C' and resid 471 through 475 removed outlier: 6.545A pdb=" N ASP C 547 " --> pdb=" O LYS C 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 480 through 482 removed outlier: 6.683A pdb=" N ILE C 540 " --> pdb=" O ILE C 481 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN C 539 " --> pdb=" O VAL C 502 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 511 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 715 through 717 removed outlier: 3.695A pdb=" N PHE B 715 " --> pdb=" O ILE B 722 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 979 through 983 removed outlier: 3.922A pdb=" N ASN B1045 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B1006 " --> pdb=" O HIS B1049 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE B1051 " --> pdb=" O ALA B1004 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B1004 " --> pdb=" O PHE B1051 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN B1053 " --> pdb=" O ILE B1002 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE B1002 " --> pdb=" O ASN B1053 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE B1055 " --> pdb=" O TYR B1000 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR B1000 " --> pdb=" O PHE B1055 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B1057 " --> pdb=" O GLU B 998 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU B 998 " --> pdb=" O LEU B1057 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL B1020 " --> pdb=" O VAL B1009 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 988 through 990 removed outlier: 6.582A pdb=" N TYR B 988 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B1048 " --> pdb=" O TYR B 988 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN B1045 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B1006 " --> pdb=" O HIS B1049 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE B1051 " --> pdb=" O ALA B1004 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B1004 " --> pdb=" O PHE B1051 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN B1053 " --> pdb=" O ILE B1002 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE B1002 " --> pdb=" O ASN B1053 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE B1055 " --> pdb=" O TYR B1000 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR B1000 " --> pdb=" O PHE B1055 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B1057 " --> pdb=" O GLU B 998 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU B 998 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 27 through 28 1164 hydrogen bonds defined for protein. 3384 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: 3.18 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4008 1.33 - 1.45: 4037 1.45 - 1.58: 10077 1.58 - 1.70: 0 1.70 - 1.82: 176 Bond restraints: 18298 Sorted by residual: bond pdb=" N ILE B 833 " pdb=" CA ILE B 833 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.57e+00 bond pdb=" N ILE B 782 " pdb=" CA ILE B 782 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 7.96e+00 bond pdb=" N VAL B 828 " pdb=" CA VAL B 828 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 7.90e+00 bond pdb=" N THR A 267 " pdb=" CA THR A 267 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.30e-02 5.92e+03 7.54e+00 bond pdb=" N VAL C 597 " pdb=" CA VAL C 597 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.24e+00 ... (remaining 18293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 24230 1.89 - 3.78: 473 3.78 - 5.66: 46 5.66 - 7.55: 15 7.55 - 9.44: 5 Bond angle restraints: 24769 Sorted by residual: angle pdb=" C HIS A 252 " pdb=" CA HIS A 252 " pdb=" CB HIS A 252 " ideal model delta sigma weight residual 111.26 117.88 -6.62 1.67e+00 3.59e-01 1.57e+01 angle pdb=" N GLY B 827 " pdb=" CA GLY B 827 " pdb=" C GLY B 827 " ideal model delta sigma weight residual 115.64 110.13 5.51 1.46e+00 4.69e-01 1.42e+01 angle pdb=" CA GLU A 586 " pdb=" C GLU A 586 " pdb=" O GLU A 586 " ideal model delta sigma weight residual 121.10 117.32 3.78 1.10e+00 8.26e-01 1.18e+01 angle pdb=" N HIS A 252 " pdb=" CA HIS A 252 " pdb=" C HIS A 252 " ideal model delta sigma weight residual 113.23 109.12 4.11 1.22e+00 6.72e-01 1.13e+01 angle pdb=" O ASN A 268 " pdb=" C ASN A 268 " pdb=" N TYR A 269 " ideal model delta sigma weight residual 122.15 125.74 -3.59 1.14e+00 7.69e-01 9.92e+00 ... (remaining 24764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 9580 17.77 - 35.54: 1089 35.54 - 53.31: 221 53.31 - 71.08: 36 71.08 - 88.85: 20 Dihedral angle restraints: 10946 sinusoidal: 4473 harmonic: 6473 Sorted by residual: dihedral pdb=" CA VAL B 952 " pdb=" C VAL B 952 " pdb=" N ASN B 953 " pdb=" CA ASN B 953 " ideal model delta harmonic sigma weight residual -180.00 -162.26 -17.74 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CG ARG D 198 " pdb=" CD ARG D 198 " pdb=" NE ARG D 198 " pdb=" CZ ARG D 198 " ideal model delta sinusoidal sigma weight residual -90.00 -40.19 -49.81 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CA LEU A 584 " pdb=" C LEU A 584 " pdb=" N ASP A 585 " pdb=" CA ASP A 585 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 10943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2131 0.045 - 0.089: 491 0.089 - 0.134: 120 0.134 - 0.179: 18 0.179 - 0.223: 7 Chirality restraints: 2767 Sorted by residual: chirality pdb=" CA LEU B1057 " pdb=" N LEU B1057 " pdb=" C LEU B1057 " pdb=" CB LEU B1057 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU A 584 " pdb=" CB LEU A 584 " pdb=" CD1 LEU A 584 " pdb=" CD2 LEU A 584 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA VAL B 828 " pdb=" N VAL B 828 " pdb=" C VAL B 828 " pdb=" CB VAL B 828 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2764 not shown) Planarity restraints: 3120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 763 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO B 764 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 147 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO D 148 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 148 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 148 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 909 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO B 910 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 910 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 910 " -0.028 5.00e-02 4.00e+02 ... (remaining 3117 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3585 2.77 - 3.30: 17043 3.30 - 3.84: 29327 3.84 - 4.37: 35993 4.37 - 4.90: 60301 Nonbonded interactions: 146249 Sorted by model distance: nonbonded pdb=" O TYR C 215 " pdb=" OG1 THR C 218 " model vdw 2.240 3.040 nonbonded pdb=" O TYR A 215 " pdb=" OG1 THR A 218 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP B 967 " pdb=" OG SER B1072 " model vdw 2.259 3.040 nonbonded pdb=" OG SER C 542 " pdb=" O GLY C 544 " model vdw 2.284 3.040 nonbonded pdb=" OD1 ASN B 776 " pdb=" OH TYR B 789 " model vdw 2.287 3.040 ... (remaining 146244 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 130 through 647) selection = (chain 'C' and (resid 130 through 232 or resid 240 through 647)) } 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: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.540 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 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 : 0.005 0.057 18298 Z= 0.223 Angle : 0.629 9.440 24769 Z= 0.362 Chirality : 0.043 0.223 2767 Planarity : 0.005 0.070 3120 Dihedral : 15.541 88.846 6784 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 18.59 % Favored : 81.41 % 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 are not related in a simple way. whole: -0.04 (0.16), residues: 2184 helix: -0.11 (0.12), residues: 1423 sheet: 3.22 (0.52), residues: 45 loop : 0.32 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 198 TYR 0.031 0.002 TYR D 289 PHE 0.014 0.002 PHE B 856 TRP 0.015 0.002 TRP B 691 HIS 0.010 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.22 (18298) covalent geometry : angle 0.62926 / 0.36 (24769) hydrogen bonds : bond 0.23879 / 15.36 ( 1156) hydrogen bonds : angle 6.68243 / 4.74 ( 3384) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8623 (t70) cc_final: 0.8266 (t0) REVERT: A 261 ASP cc_start: 0.8652 (t70) cc_final: 0.8430 (t0) REVERT: A 427 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8307 (mp0) REVERT: A 532 MET cc_start: 0.7369 (mtt) cc_final: 0.6946 (ptp) REVERT: A 608 MET cc_start: 0.5952 (mmp) cc_final: 0.5195 (tmm) REVERT: A 640 MET cc_start: -0.0031 (tpt) cc_final: -0.0459 (ttm) REVERT: D 74 TYR cc_start: 0.8381 (t80) cc_final: 0.7650 (t80) REVERT: D 102 LYS cc_start: 0.8129 (mmtp) cc_final: 0.7798 (mmtp) REVERT: D 266 SER cc_start: 0.8893 (t) cc_final: 0.8409 (m) REVERT: D 328 GLU cc_start: 0.8451 (tt0) cc_final: 0.7834 (mp0) REVERT: D 342 THR cc_start: 0.9075 (m) cc_final: 0.8794 (p) REVERT: D 384 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8008 (mt-10) REVERT: D 425 MET cc_start: 0.7690 (mtp) cc_final: 0.7423 (mtm) REVERT: C 209 LYS cc_start: 0.7858 (ttmm) cc_final: 0.7392 (ttpt) REVERT: C 216 ILE cc_start: 0.8274 (mt) cc_final: 0.8021 (mp) REVERT: C 420 LYS cc_start: 0.8523 (mttt) cc_final: 0.7952 (mmtt) REVERT: C 576 GLU cc_start: 0.6553 (tt0) cc_final: 0.6048 (mt-10) REVERT: B 722 ILE cc_start: 0.7622 (mm) cc_final: 0.7098 (mp) REVERT: B 736 ARG cc_start: 0.6414 (ttt90) cc_final: 0.5922 (ttt90) REVERT: B 778 ARG cc_start: 0.8026 (mmp80) cc_final: 0.7012 (mmm160) REVERT: B 934 SER cc_start: 0.8307 (m) cc_final: 0.7947 (p) REVERT: B 1017 SER cc_start: 0.7681 (t) cc_final: 0.7314 (p) REVERT: B 1115 MET cc_start: 0.1187 (ptt) cc_final: 0.0758 (pp-130) REVERT: B 1119 MET cc_start: 0.0585 (tpp) cc_final: -0.0414 (mmt) REVERT: H 1 MET cc_start: 0.0436 (ttm) cc_final: -0.0513 (tpp) REVERT: H 77 MET cc_start: -0.1713 (ptt) cc_final: -0.2992 (mmt) REVERT: H 110 MET cc_start: 0.1259 (mtt) cc_final: 0.0940 (mpt) REVERT: H 115 GLU cc_start: 0.2002 (mt-10) cc_final: 0.1615 (mt-10) REVERT: H 124 GLU cc_start: 0.0929 (tm-30) cc_final: 0.0495 (mm-30) outliers start: 0 outliers final: 1 residues processed: 198 average time/residue: 0.5863 time to fit residues: 129.5843 Evaluate side-chains 179 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0040 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 598 GLN ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 ASN ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 GLN C 644 ASN ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.178947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.108432 restraints weight = 20638.896| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.89 r_work: 0.3059 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18298 Z= 0.157 Angle : 0.531 7.816 24769 Z= 0.286 Chirality : 0.039 0.177 2767 Planarity : 0.004 0.056 3120 Dihedral : 3.982 35.081 2440 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.26 % Allowed : 16.64 % Favored : 81.10 % 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 are not related in a simple way. whole: 1.70 (0.17), residues: 2184 helix: 1.49 (0.13), residues: 1423 sheet: 2.90 (0.54), residues: 45 loop : 0.43 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.019 0.002 TYR C 319 PHE 0.012 0.001 PHE A 385 TRP 0.013 0.001 TRP B 811 HIS 0.011 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (18298) covalent geometry : angle 0.53133 / 0.29 (24769) hydrogen bonds : bond 0.05222 / 3.40 ( 1156) hydrogen bonds : angle 4.12857 / 2.91 ( 3384) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 196 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8621 (t70) cc_final: 0.8373 (OUTLIER) REVERT: A 426 ARG cc_start: 0.7924 (mmm160) cc_final: 0.7183 (mtt180) REVERT: A 427 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8376 (mp0) REVERT: A 532 MET cc_start: 0.7320 (mtt) cc_final: 0.6878 (ptp) REVERT: A 568 LYS cc_start: 0.7601 (ttmt) cc_final: 0.7116 (mtpp) REVERT: A 572 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: A 608 MET cc_start: 0.5953 (mmp) cc_final: 0.5233 (tmm) REVERT: D 74 TYR cc_start: 0.8385 (t80) cc_final: 0.7753 (t80) REVERT: D 301 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6982 (tpm170) REVERT: D 305 ASP cc_start: 0.7670 (m-30) cc_final: 0.7451 (m-30) REVERT: D 328 GLU cc_start: 0.8254 (tt0) cc_final: 0.7675 (mp0) REVERT: D 384 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8045 (mt-10) REVERT: D 425 MET cc_start: 0.7607 (mtp) cc_final: 0.7338 (mtm) REVERT: D 483 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6262 (pp20) REVERT: C 209 LYS cc_start: 0.7703 (ttmm) cc_final: 0.7291 (ttpt) REVERT: C 216 ILE cc_start: 0.8371 (mt) cc_final: 0.8124 (mp) REVERT: C 376 SER cc_start: 0.8503 (m) cc_final: 0.8170 (p) REVERT: C 420 LYS cc_start: 0.8544 (mttt) cc_final: 0.7985 (mptt) REVERT: C 562 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: C 576 GLU cc_start: 0.6581 (tt0) cc_final: 0.6097 (mt-10) REVERT: B 722 ILE cc_start: 0.7625 (mm) cc_final: 0.7050 (mp) REVERT: B 736 ARG cc_start: 0.6453 (ttt90) cc_final: 0.5912 (ttt90) REVERT: B 778 ARG cc_start: 0.8052 (mmp80) cc_final: 0.7007 (mmm160) REVERT: B 934 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.8061 (p) REVERT: B 1017 SER cc_start: 0.7826 (t) cc_final: 0.7491 (p) REVERT: B 1030 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: B 1119 MET cc_start: 0.0464 (tpp) cc_final: -0.0267 (mmt) REVERT: H 1 MET cc_start: 0.0215 (ttm) cc_final: -0.0535 (tpp) REVERT: H 37 MET cc_start: -0.1987 (ttp) cc_final: -0.2393 (tpt) REVERT: H 77 MET cc_start: -0.1416 (ptt) cc_final: -0.2457 (mmm) REVERT: H 110 MET cc_start: 0.0660 (mtt) cc_final: 0.0361 (mpt) REVERT: H 115 GLU cc_start: 0.2189 (mt-10) cc_final: 0.1715 (mt-10) REVERT: H 124 GLU cc_start: 0.0855 (tm-30) cc_final: 0.0528 (mm-30) outliers start: 44 outliers final: 10 residues processed: 231 average time/residue: 0.5750 time to fit residues: 148.4045 Evaluate side-chains 202 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain B residue 1030 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 90 optimal weight: 0.5980 chunk 138 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 626 GLN D 503 GLN C 379 ASN C 397 GLN C 607 ASN C 627 GLN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.178610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.107949 restraints weight = 20715.641| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.90 r_work: 0.3057 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18298 Z= 0.145 Angle : 0.487 6.601 24769 Z= 0.261 Chirality : 0.037 0.145 2767 Planarity : 0.004 0.053 3120 Dihedral : 3.797 17.036 2438 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.93 % Allowed : 16.33 % Favored : 80.74 % 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 are not related in a simple way. whole: 2.18 (0.17), residues: 2184 helix: 1.98 (0.13), residues: 1424 sheet: 2.55 (0.57), residues: 45 loop : 0.40 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 198 TYR 0.015 0.001 TYR C 319 PHE 0.011 0.001 PHE B 870 TRP 0.013 0.001 TRP A 143 HIS 0.011 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (18298) covalent geometry : angle 0.48660 / 0.26 (24769) hydrogen bonds : bond 0.04764 / 3.10 ( 1156) hydrogen bonds : angle 3.87570 / 2.73 ( 3384) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 186 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8640 (t70) cc_final: 0.8394 (OUTLIER) REVERT: A 312 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7166 (pt) REVERT: A 427 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8366 (mp0) REVERT: A 532 MET cc_start: 0.7303 (mtt) cc_final: 0.6834 (ptp) REVERT: A 568 LYS cc_start: 0.7591 (ttmt) cc_final: 0.7121 (ttmm) REVERT: A 572 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: A 608 MET cc_start: 0.5903 (mmp) cc_final: 0.5180 (tmm) REVERT: D 74 TYR cc_start: 0.8373 (t80) cc_final: 0.7757 (t80) REVERT: D 102 LYS cc_start: 0.7915 (mmtp) cc_final: 0.7644 (mmtp) REVERT: D 301 ARG cc_start: 0.7525 (tpt90) cc_final: 0.7070 (tpm170) REVERT: D 305 ASP cc_start: 0.7727 (m-30) cc_final: 0.7504 (m-30) REVERT: D 328 GLU cc_start: 0.8305 (tt0) cc_final: 0.7663 (mp0) REVERT: D 342 THR cc_start: 0.9093 (m) cc_final: 0.8846 (p) REVERT: D 384 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8136 (mt-10) REVERT: D 425 MET cc_start: 0.7579 (mtp) cc_final: 0.7320 (mtm) REVERT: D 483 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6379 (pp20) REVERT: D 517 GLU cc_start: 0.3357 (OUTLIER) cc_final: 0.2998 (pt0) REVERT: C 209 LYS cc_start: 0.7749 (ttmm) cc_final: 0.7350 (ttpt) REVERT: C 216 ILE cc_start: 0.8368 (mt) cc_final: 0.8123 (mp) REVERT: C 420 LYS cc_start: 0.8572 (mttt) cc_final: 0.7965 (mmtt) REVERT: C 562 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: C 576 GLU cc_start: 0.6597 (tt0) cc_final: 0.6085 (mt-10) REVERT: C 640 MET cc_start: 0.0363 (ttt) cc_final: -0.0493 (mtp) REVERT: B 722 ILE cc_start: 0.7653 (mm) cc_final: 0.6988 (mp) REVERT: B 728 MET cc_start: 0.6281 (mtm) cc_final: 0.5822 (mtm) REVERT: B 736 ARG cc_start: 0.6425 (ttt90) cc_final: 0.5984 (ttt90) REVERT: B 778 ARG cc_start: 0.8060 (mmp80) cc_final: 0.7029 (mmm160) REVERT: B 934 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.8094 (p) REVERT: B 1017 SER cc_start: 0.7947 (t) cc_final: 0.7569 (p) REVERT: B 1030 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8318 (mp0) REVERT: B 1058 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7953 (t70) REVERT: B 1119 MET cc_start: 0.0595 (tpp) cc_final: -0.0431 (mmt) REVERT: H 1 MET cc_start: 0.0334 (ttm) cc_final: -0.0511 (tpp) REVERT: H 37 MET cc_start: -0.1851 (OUTLIER) cc_final: -0.2233 (tpt) REVERT: H 110 MET cc_start: 0.1198 (mtt) cc_final: 0.0817 (mpt) REVERT: H 115 GLU cc_start: 0.2228 (mt-10) cc_final: 0.1713 (mt-10) REVERT: H 124 GLU cc_start: 0.0702 (tm-30) cc_final: 0.0462 (mm-30) outliers start: 57 outliers final: 24 residues processed: 223 average time/residue: 0.6274 time to fit residues: 156.1649 Evaluate side-chains 215 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain H residue 37 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 133 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 195 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 131 optimal weight: 0.5980 chunk 96 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 GLN C 397 GLN C 627 GLN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.177228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.106988 restraints weight = 20360.153| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.86 r_work: 0.3038 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18298 Z= 0.118 Angle : 0.467 8.417 24769 Z= 0.246 Chirality : 0.037 0.250 2767 Planarity : 0.004 0.052 3120 Dihedral : 3.722 16.861 2438 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.93 % Allowed : 16.13 % Favored : 80.95 % 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 are not related in a simple way. whole: 2.43 (0.18), residues: 2184 helix: 2.21 (0.13), residues: 1428 sheet: 2.35 (0.58), residues: 45 loop : 0.43 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 198 TYR 0.015 0.001 TYR C 319 PHE 0.010 0.001 PHE D 224 TRP 0.012 0.001 TRP A 143 HIS 0.011 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (18298) covalent geometry : angle 0.46695 / 0.25 (24769) hydrogen bonds : bond 0.04210 / 2.73 ( 1156) hydrogen bonds : angle 3.74840 / 2.65 ( 3384) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 189 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8415 (t70) cc_final: 0.8167 (OUTLIER) REVERT: A 312 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.6993 (pt) REVERT: A 427 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8145 (mp0) REVERT: A 532 MET cc_start: 0.7344 (mtt) cc_final: 0.6804 (ptp) REVERT: A 568 LYS cc_start: 0.7341 (ttmt) cc_final: 0.6893 (ttmm) REVERT: A 572 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6769 (mt-10) REVERT: A 608 MET cc_start: 0.5936 (mmp) cc_final: 0.5199 (tmm) REVERT: D 74 TYR cc_start: 0.8221 (t80) cc_final: 0.7597 (t80) REVERT: D 102 LYS cc_start: 0.7611 (mmtp) cc_final: 0.7320 (mmtp) REVERT: D 301 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6849 (tpm170) REVERT: D 305 ASP cc_start: 0.7563 (m-30) cc_final: 0.7319 (m-30) REVERT: D 328 GLU cc_start: 0.8090 (tt0) cc_final: 0.7348 (mp0) REVERT: D 384 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8049 (mt-10) REVERT: D 425 MET cc_start: 0.7500 (mtp) cc_final: 0.7207 (mtm) REVERT: D 466 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: D 483 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6431 (pp20) REVERT: D 517 GLU cc_start: 0.3430 (OUTLIER) cc_final: 0.3170 (pt0) REVERT: C 209 LYS cc_start: 0.7602 (ttmm) cc_final: 0.7156 (ttpt) REVERT: C 216 ILE cc_start: 0.8216 (mt) cc_final: 0.7951 (mp) REVERT: C 420 LYS cc_start: 0.8490 (mttt) cc_final: 0.7886 (mptt) REVERT: C 562 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: C 576 GLU cc_start: 0.6456 (tt0) cc_final: 0.5936 (mt-10) REVERT: C 640 MET cc_start: 0.0864 (ttt) cc_final: 0.0246 (mtt) REVERT: B 722 ILE cc_start: 0.7461 (mm) cc_final: 0.6754 (mp) REVERT: B 728 MET cc_start: 0.5998 (mtm) cc_final: 0.5587 (mtm) REVERT: B 736 ARG cc_start: 0.6267 (ttt90) cc_final: 0.5837 (ttt90) REVERT: B 778 ARG cc_start: 0.7793 (mmp80) cc_final: 0.6745 (mmm160) REVERT: B 934 SER cc_start: 0.8185 (OUTLIER) cc_final: 0.7847 (p) REVERT: B 1017 SER cc_start: 0.7817 (t) cc_final: 0.7380 (p) REVERT: B 1030 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: B 1058 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7886 (t70) REVERT: B 1119 MET cc_start: 0.0600 (tpp) cc_final: -0.0366 (mmt) REVERT: H 1 MET cc_start: 0.0277 (ttm) cc_final: -0.0503 (tpp) REVERT: H 37 MET cc_start: -0.1691 (OUTLIER) cc_final: -0.2102 (tpt) REVERT: H 110 MET cc_start: 0.1323 (mtt) cc_final: 0.0961 (mpt) REVERT: H 115 GLU cc_start: 0.2289 (mt-10) cc_final: 0.1775 (mt-10) outliers start: 57 outliers final: 20 residues processed: 226 average time/residue: 0.6473 time to fit residues: 162.9284 Evaluate side-chains 212 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain H residue 37 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 74 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 166 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 31 optimal weight: 0.1980 chunk 126 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 GLN C 627 GLN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.176835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106534 restraints weight = 20203.037| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.87 r_work: 0.3010 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18298 Z= 0.105 Angle : 0.450 10.069 24769 Z= 0.236 Chirality : 0.036 0.143 2767 Planarity : 0.003 0.053 3120 Dihedral : 3.615 16.834 2438 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.57 % Allowed : 16.90 % Favored : 80.53 % 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 are not related in a simple way. whole: 2.61 (0.18), residues: 2184 helix: 2.35 (0.13), residues: 1438 sheet: 2.31 (0.57), residues: 45 loop : 0.46 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 198 TYR 0.016 0.001 TYR C 319 PHE 0.009 0.001 PHE D 224 TRP 0.012 0.001 TRP A 143 HIS 0.010 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (18298) covalent geometry : angle 0.45001 / 0.24 (24769) hydrogen bonds : bond 0.03841 / 2.49 ( 1156) hydrogen bonds : angle 3.60538 / 2.55 ( 3384) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8338 (t70) cc_final: 0.8121 (OUTLIER) REVERT: A 312 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.6924 (pt) REVERT: A 427 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8079 (mp0) REVERT: A 532 MET cc_start: 0.7319 (mtt) cc_final: 0.6774 (ptp) REVERT: A 568 LYS cc_start: 0.7294 (ttmt) cc_final: 0.6849 (ttmm) REVERT: A 572 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6713 (mt-10) REVERT: A 608 MET cc_start: 0.5912 (mmp) cc_final: 0.5171 (tmm) REVERT: D 46 MET cc_start: 0.8816 (mmm) cc_final: 0.8551 (tpt) REVERT: D 74 TYR cc_start: 0.8157 (t80) cc_final: 0.7565 (t80) REVERT: D 97 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7288 (mp) REVERT: D 102 LYS cc_start: 0.7556 (mmtp) cc_final: 0.7262 (mmtp) REVERT: D 256 MET cc_start: 0.8522 (mmm) cc_final: 0.8150 (mmt) REVERT: D 301 ARG cc_start: 0.7281 (tpt90) cc_final: 0.6989 (tpm170) REVERT: D 328 GLU cc_start: 0.8060 (tt0) cc_final: 0.7287 (mp0) REVERT: D 329 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7589 (tpp-160) REVERT: D 384 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7980 (mt-10) REVERT: D 425 MET cc_start: 0.7447 (mtp) cc_final: 0.7121 (mtm) REVERT: D 428 ASN cc_start: 0.7981 (t0) cc_final: 0.7763 (t0) REVERT: D 483 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6521 (pp20) REVERT: C 209 LYS cc_start: 0.7509 (ttmm) cc_final: 0.7077 (ttpt) REVERT: C 216 ILE cc_start: 0.8118 (mt) cc_final: 0.7861 (mp) REVERT: C 420 LYS cc_start: 0.8421 (mttt) cc_final: 0.7744 (mmtt) REVERT: C 514 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8116 (m) REVERT: C 562 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: C 576 GLU cc_start: 0.6414 (tt0) cc_final: 0.5843 (mt-10) REVERT: C 640 MET cc_start: 0.0994 (ttt) cc_final: 0.0439 (mtt) REVERT: B 722 ILE cc_start: 0.7316 (mm) cc_final: 0.6602 (mp) REVERT: B 728 MET cc_start: 0.5752 (mtm) cc_final: 0.5343 (mtm) REVERT: B 736 ARG cc_start: 0.6187 (ttt90) cc_final: 0.5707 (ttt90) REVERT: B 778 ARG cc_start: 0.7618 (mmp80) cc_final: 0.6587 (mmm160) REVERT: B 934 SER cc_start: 0.8105 (OUTLIER) cc_final: 0.7763 (p) REVERT: B 1017 SER cc_start: 0.7723 (t) cc_final: 0.7268 (p) REVERT: B 1030 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: B 1119 MET cc_start: 0.0660 (tpp) cc_final: -0.0382 (mmt) REVERT: H 1 MET cc_start: 0.0356 (ttm) cc_final: -0.0540 (tpp) REVERT: H 37 MET cc_start: -0.2053 (OUTLIER) cc_final: -0.2338 (tpt) REVERT: H 110 MET cc_start: 0.1272 (mtt) cc_final: 0.0904 (mpt) REVERT: H 115 GLU cc_start: 0.2186 (mt-10) cc_final: 0.1630 (mt-10) outliers start: 50 outliers final: 16 residues processed: 219 average time/residue: 0.5942 time to fit residues: 145.7237 Evaluate side-chains 208 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain H residue 37 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 177 optimal weight: 0.0870 chunk 172 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 162 optimal weight: 5.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 GLN C 627 GLN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.175241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104758 restraints weight = 20018.492| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.86 r_work: 0.2998 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18298 Z= 0.149 Angle : 0.484 7.364 24769 Z= 0.255 Chirality : 0.038 0.187 2767 Planarity : 0.004 0.053 3120 Dihedral : 3.685 17.471 2438 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.21 % Allowed : 17.51 % Favored : 80.28 % 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 are not related in a simple way. whole: 2.57 (0.18), residues: 2184 helix: 2.32 (0.13), residues: 1438 sheet: 2.13 (0.58), residues: 45 loop : 0.44 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 198 TYR 0.016 0.001 TYR C 326 PHE 0.011 0.001 PHE B 870 TRP 0.012 0.001 TRP A 143 HIS 0.010 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (18298) covalent geometry : angle 0.48420 / 0.25 (24769) hydrogen bonds : bond 0.04167 / 2.70 ( 1156) hydrogen bonds : angle 3.67274 / 2.60 ( 3384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8356 (t70) cc_final: 0.8128 (OUTLIER) REVERT: A 427 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8135 (mp0) REVERT: A 532 MET cc_start: 0.7356 (mtt) cc_final: 0.6809 (ptp) REVERT: A 568 LYS cc_start: 0.7296 (ttmt) cc_final: 0.6845 (ttmm) REVERT: A 572 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6719 (mt-10) REVERT: A 608 MET cc_start: 0.5768 (mmp) cc_final: 0.5006 (tmm) REVERT: D 46 MET cc_start: 0.8815 (mmm) cc_final: 0.8574 (mmm) REVERT: D 74 TYR cc_start: 0.8172 (t80) cc_final: 0.7508 (t80) REVERT: D 97 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7307 (mp) REVERT: D 256 MET cc_start: 0.8513 (mmm) cc_final: 0.8142 (mmt) REVERT: D 301 ARG cc_start: 0.7277 (tpt90) cc_final: 0.6923 (tpm170) REVERT: D 328 GLU cc_start: 0.8092 (tt0) cc_final: 0.7292 (mp0) REVERT: D 329 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7630 (tpp-160) REVERT: D 384 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8009 (mt-10) REVERT: D 425 MET cc_start: 0.7463 (mtp) cc_final: 0.7136 (mtm) REVERT: D 428 ASN cc_start: 0.7997 (t0) cc_final: 0.7768 (t0) REVERT: C 209 LYS cc_start: 0.7516 (ttmm) cc_final: 0.7077 (ttpt) REVERT: C 216 ILE cc_start: 0.8180 (mt) cc_final: 0.7931 (mp) REVERT: C 420 LYS cc_start: 0.8408 (mttt) cc_final: 0.7736 (mmtt) REVERT: C 562 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: C 576 GLU cc_start: 0.6334 (tt0) cc_final: 0.5822 (mt-10) REVERT: C 640 MET cc_start: 0.1009 (ttt) cc_final: 0.0482 (mtt) REVERT: B 722 ILE cc_start: 0.7339 (mm) cc_final: 0.6600 (mp) REVERT: B 728 MET cc_start: 0.5819 (mtm) cc_final: 0.5352 (mtm) REVERT: B 736 ARG cc_start: 0.6265 (ttt90) cc_final: 0.5837 (ttt90) REVERT: B 778 ARG cc_start: 0.7659 (mmp80) cc_final: 0.6610 (mmm160) REVERT: B 934 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7769 (p) REVERT: B 1017 SER cc_start: 0.7823 (t) cc_final: 0.7332 (p) REVERT: B 1030 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: B 1119 MET cc_start: 0.0726 (tpp) cc_final: -0.0377 (mmt) REVERT: H 1 MET cc_start: 0.0393 (ttm) cc_final: -0.0540 (tpp) REVERT: H 37 MET cc_start: -0.2152 (OUTLIER) cc_final: -0.2400 (tpt) REVERT: H 110 MET cc_start: 0.1240 (mtt) cc_final: 0.0871 (mpt) REVERT: H 115 GLU cc_start: 0.2067 (mt-10) cc_final: 0.1547 (mt-10) outliers start: 43 outliers final: 20 residues processed: 211 average time/residue: 0.5857 time to fit residues: 138.5088 Evaluate side-chains 203 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 53 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 47 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 607 ASN C 397 GLN C 627 GLN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.175005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104568 restraints weight = 20263.590| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.86 r_work: 0.2965 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18298 Z= 0.148 Angle : 0.478 7.642 24769 Z= 0.251 Chirality : 0.038 0.198 2767 Planarity : 0.004 0.053 3120 Dihedral : 3.687 17.343 2438 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.31 % Allowed : 17.82 % Favored : 79.87 % 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 are not related in a simple way. whole: 2.61 (0.18), residues: 2184 helix: 2.38 (0.13), residues: 1432 sheet: 2.04 (0.57), residues: 45 loop : 0.43 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 198 TYR 0.015 0.001 TYR C 326 PHE 0.010 0.001 PHE B 870 TRP 0.012 0.001 TRP A 143 HIS 0.007 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (18298) covalent geometry : angle 0.47781 / 0.25 (24769) hydrogen bonds : bond 0.04141 / 2.69 ( 1156) hydrogen bonds : angle 3.64841 / 2.58 ( 3384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8305 (t70) cc_final: 0.8076 (t0) REVERT: A 427 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8075 (mp0) REVERT: A 447 SER cc_start: 0.8596 (m) cc_final: 0.8375 (p) REVERT: A 532 MET cc_start: 0.7359 (mtt) cc_final: 0.6766 (ptp) REVERT: A 568 LYS cc_start: 0.7251 (ttmt) cc_final: 0.6840 (ttmm) REVERT: A 572 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6655 (mt-10) REVERT: A 608 MET cc_start: 0.5781 (mmp) cc_final: 0.5116 (tmm) REVERT: D 46 MET cc_start: 0.8769 (mmm) cc_final: 0.8536 (mmm) REVERT: D 74 TYR cc_start: 0.8118 (t80) cc_final: 0.7500 (t80) REVERT: D 97 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7234 (mp) REVERT: D 288 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7298 (mtpp) REVERT: D 301 ARG cc_start: 0.7229 (tpt90) cc_final: 0.6833 (tpm170) REVERT: D 328 GLU cc_start: 0.8076 (tt0) cc_final: 0.7262 (mp0) REVERT: D 384 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7964 (mt-10) REVERT: D 425 MET cc_start: 0.7486 (mtp) cc_final: 0.7151 (mtm) REVERT: D 428 ASN cc_start: 0.7942 (t0) cc_final: 0.7698 (t0) REVERT: D 483 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6522 (pp20) REVERT: C 209 LYS cc_start: 0.7465 (ttmm) cc_final: 0.7015 (ttpt) REVERT: C 216 ILE cc_start: 0.8141 (mt) cc_final: 0.7882 (mp) REVERT: C 420 LYS cc_start: 0.8377 (mttt) cc_final: 0.7698 (mmtt) REVERT: C 562 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: C 576 GLU cc_start: 0.6394 (tt0) cc_final: 0.5825 (mt-10) REVERT: C 593 MET cc_start: 0.1498 (mpt) cc_final: 0.0519 (mtt) REVERT: C 640 MET cc_start: 0.0900 (ttt) cc_final: 0.0497 (mmm) REVERT: B 722 ILE cc_start: 0.7285 (mm) cc_final: 0.6520 (mp) REVERT: B 728 MET cc_start: 0.5771 (mtm) cc_final: 0.5306 (mtm) REVERT: B 736 ARG cc_start: 0.6155 (ttt90) cc_final: 0.5700 (ttt90) REVERT: B 778 ARG cc_start: 0.7629 (mmp80) cc_final: 0.6571 (mmm160) REVERT: B 934 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7738 (p) REVERT: B 1017 SER cc_start: 0.7856 (t) cc_final: 0.7343 (p) REVERT: B 1030 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: B 1119 MET cc_start: 0.0634 (tpp) cc_final: -0.0417 (mmt) REVERT: H 1 MET cc_start: 0.0418 (ttm) cc_final: -0.0529 (tpp) REVERT: H 37 MET cc_start: -0.2049 (OUTLIER) cc_final: -0.2301 (tpt) REVERT: H 110 MET cc_start: 0.1287 (mtt) cc_final: 0.0844 (mpt) REVERT: H 115 GLU cc_start: 0.2059 (mt-10) cc_final: 0.1473 (mt-10) outliers start: 45 outliers final: 21 residues processed: 214 average time/residue: 0.5730 time to fit residues: 137.0994 Evaluate side-chains 209 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 240 ARG Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 53 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 145 optimal weight: 2.9990 chunk 215 optimal weight: 30.0000 chunk 191 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 397 GLN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.173444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103127 restraints weight = 20143.829| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.84 r_work: 0.2936 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18298 Z= 0.213 Angle : 0.522 8.222 24769 Z= 0.274 Chirality : 0.040 0.166 2767 Planarity : 0.004 0.052 3120 Dihedral : 3.800 17.458 2438 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.11 % Allowed : 18.03 % Favored : 79.87 % 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 are not related in a simple way. whole: 2.43 (0.17), residues: 2184 helix: 2.24 (0.13), residues: 1432 sheet: 1.96 (0.57), residues: 45 loop : 0.36 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 198 TYR 0.020 0.002 TYR C 326 PHE 0.012 0.001 PHE D 43 TRP 0.013 0.001 TRP A 143 HIS 0.006 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.21 (18298) covalent geometry : angle 0.52233 / 0.27 (24769) hydrogen bonds : bond 0.04604 / 2.99 ( 1156) hydrogen bonds : angle 3.75692 / 2.66 ( 3384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ARG cc_start: 0.7774 (mtp85) cc_final: 0.7451 (mmt-90) REVERT: A 261 ASP cc_start: 0.8440 (t70) cc_final: 0.8234 (t0) REVERT: A 427 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8106 (mp0) REVERT: A 532 MET cc_start: 0.7367 (mtt) cc_final: 0.6825 (ptp) REVERT: A 568 LYS cc_start: 0.7273 (ttmt) cc_final: 0.6868 (ttmm) REVERT: A 572 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6694 (mt-10) REVERT: A 608 MET cc_start: 0.5686 (mmp) cc_final: 0.4975 (tmm) REVERT: D 46 MET cc_start: 0.8815 (mmm) cc_final: 0.8601 (mmm) REVERT: D 74 TYR cc_start: 0.8124 (t80) cc_final: 0.7479 (t80) REVERT: D 97 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7286 (mp) REVERT: D 288 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7278 (mtpp) REVERT: D 301 ARG cc_start: 0.7239 (tpt90) cc_final: 0.6875 (tpm170) REVERT: D 328 GLU cc_start: 0.8154 (tt0) cc_final: 0.7322 (mp0) REVERT: D 384 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7978 (mt-10) REVERT: D 425 MET cc_start: 0.7500 (mtp) cc_final: 0.7161 (mtm) REVERT: D 428 ASN cc_start: 0.7957 (t0) cc_final: 0.7689 (t0) REVERT: C 209 LYS cc_start: 0.7540 (ttmm) cc_final: 0.7085 (ttpt) REVERT: C 216 ILE cc_start: 0.8175 (mt) cc_final: 0.7909 (mp) REVERT: C 420 LYS cc_start: 0.8363 (mttt) cc_final: 0.7739 (mptt) REVERT: C 562 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: C 576 GLU cc_start: 0.6401 (tt0) cc_final: 0.5819 (mt-10) REVERT: C 640 MET cc_start: 0.0841 (ttt) cc_final: 0.0432 (mmm) REVERT: B 722 ILE cc_start: 0.7289 (mm) cc_final: 0.6532 (mp) REVERT: B 728 MET cc_start: 0.5801 (mtm) cc_final: 0.5303 (mtm) REVERT: B 736 ARG cc_start: 0.6215 (ttt90) cc_final: 0.5783 (ttt90) REVERT: B 778 ARG cc_start: 0.7669 (mmp80) cc_final: 0.6662 (mmm160) REVERT: B 934 SER cc_start: 0.8116 (OUTLIER) cc_final: 0.7781 (p) REVERT: B 1017 SER cc_start: 0.8030 (t) cc_final: 0.7500 (p) REVERT: B 1030 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: B 1119 MET cc_start: 0.0517 (tpp) cc_final: -0.0443 (mmt) REVERT: H 1 MET cc_start: 0.0381 (ttm) cc_final: -0.0514 (tpp) REVERT: H 37 MET cc_start: -0.2105 (OUTLIER) cc_final: -0.2306 (tpt) REVERT: H 110 MET cc_start: 0.1315 (mtt) cc_final: 0.0876 (mpt) REVERT: H 115 GLU cc_start: 0.2015 (mt-10) cc_final: 0.1488 (mt-10) outliers start: 41 outliers final: 20 residues processed: 209 average time/residue: 0.6146 time to fit residues: 143.5115 Evaluate side-chains 207 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 240 ARG Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 53 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 98 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 397 GLN B 653 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.175760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105748 restraints weight = 20078.928| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.85 r_work: 0.2992 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18298 Z= 0.113 Angle : 0.462 8.850 24769 Z= 0.241 Chirality : 0.037 0.196 2767 Planarity : 0.003 0.053 3120 Dihedral : 3.647 17.726 2438 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.44 % Allowed : 18.70 % Favored : 79.87 % 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 are not related in a simple way. whole: 2.69 (0.18), residues: 2184 helix: 2.45 (0.13), residues: 1431 sheet: 1.98 (0.58), residues: 45 loop : 0.42 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 198 TYR 0.015 0.001 TYR A 319 PHE 0.010 0.001 PHE B1109 TRP 0.014 0.001 TRP A 143 HIS 0.007 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (18298) covalent geometry : angle 0.46164 / 0.24 (24769) hydrogen bonds : bond 0.03782 / 2.45 ( 1156) hydrogen bonds : angle 3.61752 / 2.56 ( 3384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7396 (mmt-90) REVERT: A 261 ASP cc_start: 0.8326 (t70) cc_final: 0.8104 (OUTLIER) REVERT: A 384 GLU cc_start: 0.8384 (pt0) cc_final: 0.8166 (pt0) REVERT: A 427 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8148 (mp0) REVERT: A 532 MET cc_start: 0.7350 (mtt) cc_final: 0.6797 (ptp) REVERT: A 568 LYS cc_start: 0.7304 (ttmt) cc_final: 0.6917 (ttmm) REVERT: A 572 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: A 608 MET cc_start: 0.5648 (mmp) cc_final: 0.4946 (tmm) REVERT: D 46 MET cc_start: 0.8790 (mmm) cc_final: 0.8567 (mmm) REVERT: D 74 TYR cc_start: 0.8174 (t80) cc_final: 0.7580 (t80) REVERT: D 97 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7274 (mp) REVERT: D 102 LYS cc_start: 0.7503 (mmtp) cc_final: 0.7164 (mmtp) REVERT: D 256 MET cc_start: 0.8485 (mmm) cc_final: 0.8131 (mmt) REVERT: D 301 ARG cc_start: 0.7257 (tpt90) cc_final: 0.6930 (tpm170) REVERT: D 328 GLU cc_start: 0.8071 (tt0) cc_final: 0.7303 (mp0) REVERT: D 384 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7986 (mt-10) REVERT: D 425 MET cc_start: 0.7499 (mtp) cc_final: 0.7150 (mtm) REVERT: C 209 LYS cc_start: 0.7519 (ttmm) cc_final: 0.7069 (ttpt) REVERT: C 216 ILE cc_start: 0.8100 (mt) cc_final: 0.7836 (mp) REVERT: C 420 LYS cc_start: 0.8403 (mttt) cc_final: 0.7782 (mptt) REVERT: C 576 GLU cc_start: 0.6407 (tt0) cc_final: 0.5835 (mt-10) REVERT: C 640 MET cc_start: 0.1156 (ttt) cc_final: 0.0828 (mmm) REVERT: B 722 ILE cc_start: 0.7374 (mm) cc_final: 0.6617 (mp) REVERT: B 728 MET cc_start: 0.5813 (mtm) cc_final: 0.5344 (mtm) REVERT: B 736 ARG cc_start: 0.6144 (ttt90) cc_final: 0.5660 (ttt90) REVERT: B 778 ARG cc_start: 0.7648 (mmp80) cc_final: 0.6622 (mmm160) REVERT: B 934 SER cc_start: 0.8088 (m) cc_final: 0.7733 (p) REVERT: B 1017 SER cc_start: 0.7937 (t) cc_final: 0.7466 (p) REVERT: B 1030 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: B 1119 MET cc_start: 0.0687 (tpp) cc_final: -0.0325 (mmt) REVERT: H 1 MET cc_start: 0.0537 (ttm) cc_final: -0.0455 (tpp) REVERT: H 110 MET cc_start: 0.1281 (mtt) cc_final: 0.0890 (mpt) REVERT: H 115 GLU cc_start: 0.1959 (mt-10) cc_final: 0.1407 (mt-10) outliers start: 28 outliers final: 17 residues processed: 204 average time/residue: 0.6477 time to fit residues: 146.9280 Evaluate side-chains 198 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 1030 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 178 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 397 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.175712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105584 restraints weight = 20013.334| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.84 r_work: 0.2989 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18298 Z= 0.120 Angle : 0.474 9.405 24769 Z= 0.247 Chirality : 0.037 0.183 2767 Planarity : 0.003 0.053 3120 Dihedral : 3.620 17.445 2438 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.44 % Allowed : 18.80 % Favored : 79.76 % 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 are not related in a simple way. whole: 2.73 (0.18), residues: 2184 helix: 2.50 (0.13), residues: 1431 sheet: 1.94 (0.57), residues: 45 loop : 0.41 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 430 TYR 0.014 0.001 TYR A 319 PHE 0.010 0.001 PHE B 870 TRP 0.013 0.001 TRP A 143 HIS 0.007 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (18298) covalent geometry : angle 0.47400 / 0.25 (24769) hydrogen bonds : bond 0.03796 / 2.46 ( 1156) hydrogen bonds : angle 3.59224 / 2.54 ( 3384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7341 (mmt-90) REVERT: A 261 ASP cc_start: 0.8267 (t70) cc_final: 0.8050 (OUTLIER) REVERT: A 384 GLU cc_start: 0.8343 (pt0) cc_final: 0.8112 (pt0) REVERT: A 427 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8094 (mp0) REVERT: A 532 MET cc_start: 0.7315 (mtt) cc_final: 0.6791 (ptp) REVERT: A 568 LYS cc_start: 0.7224 (ttmt) cc_final: 0.6824 (ttmm) REVERT: A 572 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6667 (mt-10) REVERT: A 608 MET cc_start: 0.5726 (mmp) cc_final: 0.4996 (tmm) REVERT: D 46 MET cc_start: 0.8744 (mmm) cc_final: 0.8502 (mmm) REVERT: D 74 TYR cc_start: 0.8096 (t80) cc_final: 0.7489 (t80) REVERT: D 97 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7187 (mp) REVERT: D 256 MET cc_start: 0.8389 (mmm) cc_final: 0.8040 (mmt) REVERT: D 301 ARG cc_start: 0.7193 (tpt90) cc_final: 0.6850 (tpm170) REVERT: D 328 GLU cc_start: 0.8032 (tt0) cc_final: 0.7228 (mp0) REVERT: D 384 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7941 (mt-10) REVERT: D 425 MET cc_start: 0.7502 (mtp) cc_final: 0.7184 (mtm) REVERT: C 209 LYS cc_start: 0.7451 (ttmm) cc_final: 0.7002 (ttpt) REVERT: C 216 ILE cc_start: 0.8043 (mt) cc_final: 0.7776 (mp) REVERT: C 420 LYS cc_start: 0.8371 (mttt) cc_final: 0.7732 (mptt) REVERT: C 514 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.8140 (m) REVERT: C 576 GLU cc_start: 0.6372 (tt0) cc_final: 0.5790 (mt-10) REVERT: C 640 MET cc_start: 0.1327 (ttt) cc_final: 0.1012 (mmm) REVERT: B 722 ILE cc_start: 0.7292 (mm) cc_final: 0.6512 (mp) REVERT: B 728 MET cc_start: 0.5698 (mtm) cc_final: 0.5242 (mtm) REVERT: B 736 ARG cc_start: 0.6099 (ttt90) cc_final: 0.5686 (ttt90) REVERT: B 778 ARG cc_start: 0.7558 (mmp80) cc_final: 0.6504 (mmm160) REVERT: B 934 SER cc_start: 0.7926 (m) cc_final: 0.7570 (p) REVERT: B 1017 SER cc_start: 0.7808 (t) cc_final: 0.7325 (p) REVERT: B 1030 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: B 1119 MET cc_start: 0.0663 (tpp) cc_final: -0.0387 (mmt) REVERT: H 1 MET cc_start: 0.0662 (ttm) cc_final: -0.0399 (tpp) REVERT: H 110 MET cc_start: 0.1373 (mtt) cc_final: 0.0985 (mpt) REVERT: H 115 GLU cc_start: 0.1949 (mt-10) cc_final: 0.1393 (mt-10) outliers start: 28 outliers final: 19 residues processed: 197 average time/residue: 0.6294 time to fit residues: 138.0740 Evaluate side-chains 200 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1043 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 176 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 169 optimal weight: 0.0980 chunk 90 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 153 optimal weight: 30.0000 chunk 212 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 397 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.174478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.104184 restraints weight = 20068.621| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.84 r_work: 0.2962 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18298 Z= 0.164 Angle : 0.507 9.494 24769 Z= 0.263 Chirality : 0.038 0.178 2767 Planarity : 0.004 0.053 3120 Dihedral : 3.694 17.283 2438 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.49 % Allowed : 18.90 % Favored : 79.61 % 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 are not related in a simple way. whole: 2.62 (0.18), residues: 2184 helix: 2.41 (0.13), residues: 1431 sheet: 1.90 (0.58), residues: 45 loop : 0.37 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 471 TYR 0.017 0.001 TYR C 326 PHE 0.012 0.001 PHE B 870 TRP 0.013 0.001 TRP A 143 HIS 0.005 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (18298) covalent geometry : angle 0.50669 / 0.26 (24769) hydrogen bonds : bond 0.04152 / 2.70 ( 1156) hydrogen bonds : angle 3.65712 / 2.58 ( 3384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7364.23 seconds wall clock time: 125 minutes 44.76 seconds (7544.76 seconds total)