Starting phenix.real_space_refine on Thu Feb 5 15:10:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9upg_64395/02_2026/9upg_64395.cif Found real_map, /net/cci-nas-00/data/ceres_data/9upg_64395/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9upg_64395/02_2026/9upg_64395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9upg_64395/02_2026/9upg_64395.map" model { file = "/net/cci-nas-00/data/ceres_data/9upg_64395/02_2026/9upg_64395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9upg_64395/02_2026/9upg_64395.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.62, per 1000 atoms: 0.20 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: 1.40 Conformation dependent library (CDL) restraints added in 608.2 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: 0.34 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: 3.30 Time building geometry restraints manager: 1.89 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: 4.350 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.160 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 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 covalent geometry : bond 0.00450 (18298) covalent geometry : angle 0.62926 (24769) hydrogen bonds : bond 0.23879 ( 1156) hydrogen bonds : angle 6.68243 ( 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 : 0.688 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: 0.6068 time to fit residues: 133.5616 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 : 0.711 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4060 r_free = 0.4060 target = 0.178825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.108202 restraints weight = 20626.245| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.89 r_work: 0.3056 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18298 Z= 0.156 Angle : 0.533 7.820 24769 Z= 0.286 Chirality : 0.038 0.168 2767 Planarity : 0.004 0.056 3120 Dihedral : 3.975 35.093 2440 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.26 % Allowed : 16.80 % 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: 1.71 (0.17), residues: 2184 helix: 1.50 (0.13), residues: 1423 sheet: 2.94 (0.54), residues: 45 loop : 0.45 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.018 0.002 TYR C 326 PHE 0.012 0.001 PHE B 870 TRP 0.013 0.001 TRP B 811 HIS 0.010 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00355 (18298) covalent geometry : angle 0.53309 (24769) hydrogen bonds : bond 0.05491 ( 1156) hydrogen bonds : angle 4.16472 ( 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 239 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8627 (t70) cc_final: 0.8380 (OUTLIER) REVERT: A 426 ARG cc_start: 0.7926 (mmm160) cc_final: 0.7192 (mtt180) REVERT: A 427 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8374 (mp0) REVERT: A 532 MET cc_start: 0.7361 (mtt) cc_final: 0.6910 (ptp) REVERT: A 568 LYS cc_start: 0.7612 (ttmt) cc_final: 0.7111 (mtpp) REVERT: A 572 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7034 (mt-10) REVERT: A 608 MET cc_start: 0.5967 (mmp) cc_final: 0.5263 (tmm) REVERT: D 74 TYR cc_start: 0.8381 (t80) cc_final: 0.7751 (t80) REVERT: D 301 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6988 (tpm170) REVERT: D 328 GLU cc_start: 0.8243 (tt0) cc_final: 0.7673 (mp0) REVERT: D 384 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8053 (mt-10) REVERT: D 425 MET cc_start: 0.7620 (mtp) cc_final: 0.7360 (mtm) REVERT: D 483 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6223 (pp20) REVERT: C 209 LYS cc_start: 0.7712 (ttmm) cc_final: 0.7303 (ttpt) REVERT: C 216 ILE cc_start: 0.8361 (mt) cc_final: 0.8107 (mp) REVERT: C 376 SER cc_start: 0.8508 (m) cc_final: 0.8172 (p) REVERT: C 420 LYS cc_start: 0.8528 (mttt) cc_final: 0.7974 (mptt) REVERT: C 473 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8267 (mm-40) REVERT: C 562 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: C 576 GLU cc_start: 0.6626 (tt0) cc_final: 0.6145 (mt-10) REVERT: B 722 ILE cc_start: 0.7627 (mm) cc_final: 0.7062 (mp) REVERT: B 736 ARG cc_start: 0.6404 (ttt90) cc_final: 0.5864 (ttt90) REVERT: B 778 ARG cc_start: 0.8058 (mmp80) cc_final: 0.7015 (mmm160) REVERT: B 934 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.8065 (p) REVERT: B 1017 SER cc_start: 0.7814 (t) cc_final: 0.7476 (p) REVERT: B 1030 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8313 (mp0) REVERT: B 1119 MET cc_start: 0.0389 (tpp) cc_final: -0.0269 (mmt) REVERT: H 1 MET cc_start: 0.0172 (ttm) cc_final: -0.0536 (tpp) REVERT: H 37 MET cc_start: -0.2028 (OUTLIER) cc_final: -0.2555 (tpt) REVERT: H 77 MET cc_start: -0.1414 (ptt) cc_final: -0.2422 (mmt) REVERT: H 110 MET cc_start: 0.0663 (mtt) cc_final: 0.0372 (mpt) REVERT: H 115 GLU cc_start: 0.2202 (mt-10) cc_final: 0.1743 (mt-10) REVERT: H 124 GLU cc_start: 0.0841 (tm-30) cc_final: 0.0533 (mm-30) outliers start: 44 outliers final: 11 residues processed: 229 average time/residue: 0.5949 time to fit residues: 152.5723 Evaluate side-chains 205 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 1086 SER Chi-restraints excluded: chain H residue 37 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 90 optimal weight: 2.9990 chunk 138 optimal weight: 0.0370 chunk 36 optimal weight: 0.0470 chunk 167 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 188 optimal weight: 0.3980 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 GLN C 379 ASN C 397 GLN C 607 ASN C 627 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.181765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122046 restraints weight = 20644.022| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.91 r_work: 0.3145 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18298 Z= 0.105 Angle : 0.453 6.784 24769 Z= 0.242 Chirality : 0.036 0.138 2767 Planarity : 0.004 0.053 3120 Dihedral : 3.705 16.789 2438 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.31 % Allowed : 16.90 % Favored : 80.79 % 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: 2.31 (0.17), residues: 2184 helix: 2.07 (0.13), residues: 1423 sheet: 2.67 (0.57), residues: 45 loop : 0.44 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 198 TYR 0.016 0.001 TYR C 319 PHE 0.013 0.001 PHE D 224 TRP 0.011 0.001 TRP A 143 HIS 0.008 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00210 (18298) covalent geometry : angle 0.45279 (24769) hydrogen bonds : bond 0.04339 ( 1156) hydrogen bonds : angle 3.78707 ( 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: 45 poor density : 198 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8565 (t70) cc_final: 0.8324 (OUTLIER) REVERT: A 312 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7126 (pt) REVERT: A 426 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7193 (mtt180) REVERT: A 427 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8342 (mp0) REVERT: A 532 MET cc_start: 0.7301 (mtt) cc_final: 0.6816 (ptp) REVERT: A 572 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6982 (mt-10) REVERT: A 608 MET cc_start: 0.5902 (mmp) cc_final: 0.5187 (tmm) REVERT: D 46 MET cc_start: 0.8990 (mmm) cc_final: 0.8729 (tpt) REVERT: D 74 TYR cc_start: 0.8379 (t80) cc_final: 0.7796 (t80) REVERT: D 102 LYS cc_start: 0.7956 (mmtp) cc_final: 0.7708 (mmtp) REVERT: D 301 ARG cc_start: 0.7523 (tpt90) cc_final: 0.7079 (tpm170) REVERT: D 305 ASP cc_start: 0.7729 (m-30) cc_final: 0.7514 (m-30) REVERT: D 328 GLU cc_start: 0.8276 (tt0) cc_final: 0.7720 (mp0) REVERT: D 342 THR cc_start: 0.9096 (m) cc_final: 0.8857 (p) REVERT: D 384 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8078 (mt-10) REVERT: D 425 MET cc_start: 0.7552 (mtp) cc_final: 0.7309 (mtm) REVERT: D 483 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6444 (pp20) REVERT: D 517 GLU cc_start: 0.3368 (OUTLIER) cc_final: 0.3030 (pt0) REVERT: C 209 LYS cc_start: 0.7719 (ttmm) cc_final: 0.7321 (ttpt) REVERT: C 376 SER cc_start: 0.8455 (m) cc_final: 0.8139 (p) REVERT: C 420 LYS cc_start: 0.8592 (mttt) cc_final: 0.8000 (mmtt) REVERT: C 514 SER cc_start: 0.8443 (p) cc_final: 0.8223 (m) REVERT: C 562 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: C 576 GLU cc_start: 0.6588 (tt0) cc_final: 0.6086 (mt-10) REVERT: C 640 MET cc_start: 0.0986 (ttt) cc_final: 0.0401 (mtt) REVERT: B 722 ILE cc_start: 0.7662 (mm) cc_final: 0.6994 (mp) REVERT: B 728 MET cc_start: 0.6272 (mtm) cc_final: 0.5833 (mtm) REVERT: B 736 ARG cc_start: 0.6382 (ttt90) cc_final: 0.5958 (ttt90) REVERT: B 778 ARG cc_start: 0.7976 (mmp80) cc_final: 0.6986 (mmm160) REVERT: B 934 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.8031 (p) REVERT: B 1017 SER cc_start: 0.7788 (t) cc_final: 0.7479 (p) REVERT: B 1030 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: B 1119 MET cc_start: 0.0653 (tpp) cc_final: -0.0462 (mmt) REVERT: H 1 MET cc_start: 0.0479 (ttm) cc_final: -0.0527 (tpp) REVERT: H 37 MET cc_start: -0.1935 (ttp) cc_final: -0.2393 (tpt) REVERT: H 110 MET cc_start: 0.1362 (mtt) cc_final: 0.0968 (mpt) REVERT: H 115 GLU cc_start: 0.2164 (mt-10) cc_final: 0.1645 (mt-10) REVERT: H 124 GLU cc_start: 0.0599 (tm-30) cc_final: 0.0372 (mm-30) outliers start: 45 outliers final: 16 residues processed: 226 average time/residue: 0.5709 time to fit residues: 144.1551 Evaluate side-chains 205 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 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 419 ILE Chi-restraints excluded: chain D residue 448 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 934 SER Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1030 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 133 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 195 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 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 = 0.4062 r_free = 0.4062 target = 0.178707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108992 restraints weight = 20703.103| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.86 r_work: 0.3063 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18298 Z= 0.145 Angle : 0.479 7.216 24769 Z= 0.255 Chirality : 0.037 0.177 2767 Planarity : 0.004 0.052 3120 Dihedral : 3.714 16.361 2438 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.98 % Allowed : 16.54 % Favored : 80.48 % 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: 2.46 (0.18), residues: 2184 helix: 2.22 (0.13), residues: 1427 sheet: 2.37 (0.58), residues: 45 loop : 0.45 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 213 TYR 0.017 0.001 TYR C 326 PHE 0.012 0.001 PHE B 870 TRP 0.012 0.001 TRP A 143 HIS 0.011 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00340 (18298) covalent geometry : angle 0.47924 (24769) hydrogen bonds : bond 0.04406 ( 1156) hydrogen bonds : angle 3.73591 ( 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 245 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 187 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8638 (t70) cc_final: 0.8383 (OUTLIER) REVERT: A 312 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.7220 (pt) REVERT: A 427 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8335 (mp0) REVERT: A 532 MET cc_start: 0.7329 (mtt) cc_final: 0.6833 (ptp) REVERT: A 568 LYS cc_start: 0.7603 (ttmt) cc_final: 0.7148 (ttmm) REVERT: A 572 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6864 (mt-10) REVERT: A 608 MET cc_start: 0.5875 (mmp) cc_final: 0.5137 (tmm) REVERT: D 74 TYR cc_start: 0.8362 (t80) cc_final: 0.7762 (t80) REVERT: D 328 GLU cc_start: 0.8227 (tt0) cc_final: 0.7567 (mp0) REVERT: D 384 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8198 (mt-10) REVERT: D 425 MET cc_start: 0.7567 (mtp) cc_final: 0.7288 (mtm) REVERT: D 483 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6490 (pp20) REVERT: D 517 GLU cc_start: 0.3415 (OUTLIER) cc_final: 0.3190 (pt0) REVERT: C 209 LYS cc_start: 0.7759 (ttmm) cc_final: 0.7336 (ttpt) REVERT: C 216 ILE cc_start: 0.8395 (mt) cc_final: 0.8161 (mp) REVERT: C 420 LYS cc_start: 0.8559 (mttt) cc_final: 0.7949 (mmtt) REVERT: C 562 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: C 576 GLU cc_start: 0.6567 (tt0) cc_final: 0.6045 (mt-10) REVERT: C 640 MET cc_start: 0.1384 (ttt) cc_final: 0.0773 (mtt) REVERT: B 722 ILE cc_start: 0.7626 (mm) cc_final: 0.6973 (mp) REVERT: B 728 MET cc_start: 0.6248 (mtm) cc_final: 0.5759 (mtm) REVERT: B 736 ARG cc_start: 0.6435 (ttt90) cc_final: 0.5939 (ttt90) REVERT: B 778 ARG cc_start: 0.8000 (mmp80) cc_final: 0.6972 (mmm160) REVERT: B 934 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.8079 (p) REVERT: B 1017 SER cc_start: 0.7961 (t) cc_final: 0.7562 (p) REVERT: B 1030 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: B 1119 MET cc_start: 0.0642 (tpp) cc_final: -0.0458 (mmt) REVERT: H 1 MET cc_start: 0.0437 (ttm) cc_final: -0.0482 (tpp) REVERT: H 37 MET cc_start: -0.2046 (ttp) cc_final: -0.2347 (tpt) REVERT: H 110 MET cc_start: 0.1375 (mtt) cc_final: 0.0970 (mpt) REVERT: H 115 GLU cc_start: 0.2254 (mt-10) cc_final: 0.1715 (mt-10) REVERT: H 124 GLU cc_start: 0.0690 (tm-30) cc_final: 0.0457 (mm-30) outliers start: 58 outliers final: 21 residues processed: 227 average time/residue: 0.5710 time to fit residues: 145.1834 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 : 0.499 ------------------------------------------------------------------------------- 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 150 LEU Chi-restraints excluded: chain D residue 292 LEU 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 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 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 995 ILE Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain B residue 1030 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 74 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 915 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.177752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108391 restraints weight = 20240.217| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.84 r_work: 0.3053 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18298 Z= 0.112 Angle : 0.463 9.699 24769 Z= 0.242 Chirality : 0.037 0.369 2767 Planarity : 0.003 0.052 3120 Dihedral : 3.662 18.282 2438 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.52 % Allowed : 17.10 % Favored : 80.38 % 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: 1429 sheet: 2.19 (0.59), residues: 45 loop : 0.49 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 C 143 HIS 0.011 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00247 (18298) covalent geometry : angle 0.46275 (24769) hydrogen bonds : bond 0.03962 ( 1156) hydrogen bonds : angle 3.64125 ( 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 238 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8412 (t70) cc_final: 0.8175 (OUTLIER) REVERT: A 312 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.6990 (pt) REVERT: A 427 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8111 (mp0) REVERT: A 532 MET cc_start: 0.7300 (mtt) cc_final: 0.6751 (ptp) REVERT: A 568 LYS cc_start: 0.7322 (ttmt) cc_final: 0.6878 (ttmm) REVERT: A 572 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6677 (mt-10) REVERT: A 608 MET cc_start: 0.5959 (mmp) cc_final: 0.5215 (tmm) REVERT: D 74 TYR cc_start: 0.8208 (t80) cc_final: 0.7617 (t80) REVERT: D 97 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7377 (mp) REVERT: D 102 LYS cc_start: 0.7654 (mmtp) cc_final: 0.7343 (mmtp) REVERT: D 256 MET cc_start: 0.8580 (mmm) cc_final: 0.8176 (mmt) REVERT: D 301 ARG cc_start: 0.7275 (tpt90) cc_final: 0.6861 (tpm170) REVERT: D 305 ASP cc_start: 0.7511 (m-30) cc_final: 0.7289 (m-30) REVERT: D 328 GLU cc_start: 0.8084 (tt0) cc_final: 0.7330 (mp0) REVERT: D 384 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8005 (mt-10) REVERT: D 425 MET cc_start: 0.7453 (mtp) cc_final: 0.7137 (mtm) REVERT: D 428 ASN cc_start: 0.7966 (t0) cc_final: 0.7725 (t0) REVERT: D 483 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6475 (pp20) REVERT: C 209 LYS cc_start: 0.7555 (ttmm) cc_final: 0.7120 (ttpt) REVERT: C 216 ILE cc_start: 0.8216 (mt) cc_final: 0.7970 (mp) REVERT: C 420 LYS cc_start: 0.8444 (mttt) cc_final: 0.7803 (mmtt) REVERT: C 562 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: C 576 GLU cc_start: 0.6405 (tt0) cc_final: 0.5894 (mt-10) REVERT: C 640 MET cc_start: 0.1275 (ttt) cc_final: 0.0811 (mtt) REVERT: B 722 ILE cc_start: 0.7431 (mm) cc_final: 0.6734 (mp) REVERT: B 728 MET cc_start: 0.5951 (mtm) cc_final: 0.5535 (mtm) REVERT: B 736 ARG cc_start: 0.6256 (ttt90) cc_final: 0.5848 (ttt90) REVERT: B 778 ARG cc_start: 0.7709 (mmp80) cc_final: 0.6684 (mmm160) REVERT: B 934 SER cc_start: 0.8170 (OUTLIER) cc_final: 0.7810 (p) REVERT: B 1017 SER cc_start: 0.7794 (t) cc_final: 0.7355 (p) REVERT: B 1030 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: B 1119 MET cc_start: 0.0577 (tpp) cc_final: -0.0343 (mmt) REVERT: H 1 MET cc_start: 0.0254 (ttm) cc_final: -0.0545 (tpp) REVERT: H 37 MET cc_start: -0.1930 (OUTLIER) cc_final: -0.2267 (tpt) REVERT: H 110 MET cc_start: 0.1216 (mtt) cc_final: 0.0883 (mpt) REVERT: H 115 GLU cc_start: 0.2262 (mt-10) cc_final: 0.1723 (mt-10) REVERT: H 124 GLU cc_start: 0.0618 (tm-30) cc_final: 0.0385 (mm-30) outliers start: 49 outliers final: 20 residues processed: 221 average time/residue: 0.6293 time to fit residues: 154.6753 Evaluate side-chains 204 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 269 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 414 ASP 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 448 GLU Chi-restraints excluded: chain D residue 462 THR 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: 0.9980 chunk 78 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 chunk 2 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3993 r_free = 0.3993 target = 0.175768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105238 restraints weight = 20012.176| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.86 r_work: 0.2975 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18298 Z= 0.136 Angle : 0.476 9.815 24769 Z= 0.249 Chirality : 0.037 0.228 2767 Planarity : 0.004 0.053 3120 Dihedral : 3.646 16.729 2438 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.72 % Allowed : 17.10 % Favored : 80.17 % 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: 2.59 (0.18), residues: 2184 helix: 2.33 (0.13), residues: 1443 sheet: 2.16 (0.58), residues: 45 loop : 0.46 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 198 TYR 0.015 0.001 TYR C 326 PHE 0.011 0.001 PHE B 870 TRP 0.012 0.001 TRP A 143 HIS 0.011 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00320 (18298) covalent geometry : angle 0.47598 (24769) hydrogen bonds : bond 0.04087 ( 1156) hydrogen bonds : angle 3.62618 ( 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 231 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8312 (t70) cc_final: 0.8091 (OUTLIER) REVERT: A 427 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8083 (mp0) REVERT: A 532 MET cc_start: 0.7335 (mtt) cc_final: 0.6788 (ptp) REVERT: A 568 LYS cc_start: 0.7218 (ttmt) cc_final: 0.6770 (ttmm) REVERT: A 572 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6634 (mt-10) REVERT: A 608 MET cc_start: 0.5808 (mmp) cc_final: 0.5162 (tmm) REVERT: D 74 TYR cc_start: 0.8127 (t80) cc_final: 0.7524 (t80) REVERT: D 97 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7229 (mp) REVERT: D 301 ARG cc_start: 0.7178 (tpt90) cc_final: 0.6819 (tpm170) REVERT: D 328 GLU cc_start: 0.8061 (tt0) cc_final: 0.7266 (mp0) REVERT: D 329 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7559 (tpp-160) REVERT: D 384 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7992 (mt-10) REVERT: D 425 MET cc_start: 0.7427 (mtp) cc_final: 0.7096 (mtm) REVERT: D 428 ASN cc_start: 0.7971 (t0) cc_final: 0.7741 (t0) REVERT: C 209 LYS cc_start: 0.7444 (ttmm) cc_final: 0.7008 (ttpt) REVERT: C 216 ILE cc_start: 0.8121 (mt) cc_final: 0.7856 (mp) REVERT: C 420 LYS cc_start: 0.8392 (mttt) cc_final: 0.7711 (mmtt) REVERT: C 562 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: C 576 GLU cc_start: 0.6350 (tt0) cc_final: 0.5799 (mt-10) REVERT: C 640 MET cc_start: 0.1597 (ttt) cc_final: 0.1188 (mmm) REVERT: B 722 ILE cc_start: 0.7305 (mm) cc_final: 0.6550 (mp) REVERT: B 728 MET cc_start: 0.5755 (mtm) cc_final: 0.5294 (mtm) REVERT: B 736 ARG cc_start: 0.6192 (ttt90) cc_final: 0.5749 (ttt90) REVERT: B 778 ARG cc_start: 0.7640 (mmp80) cc_final: 0.6594 (mmm160) REVERT: B 934 SER cc_start: 0.8076 (OUTLIER) cc_final: 0.7719 (p) REVERT: B 1017 SER cc_start: 0.7768 (t) cc_final: 0.7274 (p) REVERT: B 1030 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: B 1119 MET cc_start: 0.0699 (tpp) cc_final: -0.0365 (mmt) REVERT: H 1 MET cc_start: 0.0354 (ttm) cc_final: -0.0545 (tpp) REVERT: H 37 MET cc_start: -0.2102 (OUTLIER) cc_final: -0.2342 (tpt) REVERT: H 110 MET cc_start: 0.1284 (mtt) cc_final: 0.0918 (mpt) REVERT: H 115 GLU cc_start: 0.2037 (mt-10) cc_final: 0.1535 (mt-10) outliers start: 53 outliers final: 23 residues processed: 211 average time/residue: 0.6957 time to fit residues: 163.4264 Evaluate side-chains 201 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 414 ASP 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 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 D residue 462 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 256 MET 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 655 MET 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 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: 5.9990 chunk 59 optimal weight: 0.0570 chunk 154 optimal weight: 0.6980 chunk 103 optimal weight: 0.0060 chunk 198 optimal weight: 4.9990 chunk 177 optimal weight: 0.0980 chunk 79 optimal weight: 3.9990 chunk 28 optimal weight: 0.0170 chunk 66 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.1552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN C 287 HIS C 397 GLN B 653 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.179973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112054 restraints weight = 20362.507| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.82 r_work: 0.3115 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 18298 Z= 0.092 Angle : 0.437 7.785 24769 Z= 0.230 Chirality : 0.036 0.197 2767 Planarity : 0.003 0.053 3120 Dihedral : 3.532 17.565 2438 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.75 % Allowed : 18.39 % 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: 2.88 (0.18), residues: 2184 helix: 2.58 (0.13), residues: 1434 sheet: 2.21 (0.57), residues: 45 loop : 0.53 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 614 TYR 0.016 0.001 TYR A 319 PHE 0.014 0.001 PHE D 224 TRP 0.013 0.001 TRP C 143 HIS 0.010 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00177 (18298) covalent geometry : angle 0.43700 (24769) hydrogen bonds : bond 0.03458 ( 1156) hydrogen bonds : angle 3.49112 ( 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 230 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 ASP cc_start: 0.7942 (m-30) cc_final: 0.7700 (t70) REVERT: A 427 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8160 (mp0) REVERT: A 532 MET cc_start: 0.7265 (mtt) cc_final: 0.6746 (ptp) REVERT: A 568 LYS cc_start: 0.7339 (ttmt) cc_final: 0.6870 (ttmm) REVERT: A 572 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6700 (mt-10) REVERT: A 608 MET cc_start: 0.5802 (mmp) cc_final: 0.5164 (tmm) REVERT: D 46 MET cc_start: 0.8798 (mmm) cc_final: 0.8564 (tpt) REVERT: D 74 TYR cc_start: 0.8179 (t80) cc_final: 0.7653 (t80) REVERT: D 97 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7360 (mp) REVERT: D 102 LYS cc_start: 0.7647 (mmtp) cc_final: 0.7324 (mmtp) REVERT: D 256 MET cc_start: 0.8572 (mmm) cc_final: 0.8154 (mmt) REVERT: D 262 MET cc_start: 0.8361 (mmp) cc_final: 0.8160 (mmp) REVERT: D 266 SER cc_start: 0.8530 (t) cc_final: 0.8060 (m) REVERT: D 301 ARG cc_start: 0.7330 (tpt90) cc_final: 0.7037 (tpm170) REVERT: D 328 GLU cc_start: 0.8067 (tt0) cc_final: 0.7336 (mp0) REVERT: D 384 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8011 (mt-10) REVERT: D 425 MET cc_start: 0.7446 (mtp) cc_final: 0.7138 (mtm) REVERT: C 209 LYS cc_start: 0.7543 (ttmm) cc_final: 0.7084 (ttpt) REVERT: C 216 ILE cc_start: 0.8205 (mt) cc_final: 0.7968 (mp) REVERT: C 420 LYS cc_start: 0.8490 (mttt) cc_final: 0.7825 (mmtt) REVERT: C 424 ASP cc_start: 0.6421 (t0) cc_final: 0.6168 (t0) REVERT: C 430 LYS cc_start: 0.8195 (ptmm) cc_final: 0.7907 (pttp) REVERT: C 514 SER cc_start: 0.8421 (p) cc_final: 0.8192 (m) REVERT: C 562 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: C 576 GLU cc_start: 0.6440 (tt0) cc_final: 0.5870 (mt-10) REVERT: C 640 MET cc_start: 0.1681 (ttt) cc_final: 0.1216 (mmm) REVERT: B 662 PHE cc_start: 0.7857 (m-80) cc_final: 0.7518 (m-10) REVERT: B 722 ILE cc_start: 0.7399 (mm) cc_final: 0.6717 (mp) REVERT: B 728 MET cc_start: 0.5895 (mtm) cc_final: 0.5591 (mtm) REVERT: B 736 ARG cc_start: 0.6168 (ttt90) cc_final: 0.5745 (ttt90) REVERT: B 778 ARG cc_start: 0.7698 (mmp80) cc_final: 0.6684 (mmm160) REVERT: B 934 SER cc_start: 0.8140 (m) cc_final: 0.7766 (p) REVERT: B 992 LYS cc_start: 0.8733 (tttt) cc_final: 0.8370 (ttpm) REVERT: B 1017 SER cc_start: 0.7743 (t) cc_final: 0.7330 (p) REVERT: B 1083 MET cc_start: 0.6607 (mtp) cc_final: 0.6386 (mtt) REVERT: B 1119 MET cc_start: 0.0643 (tpp) cc_final: -0.0403 (mmt) REVERT: H 1 MET cc_start: 0.0349 (ttm) cc_final: -0.0600 (tpp) REVERT: H 37 MET cc_start: -0.2085 (OUTLIER) cc_final: -0.2331 (tpt) REVERT: H 110 MET cc_start: 0.1261 (mtt) cc_final: 0.0951 (mpt) REVERT: H 115 GLU cc_start: 0.2030 (mt-10) cc_final: 0.1498 (mt-10) outliers start: 34 outliers final: 11 residues processed: 218 average time/residue: 0.6712 time to fit residues: 162.6251 Evaluate side-chains 198 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 261 ASP 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 317 THR Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain H residue 37 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 145 optimal weight: 0.9990 chunk 215 optimal weight: 7.9990 chunk 191 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 171 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS C 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105791 restraints weight = 20122.317| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.87 r_work: 0.2985 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18298 Z= 0.137 Angle : 0.489 8.465 24769 Z= 0.255 Chirality : 0.037 0.230 2767 Planarity : 0.003 0.052 3120 Dihedral : 3.593 19.706 2438 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.64 % Allowed : 18.64 % Favored : 79.71 % 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: 2.86 (0.18), residues: 2184 helix: 2.57 (0.13), residues: 1436 sheet: 2.12 (0.57), residues: 45 loop : 0.51 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.016 0.001 TYR C 326 PHE 0.012 0.001 PHE B 870 TRP 0.010 0.001 TRP A 143 HIS 0.009 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00324 (18298) covalent geometry : angle 0.48915 (24769) hydrogen bonds : bond 0.03950 ( 1156) hydrogen bonds : angle 3.56036 ( 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 218 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8277 (t70) cc_final: 0.8047 (t0) REVERT: A 427 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8087 (mp0) REVERT: A 447 SER cc_start: 0.8606 (m) cc_final: 0.8369 (p) REVERT: A 532 MET cc_start: 0.7334 (mtt) cc_final: 0.6748 (ptp) REVERT: A 568 LYS cc_start: 0.7244 (ttmt) cc_final: 0.6800 (ttmm) REVERT: A 572 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6652 (mt-10) REVERT: A 608 MET cc_start: 0.5789 (mmp) cc_final: 0.5141 (tmm) REVERT: D 74 TYR cc_start: 0.8082 (t80) cc_final: 0.7514 (t80) REVERT: D 97 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.7232 (mp) REVERT: D 247 MET cc_start: 0.8938 (mmp) cc_final: 0.8726 (mmm) REVERT: D 256 MET cc_start: 0.8453 (mmm) cc_final: 0.8124 (mmt) REVERT: D 266 SER cc_start: 0.8459 (t) cc_final: 0.7969 (m) REVERT: D 301 ARG cc_start: 0.7184 (tpt90) cc_final: 0.6845 (tpm170) REVERT: D 328 GLU cc_start: 0.8059 (tt0) cc_final: 0.7246 (mp0) REVERT: D 384 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8012 (mt-10) REVERT: D 425 MET cc_start: 0.7504 (mtp) cc_final: 0.7136 (mtm) REVERT: C 209 LYS cc_start: 0.7422 (ttmm) cc_final: 0.6985 (ttpt) REVERT: C 216 ILE cc_start: 0.8101 (mt) cc_final: 0.7843 (mp) REVERT: C 420 LYS cc_start: 0.8358 (mttt) cc_final: 0.7667 (mmtt) REVERT: C 562 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: C 576 GLU cc_start: 0.6387 (tt0) cc_final: 0.5803 (mt-10) REVERT: C 593 MET cc_start: 0.1122 (mpt) cc_final: 0.0714 (mmt) REVERT: C 640 MET cc_start: 0.1895 (ttt) cc_final: 0.1438 (mmm) REVERT: B 722 ILE cc_start: 0.7278 (mm) cc_final: 0.6519 (mp) REVERT: B 728 MET cc_start: 0.5723 (mtm) cc_final: 0.5267 (mtm) REVERT: B 736 ARG cc_start: 0.6118 (ttt90) cc_final: 0.5785 (ttt90) REVERT: B 778 ARG cc_start: 0.7530 (mmp80) cc_final: 0.6506 (mmm160) REVERT: B 934 SER cc_start: 0.7965 (m) cc_final: 0.7592 (p) REVERT: B 942 ASP cc_start: 0.8114 (m-30) cc_final: 0.7826 (m-30) REVERT: B 1017 SER cc_start: 0.7730 (t) cc_final: 0.7249 (p) REVERT: B 1030 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: B 1119 MET cc_start: 0.0597 (tpp) cc_final: -0.0422 (mmt) REVERT: H 1 MET cc_start: 0.0461 (ttm) cc_final: -0.0465 (tpp) REVERT: H 37 MET cc_start: -0.2005 (OUTLIER) cc_final: -0.2268 (tpt) REVERT: H 110 MET cc_start: 0.1251 (mtt) cc_final: 0.0889 (mpt) REVERT: H 115 GLU cc_start: 0.1961 (mt-10) cc_final: 0.1440 (mt-10) outliers start: 32 outliers final: 13 residues processed: 206 average time/residue: 0.6818 time to fit residues: 156.6551 Evaluate side-chains 201 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 250 ASP Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain C residue 256 MET 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 655 MET Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain H residue 37 MET 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: 4.9990 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 153 optimal weight: 30.0000 chunk 199 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS C 397 GLN H 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.174158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103707 restraints weight = 20170.365| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.85 r_work: 0.2965 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2255 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= 0.195 Angle : 0.527 9.085 24769 Z= 0.274 Chirality : 0.039 0.276 2767 Planarity : 0.004 0.052 3120 Dihedral : 3.745 17.274 2438 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.59 % Allowed : 18.75 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.60 (0.18), residues: 2184 helix: 2.37 (0.13), residues: 1437 sheet: 2.00 (0.58), residues: 45 loop : 0.41 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 471 TYR 0.019 0.002 TYR C 326 PHE 0.012 0.001 PHE D 43 TRP 0.011 0.001 TRP A 143 HIS 0.009 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00474 (18298) covalent geometry : angle 0.52662 (24769) hydrogen bonds : bond 0.04470 ( 1156) hydrogen bonds : angle 3.70794 ( 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 217 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ARG cc_start: 0.7771 (mtp85) cc_final: 0.7440 (mmt-90) REVERT: A 261 ASP cc_start: 0.8358 (t70) cc_final: 0.8133 (t0) REVERT: A 427 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8090 (mp0) REVERT: A 532 MET cc_start: 0.7352 (mtt) cc_final: 0.6806 (ptp) REVERT: A 568 LYS cc_start: 0.7298 (ttmt) cc_final: 0.6849 (ttmm) REVERT: A 572 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6642 (mt-10) REVERT: A 608 MET cc_start: 0.5671 (mmp) cc_final: 0.4977 (tmm) REVERT: D 74 TYR cc_start: 0.8128 (t80) cc_final: 0.7491 (t80) REVERT: D 97 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7259 (mp) REVERT: D 247 MET cc_start: 0.9016 (mmp) cc_final: 0.8765 (mmt) REVERT: D 266 SER cc_start: 0.8459 (t) cc_final: 0.7958 (m) REVERT: D 288 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7323 (mtpp) REVERT: D 301 ARG cc_start: 0.7209 (tpt90) cc_final: 0.6871 (tpm170) REVERT: D 328 GLU cc_start: 0.8146 (tt0) cc_final: 0.7328 (mp0) REVERT: D 384 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8006 (mt-10) REVERT: D 425 MET cc_start: 0.7513 (mtp) cc_final: 0.7169 (mtm) REVERT: C 209 LYS cc_start: 0.7492 (ttmm) cc_final: 0.7044 (ttpt) REVERT: C 216 ILE cc_start: 0.8151 (mt) cc_final: 0.7876 (mp) REVERT: C 420 LYS cc_start: 0.8371 (mttt) cc_final: 0.7707 (mmtt) REVERT: C 427 GLU cc_start: 0.7904 (tp30) cc_final: 0.7573 (tp30) REVERT: C 430 LYS cc_start: 0.8284 (ptmm) cc_final: 0.8003 (pttp) REVERT: C 471 ARG cc_start: 0.7517 (ptt90) cc_final: 0.7299 (ptt90) REVERT: C 562 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: C 576 GLU cc_start: 0.6464 (tt0) cc_final: 0.5879 (mt-10) REVERT: C 593 MET cc_start: 0.1349 (mpt) cc_final: 0.0985 (mmt) REVERT: C 640 MET cc_start: 0.1667 (ttt) cc_final: 0.1204 (mmm) REVERT: B 722 ILE cc_start: 0.7249 (mm) cc_final: 0.6495 (mp) REVERT: B 728 MET cc_start: 0.5763 (mtm) cc_final: 0.5282 (mtm) REVERT: B 736 ARG cc_start: 0.6223 (ttt90) cc_final: 0.5804 (ttt90) REVERT: B 778 ARG cc_start: 0.7615 (mmp80) cc_final: 0.6565 (mmm160) REVERT: B 934 SER cc_start: 0.8012 (m) cc_final: 0.7656 (p) REVERT: B 1017 SER cc_start: 0.7997 (t) cc_final: 0.7458 (p) REVERT: B 1030 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: B 1119 MET cc_start: 0.0668 (tpp) cc_final: -0.0300 (mmt) REVERT: H 1 MET cc_start: 0.0467 (ttm) cc_final: -0.0447 (tpp) REVERT: H 37 MET cc_start: -0.2065 (OUTLIER) cc_final: -0.2354 (tpt) REVERT: H 110 MET cc_start: 0.1325 (mtt) cc_final: 0.0927 (mpt) REVERT: H 115 GLU cc_start: 0.1956 (mt-10) cc_final: 0.1421 (mt-10) REVERT: H 146 MET cc_start: 0.0584 (OUTLIER) cc_final: -0.0130 (pmt) outliers start: 31 outliers final: 15 residues processed: 202 average time/residue: 0.6716 time to fit residues: 150.9214 Evaluate side-chains 206 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 288 LYS Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain C residue 256 MET 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 693 LEU 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 H residue 37 MET Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 146 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 178 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN C 252 HIS C 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105815 restraints weight = 20050.466| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.85 r_work: 0.2996 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18298 Z= 0.118 Angle : 0.481 9.666 24769 Z= 0.248 Chirality : 0.037 0.254 2767 Planarity : 0.003 0.053 3120 Dihedral : 3.643 17.388 2438 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.23 % Allowed : 19.26 % Favored : 79.51 % 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: 2.76 (0.18), residues: 2184 helix: 2.50 (0.13), residues: 1437 sheet: 1.97 (0.58), residues: 45 loop : 0.45 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 198 TYR 0.015 0.001 TYR A 319 PHE 0.009 0.001 PHE B 870 TRP 0.013 0.001 TRP A 143 HIS 0.009 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00272 (18298) covalent geometry : angle 0.48117 (24769) hydrogen bonds : bond 0.03831 ( 1156) hydrogen bonds : angle 3.59950 ( 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 212 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ARG cc_start: 0.7766 (mtp85) cc_final: 0.7410 (mmt-90) REVERT: A 261 ASP cc_start: 0.8305 (t70) cc_final: 0.8071 (t0) REVERT: A 414 ASP cc_start: 0.7912 (m-30) cc_final: 0.7707 (t70) REVERT: A 427 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8167 (mp0) REVERT: A 532 MET cc_start: 0.7318 (mtt) cc_final: 0.6799 (ptp) REVERT: A 568 LYS cc_start: 0.7342 (ttmt) cc_final: 0.6928 (ttmm) REVERT: A 572 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6713 (mt-10) REVERT: A 608 MET cc_start: 0.5722 (mmp) cc_final: 0.5003 (tmm) REVERT: D 74 TYR cc_start: 0.8166 (t80) cc_final: 0.7577 (t80) REVERT: D 97 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7275 (mp) REVERT: D 102 LYS cc_start: 0.7498 (mmtp) cc_final: 0.7168 (mmtp) REVERT: D 247 MET cc_start: 0.8981 (mmp) cc_final: 0.8698 (mmt) REVERT: D 256 MET cc_start: 0.8503 (mmm) cc_final: 0.8172 (mmt) REVERT: D 266 SER cc_start: 0.8511 (t) cc_final: 0.7991 (m) REVERT: D 301 ARG cc_start: 0.7257 (tpt90) cc_final: 0.6934 (tpm170) REVERT: D 328 GLU cc_start: 0.8058 (tt0) cc_final: 0.7294 (mp0) REVERT: D 384 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8010 (mt-10) REVERT: D 425 MET cc_start: 0.7495 (mtp) cc_final: 0.7187 (mtm) REVERT: C 209 LYS cc_start: 0.7541 (ttmm) cc_final: 0.7095 (ttpt) REVERT: C 216 ILE cc_start: 0.8135 (mt) cc_final: 0.7875 (mp) REVERT: C 420 LYS cc_start: 0.8420 (mttt) cc_final: 0.7757 (mmtt) REVERT: C 427 GLU cc_start: 0.7916 (tp30) cc_final: 0.7592 (tp30) REVERT: C 430 LYS cc_start: 0.8355 (ptmm) cc_final: 0.8074 (pttp) REVERT: C 471 ARG cc_start: 0.7599 (ptt90) cc_final: 0.7393 (ptt90) REVERT: C 562 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: C 576 GLU cc_start: 0.6398 (tt0) cc_final: 0.5819 (mt-10) REVERT: C 593 MET cc_start: 0.1355 (mpt) cc_final: 0.0988 (mmt) REVERT: C 640 MET cc_start: 0.1861 (ttt) cc_final: 0.1377 (mmm) REVERT: B 722 ILE cc_start: 0.7327 (mm) cc_final: 0.6571 (mp) REVERT: B 728 MET cc_start: 0.5769 (mtm) cc_final: 0.5297 (mtm) REVERT: B 736 ARG cc_start: 0.6138 (ttt90) cc_final: 0.5767 (ttt90) REVERT: B 778 ARG cc_start: 0.7632 (mmp80) cc_final: 0.6581 (mmm160) REVERT: B 934 SER cc_start: 0.8010 (m) cc_final: 0.7647 (p) REVERT: B 1017 SER cc_start: 0.7923 (t) cc_final: 0.7435 (p) REVERT: B 1030 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: B 1119 MET cc_start: 0.0685 (tpp) cc_final: -0.0304 (mmt) REVERT: H 1 MET cc_start: 0.0604 (ttm) cc_final: -0.0419 (tpp) REVERT: H 37 MET cc_start: -0.2258 (OUTLIER) cc_final: -0.2478 (tpt) REVERT: H 110 MET cc_start: 0.1379 (mtt) cc_final: 0.1019 (mpt) REVERT: H 146 MET cc_start: 0.0277 (ptp) cc_final: -0.0366 (pmt) outliers start: 24 outliers final: 15 residues processed: 201 average time/residue: 0.6595 time to fit residues: 147.0463 Evaluate side-chains 206 residues out of total 1947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 317 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain C residue 256 MET 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 693 LEU 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 H residue 37 MET Chi-restraints excluded: chain H residue 53 ILE 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: 8.9990 chunk 87 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 153 optimal weight: 30.0000 chunk 212 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN C 252 HIS C 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.175106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103973 restraints weight = 20118.511| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.88 r_work: 0.2963 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 : 0.003 0.040 18298 Z= 0.144 Angle : 0.491 9.429 24769 Z= 0.254 Chirality : 0.038 0.235 2767 Planarity : 0.003 0.053 3120 Dihedral : 3.656 17.060 2438 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.44 % Allowed : 19.16 % Favored : 79.40 % 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: 2.71 (0.18), residues: 2184 helix: 2.45 (0.13), residues: 1443 sheet: 1.92 (0.58), residues: 45 loop : 0.44 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 471 TYR 0.016 0.001 TYR C 326 PHE 0.010 0.001 PHE B 870 TRP 0.012 0.001 TRP A 143 HIS 0.009 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00343 (18298) covalent geometry : angle 0.49129 (24769) hydrogen bonds : bond 0.04020 ( 1156) hydrogen bonds : angle 3.61822 ( 3384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7863.96 seconds wall clock time: 134 minutes 11.11 seconds (8051.11 seconds total)