Starting phenix.real_space_refine on Thu Mar 5 01:26:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z8t_14563/03_2026/7z8t_14563.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z8t_14563/03_2026/7z8t_14563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z8t_14563/03_2026/7z8t_14563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z8t_14563/03_2026/7z8t_14563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z8t_14563/03_2026/7z8t_14563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z8t_14563/03_2026/7z8t_14563.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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 Zn 3 6.06 5 S 100 5.16 5 C 11480 2.51 5 N 3111 2.21 5 O 3383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18077 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 5836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5836 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 707} Chain breaks: 3 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 8882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1148, 8882 Classifications: {'peptide': 1148} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 53, 'TRANS': 1094} Chain breaks: 5 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "R" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 713 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "F" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1708 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 243} Link IDs: {'PTRANS': 13, 'TRANS': 300} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 812 Unresolved non-hydrogen angles: 1042 Unresolved non-hydrogen dihedrals: 656 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLU:plan': 14, 'GLN:plan1': 15, 'ASP:plan': 13, 'ASN:plan1': 14, 'HIS:plan': 10, 'ARG:plan': 12, 'PHE:plan': 12, 'TRP:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 418 Chain: "S" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 935 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14906 SG CYS R 42 131.763 58.690 47.783 1.00 73.68 S ATOM 14925 SG CYS R 45 134.419 57.129 50.352 1.00 77.24 S ATOM 15220 SG CYS R 83 131.475 59.033 51.574 1.00 64.89 S ATOM 15149 SG CYS R 75 123.040 65.140 40.620 1.00 51.65 S ATOM 15316 SG CYS R 94 126.379 66.203 42.410 1.00 59.30 S ATOM 14992 SG CYS R 53 130.405 56.197 54.107 1.00 86.82 S ATOM 15015 SG CYS R 56 130.590 54.836 57.670 1.00 91.87 S ATOM 15099 SG CYS R 68 128.271 53.202 54.928 1.00 80.60 S Time building chain proxies: 4.13, per 1000 atoms: 0.23 Number of scatterers: 18077 At special positions: 0 Unit cell: (147.258, 154.067, 120.87, 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) Zn 3 29.99 S 100 16.00 O 3383 8.00 N 3111 7.00 C 11480 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: 1.31 Conformation dependent library (CDL) restraints added in 823.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " Number of angles added : 6 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4614 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 11 sheets defined 72.3% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 38 through 55 removed outlier: 3.575A pdb=" N TYR C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASN C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 105 removed outlier: 3.894A pdb=" N LYS C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 113 through 137 Processing helix chain 'C' and resid 137 through 143 removed outlier: 3.700A pdb=" N ASN C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 171 through 192 removed outlier: 3.592A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS C 177 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 211 removed outlier: 3.671A pdb=" N GLY C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 232 through 253 Processing helix chain 'C' and resid 256 through 279 removed outlier: 3.601A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.512A pdb=" N THR C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 333 through 356 removed outlier: 3.894A pdb=" N CYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 362 through 385 Processing helix chain 'C' and resid 388 through 405 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 416 through 430 removed outlier: 3.528A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 456 removed outlier: 3.539A pdb=" N LYS C 454 " --> pdb=" O MET C 450 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 477 removed outlier: 3.970A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 496 removed outlier: 3.546A pdb=" N GLU C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 526 removed outlier: 3.716A pdb=" N ARG C 506 " --> pdb=" O SER C 502 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 508 " --> pdb=" O LEU C 504 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 558 No H-bonds generated for 'chain 'C' and resid 556 through 558' Processing helix chain 'C' and resid 559 through 574 Processing helix chain 'C' and resid 605 through 613 removed outlier: 3.581A pdb=" N GLN C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 630 removed outlier: 3.935A pdb=" N ASP C 627 " --> pdb=" O GLN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'C' and resid 688 through 722 removed outlier: 4.219A pdb=" N GLN C 692 " --> pdb=" O MET C 688 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 739 removed outlier: 3.779A pdb=" N LEU C 730 " --> pdb=" O LYS C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 759 Processing helix chain 'D' and resid 6 through 15 Processing helix chain 'D' and resid 19 through 35 Processing helix chain 'D' and resid 43 through 56 removed outlier: 3.740A pdb=" N ARG D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 61 through 77 removed outlier: 3.987A pdb=" N GLY D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Proline residue: D 74 - end of helix removed outlier: 4.235A pdb=" N SER D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.780A pdb=" N LEU D 96 " --> pdb=" O CYS D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 116 Processing helix chain 'D' and resid 128 through 144 removed outlier: 3.630A pdb=" N GLY D 136 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 164 removed outlier: 3.747A pdb=" N GLN D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 removed outlier: 3.693A pdb=" N LEU D 168 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 169 " --> pdb=" O GLY D 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 165 through 169' Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 188 through 205 removed outlier: 3.692A pdb=" N ARG D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 224 removed outlier: 3.537A pdb=" N PHE D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.730A pdb=" N THR D 231 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 251 removed outlier: 4.495A pdb=" N GLU D 251 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 265 Proline residue: D 258 - end of helix removed outlier: 3.879A pdb=" N ASN D 265 " --> pdb=" O VAL D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 286 removed outlier: 3.627A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 346 through 364 removed outlier: 3.909A pdb=" N ARG D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG D 364 " --> pdb=" O VAL D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 382 removed outlier: 4.868A pdb=" N SER D 376 " --> pdb=" O TYR D 372 " (cutoff:3.500A) Proline residue: D 377 - end of helix Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 387 through 406 removed outlier: 3.705A pdb=" N ARG D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 443 Proline residue: D 433 - end of helix removed outlier: 4.033A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 465 Processing helix chain 'D' and resid 472 through 485 Proline residue: D 478 - end of helix Processing helix chain 'D' and resid 490 through 507 Processing helix chain 'D' and resid 513 through 515 No H-bonds generated for 'chain 'D' and resid 513 through 515' Processing helix chain 'D' and resid 516 through 529 Proline residue: D 522 - end of helix Processing helix chain 'D' and resid 532 through 551 removed outlier: 3.593A pdb=" N GLN D 545 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 577 removed outlier: 3.613A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS D 566 " --> pdb=" O THR D 562 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP D 567 " --> pdb=" O PRO D 563 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS D 574 " --> pdb=" O THR D 570 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 601 Processing helix chain 'D' and resid 606 through 619 removed outlier: 4.348A pdb=" N ASN D 610 " --> pdb=" O SER D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 644 through 657 removed outlier: 4.951A pdb=" N GLU D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) Proline residue: D 653 - end of helix removed outlier: 3.563A pdb=" N SER D 657 " --> pdb=" O PRO D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 661 removed outlier: 3.542A pdb=" N LYS D 661 " --> pdb=" O PHE D 658 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 658 through 661' Processing helix chain 'D' and resid 663 through 681 Processing helix chain 'D' and resid 682 through 685 removed outlier: 3.681A pdb=" N LEU D 685 " --> pdb=" O SER D 682 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 682 through 685' Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 696 through 701 Proline residue: D 699 - end of helix No H-bonds generated for 'chain 'D' and resid 696 through 701' Processing helix chain 'D' and resid 706 through 723 Processing helix chain 'D' and resid 724 through 730 removed outlier: 4.294A pdb=" N SER D 728 " --> pdb=" O SER D 725 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.658A pdb=" N ASN D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 766 removed outlier: 3.684A pdb=" N VAL D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL D 764 " --> pdb=" O GLN D 760 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 786 Proline residue: D 782 - end of helix Processing helix chain 'D' and resid 792 through 810 removed outlier: 4.249A pdb=" N TYR D 796 " --> pdb=" O HIS D 792 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR D 797 " --> pdb=" O LYS D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 826 Processing helix chain 'D' and resid 831 through 847 Processing helix chain 'D' and resid 856 through 866 removed outlier: 4.210A pdb=" N SER D 866 " --> pdb=" O LEU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 887 removed outlier: 3.510A pdb=" N LYS D 873 " --> pdb=" O SER D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 902 Proline residue: D 893 - end of helix removed outlier: 3.855A pdb=" N THR D 900 " --> pdb=" O LEU D 896 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN D 902 " --> pdb=" O GLU D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 920 removed outlier: 3.603A pdb=" N HIS D 911 " --> pdb=" O TYR D 907 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 926 removed outlier: 3.614A pdb=" N LYS D 926 " --> pdb=" O VAL D 922 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 940 Processing helix chain 'D' and resid 946 through 961 removed outlier: 3.656A pdb=" N VAL D 950 " --> pdb=" O GLY D 946 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE D 961 " --> pdb=" O LYS D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 973 removed outlier: 3.642A pdb=" N TYR D 973 " --> pdb=" O ARG D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 991 removed outlier: 3.700A pdb=" N ARG D 982 " --> pdb=" O SER D 978 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER D 983 " --> pdb=" O SER D 979 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS D 990 " --> pdb=" O VAL D 986 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE D 991 " --> pdb=" O THR D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1013 removed outlier: 3.701A pdb=" N ASN D1006 " --> pdb=" O PRO D1002 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLY D1009 " --> pdb=" O LYS D1005 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASP D1010 " --> pdb=" O ASN D1006 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE D1011 " --> pdb=" O CYS D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1014 through 1016 No H-bonds generated for 'chain 'D' and resid 1014 through 1016' Processing helix chain 'D' and resid 1019 through 1037 removed outlier: 3.967A pdb=" N ARG D1023 " --> pdb=" O ASP D1019 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG D1024 " --> pdb=" O LEU D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1043 removed outlier: 3.600A pdb=" N ILE D1041 " --> pdb=" O PRO D1038 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG D1042 " --> pdb=" O SER D1039 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP D1043 " --> pdb=" O LEU D1040 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1038 through 1043' Processing helix chain 'D' and resid 1044 through 1054 Proline residue: D1050 - end of helix Processing helix chain 'D' and resid 1055 through 1057 No H-bonds generated for 'chain 'D' and resid 1055 through 1057' Processing helix chain 'D' and resid 1059 through 1061 No H-bonds generated for 'chain 'D' and resid 1059 through 1061' Processing helix chain 'D' and resid 1078 through 1093 removed outlier: 3.646A pdb=" N LEU D1093 " --> pdb=" O MET D1089 " (cutoff:3.500A) Processing helix chain 'D' and resid 1103 through 1113 Processing helix chain 'D' and resid 1116 through 1133 removed outlier: 4.042A pdb=" N THR D1132 " --> pdb=" O VAL D1128 " (cutoff:3.500A) Processing helix chain 'D' and resid 1134 through 1142 removed outlier: 4.133A pdb=" N VAL D1138 " --> pdb=" O CYS D1134 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1146 through 1154 Processing helix chain 'D' and resid 1162 through 1185 removed outlier: 4.141A pdb=" N PHE D1166 " --> pdb=" O VAL D1162 " (cutoff:3.500A) Processing helix chain 'D' and resid 1194 through 1205 Processing helix chain 'D' and resid 1205 through 1216 removed outlier: 3.625A pdb=" N ILE D1211 " --> pdb=" O GLU D1207 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D1216 " --> pdb=" O PHE D1212 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 59 Processing helix chain 'R' and resid 62 through 67 removed outlier: 3.684A pdb=" N GLU R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 67' Processing helix chain 'R' and resid 81 through 88 Processing helix chain 'F' and resid 96 through 100 removed outlier: 3.580A pdb=" N SER F 99 " --> pdb=" O SER F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 110 Processing helix chain 'F' and resid 113 through 121 Processing helix chain 'F' and resid 124 through 131 Processing helix chain 'F' and resid 148 through 157 Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 219 through 227 Processing helix chain 'F' and resid 244 through 255 Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 298 through 309 Processing helix chain 'F' and resid 324 through 334 removed outlier: 3.542A pdb=" N LEU F 334 " --> pdb=" O GLU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 359 Processing helix chain 'F' and resid 374 through 383 removed outlier: 3.873A pdb=" N LEU F 378 " --> pdb=" O GLY F 374 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 22 Processing helix chain 'S' and resid 24 through 31 Processing helix chain 'S' and resid 51 through 65 Processing helix chain 'S' and resid 87 through 94 removed outlier: 4.085A pdb=" N GLU S 91 " --> pdb=" O VAL S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 111 Processing helix chain 'S' and resid 112 through 127 Processing helix chain 'S' and resid 131 through 140 Processing helix chain 'S' and resid 146 through 157 removed outlier: 4.155A pdb=" N GLU S 150 " --> pdb=" O THR S 146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 541 removed outlier: 6.270A pdb=" N ASP C 534 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA R 29 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 536 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ALA R 31 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN C 538 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TRP R 33 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU C 540 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N TRP R 35 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 534 through 541 removed outlier: 6.270A pdb=" N ASP C 534 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA R 29 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 536 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ALA R 31 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN C 538 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TRP R 33 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU C 540 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N TRP R 35 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL R 24 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C 591 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS R 26 " --> pdb=" O GLU C 589 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 619 through 621 Processing sheet with id=AA4, first strand: chain 'C' and resid 724 through 725 Processing sheet with id=AA5, first strand: chain 'D' and resid 1063 through 1068 Processing sheet with id=AA6, first strand: chain 'R' and resid 78 through 80 removed outlier: 6.595A pdb=" N TRP R 72 " --> pdb=" O GLN R 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 139 through 141 removed outlier: 3.732A pdb=" N ARG F 164 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE F 163 " --> pdb=" O ASP F 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AA9, first strand: chain 'F' and resid 260 through 262 removed outlier: 3.558A pdb=" N ASN F 289 " --> pdb=" O LEU F 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 339 through 341 removed outlier: 7.343A pdb=" N LEU F 340 " --> pdb=" O GLN F 366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 13 through 17 1113 hydrogen bonds defined for protein. 3273 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: 3.43 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5098 1.33 - 1.45: 2554 1.45 - 1.57: 10561 1.57 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 18360 Sorted by residual: bond pdb=" N LEU S 105 " pdb=" CA LEU S 105 " ideal model delta sigma weight residual 1.459 1.481 -0.023 1.28e-02 6.10e+03 3.15e+00 bond pdb=" C LEU S 105 " pdb=" O LEU S 105 " ideal model delta sigma weight residual 1.236 1.216 0.020 1.26e-02 6.30e+03 2.64e+00 bond pdb=" CA LEU S 105 " pdb=" C LEU S 105 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.35e-02 5.49e+03 1.78e+00 bond pdb=" CG1 ILE S 59 " pdb=" CD1 ILE S 59 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" C ILE S 104 " pdb=" N LEU S 105 " ideal model delta sigma weight residual 1.335 1.320 0.015 1.38e-02 5.25e+03 1.13e+00 ... (remaining 18355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 24600 1.83 - 3.66: 243 3.66 - 5.49: 53 5.49 - 7.33: 9 7.33 - 9.16: 2 Bond angle restraints: 24907 Sorted by residual: angle pdb=" C LYS D 661 " pdb=" N ASN D 662 " pdb=" CA ASN D 662 " ideal model delta sigma weight residual 121.54 127.55 -6.01 1.91e+00 2.74e-01 9.92e+00 angle pdb=" C ILE S 104 " pdb=" N LEU S 105 " pdb=" CA LEU S 105 " ideal model delta sigma weight residual 120.31 115.62 4.69 1.52e+00 4.33e-01 9.52e+00 angle pdb=" N GLU C 705 " pdb=" CA GLU C 705 " pdb=" CB GLU C 705 " ideal model delta sigma weight residual 110.22 114.86 -4.64 1.54e+00 4.22e-01 9.08e+00 angle pdb=" C ARG C 401 " pdb=" N PHE C 402 " pdb=" CA PHE C 402 " ideal model delta sigma weight residual 122.06 116.53 5.53 1.86e+00 2.89e-01 8.85e+00 angle pdb=" N ILE C 684 " pdb=" CA ILE C 684 " pdb=" C ILE C 684 " ideal model delta sigma weight residual 112.29 109.50 2.79 9.40e-01 1.13e+00 8.81e+00 ... (remaining 24902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10319 17.92 - 35.84: 766 35.84 - 53.76: 109 53.76 - 71.67: 25 71.67 - 89.59: 14 Dihedral angle restraints: 11233 sinusoidal: 4173 harmonic: 7060 Sorted by residual: dihedral pdb=" CA THR C 47 " pdb=" C THR C 47 " pdb=" N HIS C 48 " pdb=" CA HIS C 48 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA THR S 146 " pdb=" C THR S 146 " pdb=" N GLU S 147 " pdb=" CA GLU S 147 " ideal model delta harmonic sigma weight residual -180.00 -161.68 -18.32 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA PHE C 232 " pdb=" C PHE C 232 " pdb=" N GLU C 233 " pdb=" CA GLU C 233 " ideal model delta harmonic sigma weight residual 180.00 -162.85 -17.15 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 11230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2353 0.046 - 0.092: 527 0.092 - 0.137: 99 0.137 - 0.183: 3 0.183 - 0.229: 1 Chirality restraints: 2983 Sorted by residual: chirality pdb=" CG LEU D1113 " pdb=" CB LEU D1113 " pdb=" CD1 LEU D1113 " pdb=" CD2 LEU D1113 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLU D 216 " pdb=" N GLU D 216 " pdb=" C GLU D 216 " pdb=" CB GLU D 216 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ASN D 662 " pdb=" N ASN D 662 " pdb=" C ASN D 662 " pdb=" CB ASN D 662 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 2980 not shown) Planarity restraints: 3171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 814 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO D 815 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 815 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 815 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 545 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO C 546 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 546 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 546 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 179 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO F 180 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO F 180 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 180 " 0.020 5.00e-02 4.00e+02 ... (remaining 3168 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 90 2.57 - 3.15: 14320 3.15 - 3.74: 27468 3.74 - 4.32: 35061 4.32 - 4.90: 61169 Nonbonded interactions: 138108 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.988 2.230 nonbonded pdb=" O PHE S 101 " pdb=" CD1 LEU S 105 " model vdw 2.094 3.460 nonbonded pdb=" OG SER D 979 " pdb=" OD2 ASP D1019 " model vdw 2.196 3.040 nonbonded pdb=" O GLY D 819 " pdb=" NE2 GLN D 823 " model vdw 2.210 3.120 nonbonded pdb=" OD1 ASP D 582 " pdb=" N GLN D 583 " model vdw 2.251 3.120 ... (remaining 138103 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.570 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.030 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 : 0.003 0.272 18371 Z= 0.129 Angle : 0.508 9.156 24913 Z= 0.269 Chirality : 0.038 0.229 2983 Planarity : 0.004 0.043 3171 Dihedral : 13.081 89.593 6619 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.05 % Allowed : 0.21 % Favored : 99.73 % 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: 1.77 (0.18), residues: 2363 helix: 2.21 (0.14), residues: 1553 sheet: -0.84 (0.70), residues: 74 loop : -0.91 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 645 TYR 0.013 0.001 TYR C 377 PHE 0.016 0.001 PHE C 402 TRP 0.010 0.001 TRP R 33 HIS 0.003 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00223 (18360) covalent geometry : angle 0.50323 (24907) hydrogen bonds : bond 0.14604 ( 1113) hydrogen bonds : angle 4.64927 ( 3273) metal coordination : bond 0.08421 ( 11) metal coordination : angle 4.68391 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 450 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: C 271 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7369 (mm-30) REVERT: C 289 ARG cc_start: 0.7026 (ttt-90) cc_final: 0.6807 (ttt-90) REVERT: C 410 LYS cc_start: 0.8022 (tttm) cc_final: 0.7734 (mtpp) REVERT: C 478 ASN cc_start: 0.8029 (p0) cc_final: 0.7660 (p0) REVERT: C 488 MET cc_start: 0.8119 (tpt) cc_final: 0.7891 (tpt) REVERT: C 565 ARG cc_start: 0.8023 (tpp80) cc_final: 0.7773 (tpp80) REVERT: C 612 LEU cc_start: 0.8318 (tt) cc_final: 0.7699 (tt) REVERT: D 213 ASP cc_start: 0.6820 (p0) cc_final: 0.6311 (p0) REVERT: D 216 GLU cc_start: 0.7087 (mp0) cc_final: 0.6838 (pm20) REVERT: D 362 SER cc_start: 0.8404 (p) cc_final: 0.8167 (p) REVERT: D 691 ASP cc_start: 0.6924 (m-30) cc_final: 0.6615 (m-30) REVERT: D 884 SER cc_start: 0.8208 (t) cc_final: 0.7733 (m) REVERT: D 979 SER cc_start: 0.8198 (t) cc_final: 0.7902 (t) REVERT: D 1046 ASP cc_start: 0.7409 (m-30) cc_final: 0.7169 (m-30) REVERT: D 1175 SER cc_start: 0.8070 (m) cc_final: 0.7864 (m) REVERT: R 89 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8376 (tttm) outliers start: 1 outliers final: 1 residues processed: 451 average time/residue: 0.6408 time to fit residues: 321.1468 Evaluate side-chains 394 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 393 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 496 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 40.0000 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 235 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 141 ASN C 178 GLN C 206 GLN C 254 GLN C 638 GLN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 GLN D 768 ASN D1006 ASN D1140 GLN D1199 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.108895 restraints weight = 26391.107| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.91 r_work: 0.3235 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18371 Z= 0.182 Angle : 0.566 8.953 24913 Z= 0.294 Chirality : 0.041 0.201 2983 Planarity : 0.004 0.046 3171 Dihedral : 3.658 30.700 2541 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.25 % Allowed : 12.10 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.18), residues: 2363 helix: 2.10 (0.13), residues: 1579 sheet: -0.91 (0.68), residues: 74 loop : -0.89 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 285 TYR 0.022 0.002 TYR C 278 PHE 0.027 0.002 PHE C 402 TRP 0.012 0.001 TRP R 33 HIS 0.005 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00438 (18360) covalent geometry : angle 0.56513 (24907) hydrogen bonds : bond 0.05613 ( 1113) hydrogen bonds : angle 3.95233 ( 3273) metal coordination : bond 0.00810 ( 11) metal coordination : angle 2.53240 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 398 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 271 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7958 (mm-30) REVERT: C 289 ARG cc_start: 0.8268 (ttt-90) cc_final: 0.7986 (ttt-90) REVERT: C 565 ARG cc_start: 0.8610 (tpp80) cc_final: 0.8312 (tpp80) REVERT: D 58 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: D 137 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.5970 (mmm-85) REVERT: D 162 LEU cc_start: 0.8280 (mp) cc_final: 0.7997 (mt) REVERT: D 213 ASP cc_start: 0.7404 (p0) cc_final: 0.7042 (p0) REVERT: D 216 GLU cc_start: 0.7946 (mp0) cc_final: 0.7548 (mp0) REVERT: D 362 SER cc_start: 0.8346 (p) cc_final: 0.8105 (p) REVERT: D 627 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8131 (m) REVERT: D 696 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: D 884 SER cc_start: 0.8469 (t) cc_final: 0.8065 (m) REVERT: D 953 GLU cc_start: 0.8169 (tp30) cc_final: 0.7917 (tp30) REVERT: D 1001 ASP cc_start: 0.7727 (m-30) cc_final: 0.7333 (m-30) REVERT: D 1046 ASP cc_start: 0.8338 (m-30) cc_final: 0.8061 (m-30) REVERT: D 1201 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7196 (tp-100) REVERT: F 129 ARG cc_start: 0.7694 (tpm-80) cc_final: 0.7408 (tpm-80) REVERT: S 4 ILE cc_start: 0.8426 (mt) cc_final: 0.8215 (mm) outliers start: 42 outliers final: 16 residues processed: 413 average time/residue: 0.6477 time to fit residues: 296.6649 Evaluate side-chains 410 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 389 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 548 GLN Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1201 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 199 optimal weight: 2.9990 chunk 40 optimal weight: 0.0270 chunk 29 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 130 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 308 GLN C 638 GLN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 GLN D 662 ASN D 768 ASN D1140 GLN D1199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.136837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109399 restraints weight = 26410.628| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.92 r_work: 0.3255 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 18371 Z= 0.146 Angle : 0.532 9.444 24913 Z= 0.274 Chirality : 0.040 0.166 2983 Planarity : 0.004 0.044 3171 Dihedral : 3.626 29.444 2541 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.46 % Allowed : 14.35 % Favored : 83.19 % 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: 1.74 (0.18), residues: 2363 helix: 2.14 (0.13), residues: 1582 sheet: -1.02 (0.66), residues: 74 loop : -0.93 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 285 TYR 0.019 0.002 TYR C 563 PHE 0.025 0.001 PHE C 402 TRP 0.012 0.001 TRP R 33 HIS 0.005 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00346 (18360) covalent geometry : angle 0.53086 (24907) hydrogen bonds : bond 0.05034 ( 1113) hydrogen bonds : angle 3.80238 ( 3273) metal coordination : bond 0.00456 ( 11) metal coordination : angle 2.28444 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 393 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 ARG cc_start: 0.8262 (ttt-90) cc_final: 0.7977 (ttt-90) REVERT: C 451 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8530 (p) REVERT: C 565 ARG cc_start: 0.8623 (tpp80) cc_final: 0.8306 (tpp80) REVERT: D 137 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.6048 (mmm-85) REVERT: D 162 LEU cc_start: 0.8369 (mp) cc_final: 0.8097 (mt) REVERT: D 213 ASP cc_start: 0.7377 (p0) cc_final: 0.7099 (p0) REVERT: D 251 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: D 257 ILE cc_start: 0.8499 (mm) cc_final: 0.8258 (mp) REVERT: D 362 SER cc_start: 0.8349 (p) cc_final: 0.8123 (p) REVERT: D 696 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: D 884 SER cc_start: 0.8423 (t) cc_final: 0.7959 (m) REVERT: D 898 GLU cc_start: 0.8280 (tp30) cc_final: 0.8020 (mm-30) REVERT: D 953 GLU cc_start: 0.8186 (tp30) cc_final: 0.7894 (tp30) REVERT: D 1001 ASP cc_start: 0.7733 (m-30) cc_final: 0.7335 (m-30) REVERT: D 1044 LEU cc_start: 0.8440 (mp) cc_final: 0.8223 (mt) REVERT: D 1046 ASP cc_start: 0.8314 (m-30) cc_final: 0.8050 (m-30) REVERT: D 1201 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7169 (tp-100) REVERT: F 129 ARG cc_start: 0.7700 (tpm-80) cc_final: 0.7307 (tpm-80) REVERT: S 4 ILE cc_start: 0.8418 (mt) cc_final: 0.8210 (mm) outliers start: 46 outliers final: 27 residues processed: 413 average time/residue: 0.6379 time to fit residues: 293.2085 Evaluate side-chains 415 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 383 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 548 GLN Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 726 SER Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 971 LYS Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 34 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 518 ASN C 638 GLN C 683 ASN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 ASN D 768 ASN D1107 ASN D1140 GLN D1199 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.133979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106484 restraints weight = 26461.831| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.92 r_work: 0.3216 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18371 Z= 0.193 Angle : 0.566 10.525 24913 Z= 0.292 Chirality : 0.042 0.188 2983 Planarity : 0.004 0.045 3171 Dihedral : 3.689 21.813 2539 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.59 % Allowed : 14.13 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.18), residues: 2363 helix: 2.07 (0.13), residues: 1572 sheet: -0.39 (0.70), residues: 64 loop : -0.98 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 285 TYR 0.022 0.002 TYR D 398 PHE 0.024 0.002 PHE C 402 TRP 0.014 0.001 TRP R 33 HIS 0.006 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00466 (18360) covalent geometry : angle 0.56366 (24907) hydrogen bonds : bond 0.05872 ( 1113) hydrogen bonds : angle 3.86211 ( 3273) metal coordination : bond 0.00593 ( 11) metal coordination : angle 3.08701 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 389 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 ARG cc_start: 0.8284 (ttt-90) cc_final: 0.8000 (ttt-90) REVERT: C 538 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8152 (mm110) REVERT: C 565 ARG cc_start: 0.8624 (tpp80) cc_final: 0.8305 (tpp80) REVERT: C 641 GLN cc_start: 0.7587 (tm130) cc_final: 0.7263 (tm130) REVERT: D 67 LEU cc_start: 0.8539 (mm) cc_final: 0.8276 (mt) REVERT: D 137 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.6046 (mmm-85) REVERT: D 162 LEU cc_start: 0.8416 (mp) cc_final: 0.8142 (mt) REVERT: D 204 MET cc_start: 0.8561 (tpp) cc_final: 0.8154 (tpp) REVERT: D 213 ASP cc_start: 0.7449 (p0) cc_final: 0.7155 (p0) REVERT: D 251 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: D 254 GLU cc_start: 0.7361 (mp0) cc_final: 0.7093 (mm-30) REVERT: D 270 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7987 (tp30) REVERT: D 362 SER cc_start: 0.8488 (p) cc_final: 0.8253 (p) REVERT: D 386 ARG cc_start: 0.8672 (ptt-90) cc_final: 0.8418 (ttp80) REVERT: D 696 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: D 755 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8164 (mtp) REVERT: D 863 GLU cc_start: 0.8048 (tp30) cc_final: 0.7779 (tp30) REVERT: D 884 SER cc_start: 0.8469 (t) cc_final: 0.8026 (m) REVERT: D 941 GLU cc_start: 0.7182 (mp0) cc_final: 0.6906 (mp0) REVERT: D 953 GLU cc_start: 0.8213 (tp30) cc_final: 0.7907 (tp30) REVERT: D 1001 ASP cc_start: 0.7743 (m-30) cc_final: 0.7350 (m-30) REVERT: D 1015 LEU cc_start: 0.8761 (mt) cc_final: 0.8484 (mt) REVERT: D 1046 ASP cc_start: 0.8279 (m-30) cc_final: 0.8043 (m-30) REVERT: D 1060 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8219 (tptm) REVERT: D 1178 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.8086 (mtt180) REVERT: D 1201 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7154 (tp-100) REVERT: F 129 ARG cc_start: 0.7757 (tpm-80) cc_final: 0.7310 (tpm-80) REVERT: S 12 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7636 (mm-30) outliers start: 67 outliers final: 34 residues processed: 422 average time/residue: 0.6540 time to fit residues: 305.3469 Evaluate side-chains 429 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 387 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 538 GLN Chi-restraints excluded: chain C residue 548 GLN Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 726 SER Chi-restraints excluded: chain D residue 755 MET Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 971 LYS Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1060 LYS Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1178 ARG Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 121 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 84 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 225 optimal weight: 7.9990 chunk 182 optimal weight: 0.7980 chunk 177 optimal weight: 0.5980 chunk 221 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 308 GLN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 ASN D1199 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109862 restraints weight = 26199.651| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.94 r_work: 0.3256 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18371 Z= 0.122 Angle : 0.518 10.542 24913 Z= 0.266 Chirality : 0.039 0.162 2983 Planarity : 0.004 0.043 3171 Dihedral : 3.543 22.562 2539 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.94 % Allowed : 16.01 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.18), residues: 2363 helix: 2.21 (0.13), residues: 1582 sheet: -0.29 (0.71), residues: 64 loop : -0.99 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 285 TYR 0.015 0.001 TYR C 377 PHE 0.020 0.001 PHE C 402 TRP 0.012 0.001 TRP R 33 HIS 0.006 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00278 (18360) covalent geometry : angle 0.51666 (24907) hydrogen bonds : bond 0.04466 ( 1113) hydrogen bonds : angle 3.66461 ( 3273) metal coordination : bond 0.00433 ( 11) metal coordination : angle 2.12608 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 386 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 ARG cc_start: 0.8276 (ttt-90) cc_final: 0.8008 (ttt-90) REVERT: C 330 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: C 565 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8277 (tpp80) REVERT: C 641 GLN cc_start: 0.7554 (tm130) cc_final: 0.7040 (tm130) REVERT: C 762 LEU cc_start: 0.8437 (pt) cc_final: 0.8100 (pp) REVERT: C 763 GLU cc_start: 0.7411 (pp20) cc_final: 0.6999 (pp20) REVERT: D 162 LEU cc_start: 0.8357 (mp) cc_final: 0.8093 (mt) REVERT: D 204 MET cc_start: 0.8539 (tpp) cc_final: 0.8109 (tpp) REVERT: D 213 ASP cc_start: 0.7356 (p0) cc_final: 0.6889 (p0) REVERT: D 216 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: D 251 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: D 252 TYR cc_start: 0.8645 (m-80) cc_final: 0.8374 (m-80) REVERT: D 362 SER cc_start: 0.8375 (p) cc_final: 0.8148 (p) REVERT: D 386 ARG cc_start: 0.8642 (ptt-90) cc_final: 0.8410 (ttp80) REVERT: D 696 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: D 863 GLU cc_start: 0.7977 (tp30) cc_final: 0.7672 (tp30) REVERT: D 884 SER cc_start: 0.8361 (t) cc_final: 0.7886 (m) REVERT: D 938 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7841 (tmmm) REVERT: D 953 GLU cc_start: 0.8204 (tp30) cc_final: 0.7904 (tp30) REVERT: D 1001 ASP cc_start: 0.7777 (m-30) cc_final: 0.7356 (m-30) REVERT: D 1015 LEU cc_start: 0.8693 (mt) cc_final: 0.8394 (mt) REVERT: D 1044 LEU cc_start: 0.8433 (mp) cc_final: 0.8195 (mt) REVERT: D 1046 ASP cc_start: 0.8276 (m-30) cc_final: 0.8006 (m-30) REVERT: D 1201 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7145 (tp-100) REVERT: F 129 ARG cc_start: 0.7736 (tpm-80) cc_final: 0.7239 (tpm-80) REVERT: S 113 LYS cc_start: 0.8101 (pptt) cc_final: 0.7766 (pptt) REVERT: S 119 THR cc_start: 0.8502 (m) cc_final: 0.8256 (t) outliers start: 55 outliers final: 31 residues processed: 407 average time/residue: 0.6473 time to fit residues: 291.8659 Evaluate side-chains 418 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 381 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 726 SER Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 938 LYS Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 971 LYS Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain F residue 114 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 75 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 308 GLN C 509 GLN C 683 ASN D 217 HIS D 662 ASN D1140 GLN D1199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.109099 restraints weight = 26171.114| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.91 r_work: 0.3261 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18371 Z= 0.126 Angle : 0.514 11.284 24913 Z= 0.262 Chirality : 0.039 0.168 2983 Planarity : 0.004 0.043 3171 Dihedral : 3.473 21.054 2539 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.94 % Allowed : 16.54 % Favored : 80.51 % 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: 1.87 (0.18), residues: 2363 helix: 2.23 (0.13), residues: 1586 sheet: -0.22 (0.72), residues: 64 loop : -0.95 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 285 TYR 0.017 0.001 TYR C 377 PHE 0.020 0.001 PHE C 402 TRP 0.012 0.001 TRP R 33 HIS 0.006 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00291 (18360) covalent geometry : angle 0.51273 (24907) hydrogen bonds : bond 0.04478 ( 1113) hydrogen bonds : angle 3.62020 ( 3273) metal coordination : bond 0.00409 ( 11) metal coordination : angle 2.12807 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 395 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 ASN cc_start: 0.8292 (t0) cc_final: 0.8079 (t0) REVERT: C 110 LEU cc_start: 0.8387 (mt) cc_final: 0.8137 (mt) REVERT: C 289 ARG cc_start: 0.8258 (ttt-90) cc_final: 0.7986 (ttt-90) REVERT: C 330 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: C 565 ARG cc_start: 0.8601 (tpp80) cc_final: 0.8282 (tpp80) REVERT: C 641 GLN cc_start: 0.7561 (tm130) cc_final: 0.7232 (tm130) REVERT: C 763 GLU cc_start: 0.7387 (pp20) cc_final: 0.6965 (pp20) REVERT: D 67 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8265 (mt) REVERT: D 137 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.6068 (mmm-85) REVERT: D 162 LEU cc_start: 0.8361 (mp) cc_final: 0.8086 (mt) REVERT: D 204 MET cc_start: 0.8544 (tpp) cc_final: 0.8088 (tpp) REVERT: D 213 ASP cc_start: 0.7339 (p0) cc_final: 0.6871 (p0) REVERT: D 251 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: D 362 SER cc_start: 0.8362 (p) cc_final: 0.8144 (p) REVERT: D 386 ARG cc_start: 0.8625 (ptt-90) cc_final: 0.8406 (ttp80) REVERT: D 755 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8164 (mtp) REVERT: D 863 GLU cc_start: 0.7941 (tp30) cc_final: 0.7643 (tp30) REVERT: D 884 SER cc_start: 0.8359 (t) cc_final: 0.7883 (m) REVERT: D 941 GLU cc_start: 0.7122 (mp0) cc_final: 0.6765 (mp0) REVERT: D 953 GLU cc_start: 0.8208 (tp30) cc_final: 0.7895 (tp30) REVERT: D 1001 ASP cc_start: 0.7779 (m-30) cc_final: 0.7330 (m-30) REVERT: D 1015 LEU cc_start: 0.8631 (mt) cc_final: 0.8388 (mt) REVERT: D 1046 ASP cc_start: 0.8273 (m-30) cc_final: 0.8014 (m-30) REVERT: D 1201 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7087 (tp-100) REVERT: F 129 ARG cc_start: 0.7737 (tpm-80) cc_final: 0.7225 (tpm-80) REVERT: S 113 LYS cc_start: 0.8127 (pptt) cc_final: 0.7800 (pptt) REVERT: S 119 THR cc_start: 0.8527 (m) cc_final: 0.8289 (t) outliers start: 55 outliers final: 30 residues processed: 419 average time/residue: 0.6496 time to fit residues: 301.8528 Evaluate side-chains 424 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 388 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 726 SER Chi-restraints excluded: chain D residue 755 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain F residue 114 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 164 optimal weight: 0.5980 chunk 180 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 206 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 185 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN C 509 GLN C 638 GLN D 66 ASN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1140 GLN D1199 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.108621 restraints weight = 26380.075| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.92 r_work: 0.3253 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18371 Z= 0.138 Angle : 0.529 11.276 24913 Z= 0.269 Chirality : 0.039 0.173 2983 Planarity : 0.004 0.043 3171 Dihedral : 3.502 21.936 2539 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.05 % Allowed : 17.51 % Favored : 79.44 % 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: 1.80 (0.18), residues: 2363 helix: 2.18 (0.13), residues: 1597 sheet: -0.23 (0.71), residues: 64 loop : -1.05 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 285 TYR 0.018 0.001 TYR C 377 PHE 0.021 0.001 PHE C 402 TRP 0.011 0.001 TRP R 33 HIS 0.007 0.001 HIS D1051 Details of bonding type rmsd covalent geometry : bond 0.00324 (18360) covalent geometry : angle 0.52755 (24907) hydrogen bonds : bond 0.04689 ( 1113) hydrogen bonds : angle 3.64564 ( 3273) metal coordination : bond 0.00419 ( 11) metal coordination : angle 2.24243 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 388 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 ASN cc_start: 0.8300 (t0) cc_final: 0.8089 (t0) REVERT: C 110 LEU cc_start: 0.8388 (mt) cc_final: 0.8118 (mt) REVERT: C 289 ARG cc_start: 0.8250 (ttt-90) cc_final: 0.7980 (ttt-90) REVERT: C 330 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: C 478 ASN cc_start: 0.8251 (p0) cc_final: 0.7904 (p0) REVERT: C 538 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8141 (mm110) REVERT: C 565 ARG cc_start: 0.8589 (tpp80) cc_final: 0.8278 (tpp80) REVERT: C 641 GLN cc_start: 0.7581 (tm130) cc_final: 0.7065 (tm130) REVERT: C 763 GLU cc_start: 0.7415 (pp20) cc_final: 0.6993 (pp20) REVERT: D 67 LEU cc_start: 0.8512 (mm) cc_final: 0.8270 (mt) REVERT: D 78 LYS cc_start: 0.8197 (mtpm) cc_final: 0.7655 (mttm) REVERT: D 137 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.6096 (mmm-85) REVERT: D 162 LEU cc_start: 0.8373 (mp) cc_final: 0.8103 (mt) REVERT: D 213 ASP cc_start: 0.7341 (p0) cc_final: 0.6884 (p0) REVERT: D 216 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: D 251 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7552 (mp0) REVERT: D 307 TYR cc_start: 0.8469 (t80) cc_final: 0.8080 (t80) REVERT: D 362 SER cc_start: 0.8369 (p) cc_final: 0.8150 (p) REVERT: D 386 ARG cc_start: 0.8620 (ptt-90) cc_final: 0.8409 (ttp80) REVERT: D 696 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: D 721 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8523 (mttt) REVERT: D 863 GLU cc_start: 0.7925 (tp30) cc_final: 0.7598 (tp30) REVERT: D 884 SER cc_start: 0.8388 (t) cc_final: 0.7914 (m) REVERT: D 941 GLU cc_start: 0.7130 (mp0) cc_final: 0.6804 (mp0) REVERT: D 953 GLU cc_start: 0.8213 (tp30) cc_final: 0.7927 (tp30) REVERT: D 1001 ASP cc_start: 0.7784 (m-30) cc_final: 0.7320 (m-30) REVERT: D 1015 LEU cc_start: 0.8635 (mt) cc_final: 0.8406 (mt) REVERT: D 1046 ASP cc_start: 0.8263 (m-30) cc_final: 0.7997 (m-30) REVERT: D 1201 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7145 (tp-100) REVERT: F 129 ARG cc_start: 0.7755 (tpm-80) cc_final: 0.7229 (tpm-80) REVERT: S 113 LYS cc_start: 0.8150 (pptt) cc_final: 0.7839 (pptt) REVERT: S 119 THR cc_start: 0.8532 (m) cc_final: 0.8304 (t) outliers start: 57 outliers final: 33 residues processed: 416 average time/residue: 0.6573 time to fit residues: 303.2788 Evaluate side-chains 428 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 388 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 538 GLN Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 721 LYS Chi-restraints excluded: chain D residue 726 SER Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain F residue 114 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 224 optimal weight: 30.0000 chunk 214 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 233 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 223 optimal weight: 40.0000 chunk 44 optimal weight: 0.0030 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN C 254 GLN C 509 GLN D 151 GLN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1140 GLN D1199 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.136574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.109233 restraints weight = 26333.014| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.95 r_work: 0.3263 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18371 Z= 0.124 Angle : 0.524 11.722 24913 Z= 0.266 Chirality : 0.039 0.164 2983 Planarity : 0.004 0.043 3171 Dihedral : 3.465 21.880 2539 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.89 % Allowed : 18.04 % Favored : 79.07 % 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: 1.83 (0.18), residues: 2363 helix: 2.21 (0.13), residues: 1598 sheet: -0.71 (0.66), residues: 74 loop : -1.01 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 285 TYR 0.017 0.001 TYR S 109 PHE 0.019 0.001 PHE C 402 TRP 0.011 0.001 TRP R 33 HIS 0.006 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00287 (18360) covalent geometry : angle 0.52280 (24907) hydrogen bonds : bond 0.04364 ( 1113) hydrogen bonds : angle 3.59648 ( 3273) metal coordination : bond 0.00411 ( 11) metal coordination : angle 2.01484 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 389 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 ASN cc_start: 0.8295 (t0) cc_final: 0.8085 (t0) REVERT: C 110 LEU cc_start: 0.8377 (mt) cc_final: 0.8115 (mt) REVERT: C 289 ARG cc_start: 0.8270 (ttt-90) cc_final: 0.8006 (ttt-90) REVERT: C 330 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: C 451 VAL cc_start: 0.8803 (t) cc_final: 0.8527 (p) REVERT: C 478 ASN cc_start: 0.8241 (p0) cc_final: 0.7913 (p0) REVERT: C 565 ARG cc_start: 0.8609 (tpp80) cc_final: 0.8266 (tpp80) REVERT: C 641 GLN cc_start: 0.7604 (tm130) cc_final: 0.7279 (tm130) REVERT: C 763 GLU cc_start: 0.7403 (pp20) cc_final: 0.6980 (pp20) REVERT: D 67 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8282 (mt) REVERT: D 78 LYS cc_start: 0.8198 (mtpm) cc_final: 0.7694 (mttm) REVERT: D 137 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.6091 (mmm-85) REVERT: D 162 LEU cc_start: 0.8390 (mp) cc_final: 0.8112 (mt) REVERT: D 177 LEU cc_start: 0.8390 (tp) cc_final: 0.8157 (tp) REVERT: D 204 MET cc_start: 0.8533 (tpp) cc_final: 0.8126 (tpp) REVERT: D 213 ASP cc_start: 0.7333 (p0) cc_final: 0.6925 (p0) REVERT: D 251 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7538 (mp0) REVERT: D 362 SER cc_start: 0.8350 (p) cc_final: 0.8135 (p) REVERT: D 863 GLU cc_start: 0.7910 (tp30) cc_final: 0.7587 (tp30) REVERT: D 884 SER cc_start: 0.8357 (t) cc_final: 0.7880 (m) REVERT: D 941 GLU cc_start: 0.7173 (mp0) cc_final: 0.6813 (mp0) REVERT: D 953 GLU cc_start: 0.8221 (tp30) cc_final: 0.7925 (tp30) REVERT: D 1001 ASP cc_start: 0.7762 (m-30) cc_final: 0.7430 (m-30) REVERT: D 1015 LEU cc_start: 0.8589 (mt) cc_final: 0.8379 (mt) REVERT: D 1046 ASP cc_start: 0.8261 (m-30) cc_final: 0.7997 (m-30) REVERT: D 1201 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7212 (tp-100) REVERT: F 129 ARG cc_start: 0.7752 (tpm-80) cc_final: 0.7217 (tpm-80) REVERT: S 113 LYS cc_start: 0.8136 (pptt) cc_final: 0.7835 (pptt) REVERT: S 119 THR cc_start: 0.8527 (m) cc_final: 0.8309 (t) outliers start: 54 outliers final: 34 residues processed: 413 average time/residue: 0.6401 time to fit residues: 293.5413 Evaluate side-chains 426 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 388 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 726 SER Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain F residue 114 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 83 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 220 optimal weight: 50.0000 chunk 115 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN C 206 GLN C 509 GLN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1140 GLN D1199 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.108980 restraints weight = 26281.724| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.96 r_work: 0.3251 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18371 Z= 0.133 Angle : 0.536 11.789 24913 Z= 0.273 Chirality : 0.039 0.174 2983 Planarity : 0.004 0.043 3171 Dihedral : 3.484 21.266 2539 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.30 % Allowed : 18.79 % Favored : 78.91 % 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: 1.81 (0.18), residues: 2363 helix: 2.21 (0.13), residues: 1596 sheet: -0.69 (0.65), residues: 74 loop : -1.02 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 285 TYR 0.016 0.001 TYR D 398 PHE 0.021 0.001 PHE C 402 TRP 0.011 0.001 TRP R 33 HIS 0.006 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00309 (18360) covalent geometry : angle 0.53510 (24907) hydrogen bonds : bond 0.04550 ( 1113) hydrogen bonds : angle 3.60988 ( 3273) metal coordination : bond 0.00405 ( 11) metal coordination : angle 2.13318 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 385 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 ASN cc_start: 0.8323 (t0) cc_final: 0.8116 (t0) REVERT: C 110 LEU cc_start: 0.8371 (mt) cc_final: 0.8116 (mt) REVERT: C 289 ARG cc_start: 0.8289 (ttt-90) cc_final: 0.8028 (ttt-90) REVERT: C 330 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: C 478 ASN cc_start: 0.8231 (p0) cc_final: 0.7905 (p0) REVERT: C 538 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8135 (mm110) REVERT: C 565 ARG cc_start: 0.8595 (tpp80) cc_final: 0.8262 (tpp80) REVERT: C 641 GLN cc_start: 0.7613 (tm130) cc_final: 0.7089 (tm130) REVERT: C 763 GLU cc_start: 0.7397 (pp20) cc_final: 0.6975 (pp20) REVERT: D 67 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8292 (mt) REVERT: D 78 LYS cc_start: 0.8202 (mtpm) cc_final: 0.7729 (mttm) REVERT: D 137 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.6105 (mmm-85) REVERT: D 162 LEU cc_start: 0.8402 (mp) cc_final: 0.8134 (mt) REVERT: D 204 MET cc_start: 0.8556 (tpp) cc_final: 0.8135 (tpp) REVERT: D 213 ASP cc_start: 0.7453 (p0) cc_final: 0.7007 (p0) REVERT: D 251 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7558 (mp0) REVERT: D 307 TYR cc_start: 0.8466 (t80) cc_final: 0.8109 (t80) REVERT: D 362 SER cc_start: 0.8357 (p) cc_final: 0.8142 (p) REVERT: D 721 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8558 (mttt) REVERT: D 863 GLU cc_start: 0.7901 (tp30) cc_final: 0.7627 (tp30) REVERT: D 884 SER cc_start: 0.8391 (t) cc_final: 0.7917 (m) REVERT: D 941 GLU cc_start: 0.7195 (mp0) cc_final: 0.6734 (mp0) REVERT: D 953 GLU cc_start: 0.8210 (tp30) cc_final: 0.7911 (tp30) REVERT: D 1001 ASP cc_start: 0.7774 (m-30) cc_final: 0.7441 (m-30) REVERT: D 1015 LEU cc_start: 0.8585 (mt) cc_final: 0.8383 (mt) REVERT: D 1044 LEU cc_start: 0.8397 (mp) cc_final: 0.8173 (mt) REVERT: D 1046 ASP cc_start: 0.8254 (m-30) cc_final: 0.7991 (m-30) REVERT: D 1201 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7133 (tp-100) REVERT: F 129 ARG cc_start: 0.7760 (tpm-80) cc_final: 0.7230 (tpm-80) REVERT: S 113 LYS cc_start: 0.8152 (pptt) cc_final: 0.7862 (pptt) REVERT: S 119 THR cc_start: 0.8518 (m) cc_final: 0.8309 (t) outliers start: 43 outliers final: 33 residues processed: 406 average time/residue: 0.6369 time to fit residues: 287.0738 Evaluate side-chains 421 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 382 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 538 GLN Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 721 LYS Chi-restraints excluded: chain D residue 726 SER Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain F residue 114 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 147 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 179 optimal weight: 0.4980 chunk 176 optimal weight: 0.9980 chunk 222 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 155 optimal weight: 0.0170 chunk 226 optimal weight: 7.9990 chunk 129 optimal weight: 0.0370 chunk 177 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN C 206 GLN C 509 GLN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 GLN D 507 ASN D1140 GLN D1199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.137962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.110564 restraints weight = 26331.881| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.97 r_work: 0.3281 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18371 Z= 0.109 Angle : 0.516 9.937 24913 Z= 0.263 Chirality : 0.038 0.199 2983 Planarity : 0.004 0.042 3171 Dihedral : 3.417 21.513 2539 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.09 % Allowed : 19.38 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.18), residues: 2363 helix: 2.30 (0.13), residues: 1591 sheet: -0.79 (0.65), residues: 74 loop : -0.98 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 285 TYR 0.012 0.001 TYR D 398 PHE 0.018 0.001 PHE C 402 TRP 0.012 0.001 TRP R 33 HIS 0.008 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00241 (18360) covalent geometry : angle 0.51569 (24907) hydrogen bonds : bond 0.03838 ( 1113) hydrogen bonds : angle 3.53025 ( 3273) metal coordination : bond 0.00435 ( 11) metal coordination : angle 1.63693 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 387 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 ASN cc_start: 0.8300 (t0) cc_final: 0.8085 (t0) REVERT: C 110 LEU cc_start: 0.8335 (mt) cc_final: 0.8061 (mt) REVERT: C 289 ARG cc_start: 0.8294 (ttt-90) cc_final: 0.8039 (ttt-90) REVERT: C 451 VAL cc_start: 0.8796 (t) cc_final: 0.8532 (p) REVERT: C 538 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8062 (mm110) REVERT: C 565 ARG cc_start: 0.8609 (tpp80) cc_final: 0.8281 (tpp80) REVERT: C 612 LEU cc_start: 0.8296 (pp) cc_final: 0.8084 (tt) REVERT: C 641 GLN cc_start: 0.7606 (tm130) cc_final: 0.7088 (tm130) REVERT: C 762 LEU cc_start: 0.8465 (pt) cc_final: 0.8126 (pp) REVERT: C 763 GLU cc_start: 0.7372 (pp20) cc_final: 0.6955 (pp20) REVERT: D 67 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8283 (mt) REVERT: D 78 LYS cc_start: 0.8185 (mtpm) cc_final: 0.7733 (mttm) REVERT: D 137 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.6084 (mmm-85) REVERT: D 162 LEU cc_start: 0.8375 (mp) cc_final: 0.8113 (mt) REVERT: D 177 LEU cc_start: 0.8378 (tp) cc_final: 0.8176 (tp) REVERT: D 204 MET cc_start: 0.8530 (tpp) cc_final: 0.8118 (tpp) REVERT: D 213 ASP cc_start: 0.7397 (p0) cc_final: 0.6953 (p0) REVERT: D 251 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7570 (mp0) REVERT: D 362 SER cc_start: 0.8325 (p) cc_final: 0.8118 (p) REVERT: D 863 GLU cc_start: 0.7880 (tp30) cc_final: 0.7609 (tp30) REVERT: D 884 SER cc_start: 0.8274 (t) cc_final: 0.7792 (m) REVERT: D 941 GLU cc_start: 0.7110 (mp0) cc_final: 0.6646 (mp0) REVERT: D 953 GLU cc_start: 0.8213 (tp30) cc_final: 0.7921 (tp30) REVERT: D 1001 ASP cc_start: 0.7739 (m-30) cc_final: 0.7408 (m-30) REVERT: D 1046 ASP cc_start: 0.8235 (m-30) cc_final: 0.7964 (m-30) REVERT: D 1060 LYS cc_start: 0.8402 (tptm) cc_final: 0.7565 (tptp) REVERT: D 1201 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7161 (tp40) REVERT: F 129 ARG cc_start: 0.7728 (tpm-80) cc_final: 0.7176 (tpm-80) REVERT: S 113 LYS cc_start: 0.8113 (pptt) cc_final: 0.7866 (pptt) REVERT: S 119 THR cc_start: 0.8516 (m) cc_final: 0.8310 (t) outliers start: 39 outliers final: 27 residues processed: 404 average time/residue: 0.6341 time to fit residues: 285.2240 Evaluate side-chains 412 residues out of total 2165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 381 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 538 GLN Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 1072 LYS Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain F residue 114 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 158 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 236 optimal weight: 0.3980 chunk 129 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 GLN D 507 ASN D 768 ASN D1107 ASN D1140 GLN D1199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.136641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109340 restraints weight = 26405.090| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.94 r_work: 0.3261 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18371 Z= 0.135 Angle : 0.542 11.898 24913 Z= 0.275 Chirality : 0.039 0.204 2983 Planarity : 0.004 0.043 3171 Dihedral : 3.474 20.634 2539 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.93 % Allowed : 19.75 % Favored : 78.32 % 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: 1.85 (0.18), residues: 2363 helix: 2.26 (0.13), residues: 1592 sheet: -0.75 (0.67), residues: 69 loop : -1.03 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 285 TYR 0.019 0.001 TYR D 274 PHE 0.021 0.001 PHE C 402 TRP 0.010 0.001 TRP R 33 HIS 0.007 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00318 (18360) covalent geometry : angle 0.54079 (24907) hydrogen bonds : bond 0.04501 ( 1113) hydrogen bonds : angle 3.58993 ( 3273) metal coordination : bond 0.00403 ( 11) metal coordination : angle 2.04999 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7962.28 seconds wall clock time: 135 minutes 55.25 seconds (8155.25 seconds total)