Starting phenix.real_space_refine on Thu Mar 5 01:55:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z8v_14564/03_2026/7z8v_14564.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z8v_14564/03_2026/7z8v_14564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z8v_14564/03_2026/7z8v_14564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z8v_14564/03_2026/7z8v_14564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z8v_14564/03_2026/7z8v_14564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z8v_14564/03_2026/7z8v_14564.map" } resolution = 2.7 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= 0.029 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 102 5.16 5 C 11621 2.51 5 N 3140 2.21 5 O 3447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s 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: 18313 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 5893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5893 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 713} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 8982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1158, 8982 Classifications: {'peptide': 1158} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 55, 'TRANS': 1102} Chain breaks: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 28 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: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1728 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 13, 'TRANS': 300} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 791 Unresolved non-hydrogen angles: 1017 Unresolved non-hydrogen dihedrals: 637 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 13, 'ASN:plan1': 14, 'HIS:plan': 10, 'ARG:plan': 12, 'PHE:plan': 11, 'GLU:plan': 12, 'TRP:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 404 Chain: "S" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 994 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 45 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 15063 SG CYS R 42 136.885 54.531 49.334 1.00 72.48 S ATOM 15082 SG CYS R 45 139.140 52.701 52.097 1.00 76.62 S ATOM 15377 SG CYS R 83 136.157 54.683 53.076 1.00 64.65 S ATOM 15306 SG CYS R 75 129.834 62.575 41.901 1.00 49.02 S ATOM 15473 SG CYS R 94 132.944 63.086 44.257 1.00 56.21 S ATOM 15149 SG CYS R 53 134.471 51.590 55.315 1.00 83.93 S ATOM 15172 SG CYS R 56 133.871 49.886 58.679 1.00 86.67 S ATOM 15256 SG CYS R 68 131.941 48.803 55.413 1.00 80.23 S Time building chain proxies: 4.06, per 1000 atoms: 0.22 Number of scatterers: 18313 At special positions: 0 Unit cell: (151.514, 154.918, 118.317, 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 102 16.00 O 3447 8.00 N 3140 7.00 C 11621 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: 1.70 Conformation dependent library (CDL) restraints added in 689.7 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 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " 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 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4652 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 10 sheets defined 71.2% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 38 through 54 Processing helix chain 'C' and resid 87 through 105 removed outlier: 3.883A pdb=" N LYS C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 137 removed outlier: 3.578A pdb=" N ASP C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 152 removed outlier: 4.559A pdb=" N VAL C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARG C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 175 through 192 Processing helix chain 'C' and resid 198 through 211 removed outlier: 3.802A pdb=" N GLY C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 4.426A 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 255 Processing helix chain 'C' and resid 256 through 279 removed outlier: 3.662A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.709A 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 297 Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.529A 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 354 Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.911A pdb=" N ALA C 358 " --> pdb=" O CYS C 355 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 359 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 385 Processing helix chain 'C' and resid 388 through 405 removed outlier: 3.779A pdb=" N ASN C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 416 through 431 removed outlier: 3.638A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 454 removed outlier: 3.617A pdb=" N LYS C 454 " --> pdb=" O MET C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 477 removed outlier: 3.937A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 496 removed outlier: 3.652A pdb=" N GLU C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 527 removed outlier: 3.749A pdb=" N MET C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 512 " --> pdb=" O PHE C 508 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASN C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 574 Processing helix chain 'C' and resid 605 through 613 Processing helix chain 'C' and resid 622 through 630 Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'C' and resid 688 through 722 removed outlier: 4.258A pdb=" N GLN C 692 " --> pdb=" O MET C 688 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 739 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 36 Processing helix chain 'D' and resid 42 through 57 removed outlier: 3.831A pdb=" N GLU D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 78 removed outlier: 4.108A pdb=" N GLY D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Proline residue: D 74 - end of helix removed outlier: 4.209A pdb=" N SER D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS D 78 " --> pdb=" O PRO D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.733A pdb=" N VAL D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR D 86 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU D 96 " --> pdb=" O CYS D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 117 removed outlier: 3.531A pdb=" N LEU D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 144 removed outlier: 3.737A pdb=" N SER D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 164 removed outlier: 3.676A pdb=" N ARG D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.540A pdb=" N THR D 185 " --> pdb=" O PRO D 182 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER D 186 " --> pdb=" O GLN D 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 182 through 186' Processing helix chain 'D' and resid 188 through 205 removed outlier: 3.590A pdb=" N ARG D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 224 removed outlier: 3.548A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.539A pdb=" N THR D 231 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 251 removed outlier: 4.427A 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: 3.865A pdb=" N ASN D 265 " --> pdb=" O VAL D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 286 Processing helix chain 'D' and resid 287 through 292 removed outlier: 3.682A pdb=" N VAL D 290 " --> pdb=" O PRO D 287 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR D 291 " --> pdb=" O LYS D 288 " (cutoff:3.500A) Proline residue: D 292 - end of helix No H-bonds generated for 'chain 'D' and resid 287 through 292' Processing helix chain 'D' and resid 293 through 306 removed outlier: 4.332A pdb=" N THR D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 364 removed outlier: 3.872A pdb=" N ARG D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 382 removed outlier: 4.932A 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: 3.883A 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: 3.973A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 465 removed outlier: 3.569A pdb=" N ARG D 451 " --> pdb=" O SER D 447 " (cutoff:3.500A) 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 508 through 515 removed outlier: 6.112A pdb=" N GLN D 511 " --> pdb=" O HIS D 508 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D 512 " --> pdb=" O SER D 509 " (cutoff:3.500A) Proline residue: D 515 - end of helix Processing helix chain 'D' and resid 516 through 529 Proline residue: D 522 - end of helix removed outlier: 3.607A pdb=" N GLY D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 551 removed outlier: 3.531A pdb=" N GLU D 538 " --> pdb=" O LYS D 534 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D 545 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 563 No H-bonds generated for 'chain 'D' and resid 561 through 563' Processing helix chain 'D' and resid 564 through 577 removed outlier: 3.579A pdb=" N LEU D 568 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D 574 " --> pdb=" O THR D 570 " (cutoff:3.500A) removed outlier: 4.131A 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: 4.525A 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 658 removed outlier: 3.585A pdb=" N LEU D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY D 649 " --> pdb=" O ARG D 645 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLU D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) Proline residue: D 653 - end of helix removed outlier: 3.508A pdb=" N PHE D 658 " --> pdb=" O ILE D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 681 Processing helix chain 'D' and resid 682 through 685 Processing helix chain 'D' and resid 686 through 695 removed outlier: 4.472A pdb=" N ALA D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL D 693 " --> pdb=" O MET D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 701 Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.693A pdb=" N SER D 709 " --> pdb=" O ASP D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 731 removed outlier: 4.299A pdb=" N SER D 728 " --> pdb=" O SER D 725 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 729 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER D 731 " --> pdb=" O SER D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.573A pdb=" N ASN D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 766 removed outlier: 3.828A pdb=" N VAL D 764 " --> pdb=" O GLN D 760 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) removed outlier: 4.327A 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 793 through 810 removed outlier: 3.688A pdb=" N TYR D 797 " --> pdb=" O LYS D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 826 removed outlier: 3.694A pdb=" N VAL D 817 " --> pdb=" O GLU D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 849 removed outlier: 4.386A pdb=" N HIS D 848 " --> pdb=" O GLU D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 864 removed outlier: 3.631A pdb=" N ALA D 864 " --> pdb=" O VAL D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 887 removed outlier: 3.539A pdb=" N SER D 884 " --> pdb=" O LEU D 880 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL D 885 " --> pdb=" O GLY D 881 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY D 886 " --> pdb=" O SER D 882 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN D 887 " --> pdb=" O ILE D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 902 removed outlier: 3.914A pdb=" N THR D 900 " --> pdb=" O LEU D 896 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D 902 " --> pdb=" O GLU D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 919 Processing helix chain 'D' and resid 921 through 926 Processing helix chain 'D' and resid 928 through 940 removed outlier: 3.559A pdb=" N LYS D 938 " --> pdb=" O ALA D 934 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS D 939 " --> pdb=" O LEU D 935 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 961 removed outlier: 3.598A pdb=" N VAL D 950 " --> pdb=" O GLY D 946 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE D 961 " --> pdb=" O LYS D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 972 Processing helix chain 'D' and resid 978 through 991 removed outlier: 3.516A pdb=" N ARG D 982 " --> pdb=" O SER D 978 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 983 " --> pdb=" O SER D 979 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 990 " --> pdb=" O VAL D 986 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE D 991 " --> pdb=" O THR D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1013 removed outlier: 3.864A pdb=" N ASN D1006 " --> pdb=" O PRO D1002 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS D1007 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLY D1009 " --> pdb=" O LYS D1005 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASP D1010 " --> pdb=" O ASN D1006 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE D1011 " --> pdb=" O CYS D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1014 through 1017 Processing helix chain 'D' and resid 1019 through 1037 removed outlier: 3.847A pdb=" N ARG D1023 " --> pdb=" O ASP D1019 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG D1024 " --> pdb=" O LEU D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1043 removed outlier: 4.461A 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) Processing helix chain 'D' and resid 1044 through 1055 Proline residue: D1050 - end of helix 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 1095 removed outlier: 3.735A pdb=" N LEU D1093 " --> pdb=" O MET D1089 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP D1094 " --> pdb=" O TYR D1090 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER D1095 " --> pdb=" O THR D1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 1101 through 1113 removed outlier: 3.812A pdb=" N PHE D1105 " --> pdb=" O ASP D1101 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1133 removed outlier: 3.519A pdb=" N LEU D1122 " --> pdb=" O ASP D1118 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU D1125 " --> pdb=" O MET D1121 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR D1132 " --> pdb=" O VAL D1128 " (cutoff:3.500A) Processing helix chain 'D' and resid 1134 through 1141 removed outlier: 4.015A pdb=" N VAL D1138 " --> pdb=" O CYS D1134 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1155 Proline residue: D1148 - end of helix Processing helix chain 'D' and resid 1162 through 1185 removed outlier: 3.625A pdb=" N PHE D1166 " --> pdb=" O VAL D1162 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D1185 " --> pdb=" O ALA D1181 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1205 removed outlier: 3.732A pdb=" N GLU D1197 " --> pdb=" O PRO D1193 " (cutoff:3.500A) Processing helix chain 'D' and resid 1205 through 1215 removed outlier: 3.506A pdb=" N ILE D1211 " --> pdb=" O GLU D1207 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D1215 " --> pdb=" O ILE D1211 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 59 Processing helix chain 'R' and resid 62 through 67 removed outlier: 3.593A pdb=" N GLU R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 88 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 158 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: 3.527A 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: 3.910A 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 29 Processing helix chain 'S' and resid 51 through 65 Processing helix chain 'S' and resid 87 through 94 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 Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 541 removed outlier: 6.192A pdb=" N ASP C 534 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ALA R 29 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER C 536 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ALA R 31 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLN C 538 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N TRP R 33 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU C 540 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N TRP R 35 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N PHE R 22 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU C 590 " --> pdb=" O PHE R 22 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N VAL R 24 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N GLY C 588 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 11.498A pdb=" N LYS R 26 " --> pdb=" O SER C 586 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N SER C 586 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N ASN R 28 " --> pdb=" O GLN C 584 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N GLN C 584 " --> pdb=" O ASN R 28 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL R 30 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 599 " --> pdb=" O THR C 592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 619 through 621 Processing sheet with id=AA3, first strand: chain 'C' and resid 724 through 726 Processing sheet with id=AA4, first strand: chain 'D' and resid 1063 through 1068 Processing sheet with id=AA5, first strand: chain 'R' and resid 78 through 80 removed outlier: 6.643A pdb=" N TRP R 72 " --> pdb=" O GLN R 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 139 through 141 removed outlier: 3.521A pdb=" N ARG F 164 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET F 186 " --> pdb=" O ASN F 210 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER F 212 " --> pdb=" O MET F 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AA8, first strand: chain 'F' and resid 260 through 262 Processing sheet with id=AA9, first strand: chain 'F' and resid 339 through 341 removed outlier: 7.353A pdb=" N LEU F 340 " --> pdb=" O GLN F 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 13 through 17 1118 hydrogen bonds defined for protein. 3288 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: 3.20 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6054 1.34 - 1.46: 2797 1.46 - 1.58: 9603 1.58 - 1.69: 0 1.69 - 1.81: 149 Bond restraints: 18603 Sorted by residual: bond pdb=" CA ASN C 478 " pdb=" CB ASN C 478 " ideal model delta sigma weight residual 1.527 1.555 -0.028 2.48e-02 1.63e+03 1.25e+00 bond pdb=" CB PRO C 556 " pdb=" CG PRO C 556 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.25e+00 bond pdb=" C SER F 179 " pdb=" N PRO F 180 " ideal model delta sigma weight residual 1.331 1.345 -0.014 1.27e-02 6.20e+03 1.16e+00 bond pdb=" CB ASN C 683 " pdb=" CG ASN C 683 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.05e-01 bond pdb=" CG LEU C 116 " pdb=" CD1 LEU C 116 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.11e-01 ... (remaining 18598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 25003 2.16 - 4.32: 196 4.32 - 6.48: 32 6.48 - 8.64: 2 8.64 - 10.80: 1 Bond angle restraints: 25234 Sorted by residual: angle pdb=" N GLU D1171 " pdb=" CA GLU D1171 " pdb=" CB GLU D1171 " ideal model delta sigma weight residual 110.28 115.46 -5.18 1.55e+00 4.16e-01 1.11e+01 angle pdb=" CA LEU D1184 " pdb=" CB LEU D1184 " pdb=" CG LEU D1184 " ideal model delta sigma weight residual 116.30 127.10 -10.80 3.50e+00 8.16e-02 9.52e+00 angle pdb=" C LYS D 661 " pdb=" N ASN D 662 " pdb=" CA ASN D 662 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.03e+00 angle pdb=" C GLY C 85 " pdb=" N LEU C 86 " pdb=" CA LEU C 86 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 8.99e+00 angle pdb=" C VAL R 39 " pdb=" N ASP R 40 " pdb=" CA ASP R 40 " ideal model delta sigma weight residual 121.54 126.86 -5.32 1.91e+00 2.74e-01 7.74e+00 ... (remaining 25229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10311 17.95 - 35.90: 894 35.90 - 53.85: 139 53.85 - 71.80: 34 71.80 - 89.75: 14 Dihedral angle restraints: 11392 sinusoidal: 4268 harmonic: 7124 Sorted by residual: dihedral pdb=" CA MET C 111 " pdb=" C MET C 111 " pdb=" N ASP C 112 " pdb=" CA ASP C 112 " ideal model delta harmonic sigma weight residual -180.00 -160.59 -19.41 0 5.00e+00 4.00e-02 1.51e+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 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CB GLU D 270 " pdb=" CG GLU D 270 " pdb=" CD GLU D 270 " pdb=" OE1 GLU D 270 " ideal model delta sinusoidal sigma weight residual 0.00 -88.96 88.96 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 11389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1962 0.032 - 0.064: 746 0.064 - 0.096: 216 0.096 - 0.129: 80 0.129 - 0.161: 5 Chirality restraints: 3009 Sorted by residual: chirality pdb=" CA GLU S 102 " pdb=" N GLU S 102 " pdb=" C GLU S 102 " pdb=" CB GLU S 102 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA TYR C 377 " pdb=" N TYR C 377 " pdb=" C TYR C 377 " pdb=" CB TYR C 377 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.54e-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 5.20e-01 ... (remaining 3006 not shown) Planarity restraints: 3221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 555 " -0.068 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO C 556 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 556 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 556 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 173 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO D 174 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 174 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 174 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 545 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO C 546 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 546 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 546 " 0.027 5.00e-02 4.00e+02 ... (remaining 3218 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 73 2.57 - 3.15: 14436 3.15 - 3.74: 27764 3.74 - 4.32: 35852 4.32 - 4.90: 62212 Nonbonded interactions: 140337 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.989 2.230 nonbonded pdb=" OG SER S 8 " pdb=" OD1 ASP S 10 " model vdw 2.276 3.040 nonbonded pdb=" NH1 ARG C 127 " pdb=" OE1 GLU C 210 " model vdw 2.310 3.120 nonbonded pdb=" OH TYR D 372 " pdb=" OG1 THR D 405 " model vdw 2.318 3.040 nonbonded pdb=" OE1 GLU C 190 " pdb=" OH TYR C 278 " model vdw 2.331 3.040 ... (remaining 140332 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: 3.140 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.220 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 18614 Z= 0.138 Angle : 0.512 10.798 25240 Z= 0.270 Chirality : 0.039 0.161 3009 Planarity : 0.004 0.103 3221 Dihedral : 13.968 89.753 6740 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 1.51 (0.18), residues: 2391 helix: 2.05 (0.14), residues: 1543 sheet: -1.33 (0.64), residues: 78 loop : -0.93 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 91 TYR 0.018 0.001 TYR C 377 PHE 0.019 0.001 PHE C 402 TRP 0.017 0.001 TRP S 88 HIS 0.004 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00266 (18603) covalent geometry : angle 0.50736 (25234) hydrogen bonds : bond 0.15519 ( 1118) hydrogen bonds : angle 4.68631 ( 3288) metal coordination : bond 0.08428 ( 11) metal coordination : angle 4.67983 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 0.633 Fit side-chains REVERT: C 331 ASP cc_start: 0.7154 (t0) cc_final: 0.6849 (t0) REVERT: C 763 GLU cc_start: 0.6859 (pp20) cc_final: 0.6107 (pp20) REVERT: D 429 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7650 (mm-40) REVERT: D 593 MET cc_start: 0.8362 (tpp) cc_final: 0.8124 (tpp) REVERT: D 1171 GLU cc_start: 0.7115 (mp0) cc_final: 0.6529 (mp0) REVERT: S 88 TRP cc_start: 0.5836 (t60) cc_final: 0.4493 (t60) outliers start: 0 outliers final: 1 residues processed: 437 average time/residue: 0.6147 time to fit residues: 299.3802 Evaluate side-chains 389 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 388 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 850 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 50.0000 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 98 ASN C 206 GLN C 448 GLN C 505 GLN C 520 GLN C 615 ASN C 641 GLN D 66 ASN D 83 GLN D 599 ASN D 663 GLN D 823 GLN D 931 ASN D1199 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.137313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.111966 restraints weight = 25950.137| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.76 r_work: 0.3335 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18614 Z= 0.173 Angle : 0.541 8.206 25240 Z= 0.286 Chirality : 0.042 0.174 3009 Planarity : 0.004 0.071 3221 Dihedral : 3.696 29.058 2568 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.78 % Allowed : 10.12 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.18), residues: 2391 helix: 2.03 (0.13), residues: 1572 sheet: -0.98 (0.67), residues: 78 loop : -0.95 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 91 TYR 0.023 0.002 TYR C 377 PHE 0.024 0.002 PHE D 894 TRP 0.013 0.001 TRP R 33 HIS 0.005 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00418 (18603) covalent geometry : angle 0.54048 (25234) hydrogen bonds : bond 0.05820 ( 1118) hydrogen bonds : angle 3.97577 ( 3288) metal coordination : bond 0.00576 ( 11) metal coordination : angle 1.87797 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 421 time to evaluate : 0.516 Fit side-chains REVERT: C 175 LEU cc_start: 0.8086 (mt) cc_final: 0.7860 (mt) REVERT: C 241 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7844 (tp30) REVERT: C 259 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7931 (mm-30) REVERT: C 331 ASP cc_start: 0.7852 (t0) cc_final: 0.7496 (t0) REVERT: C 478 ASN cc_start: 0.8325 (p0) cc_final: 0.8059 (p0) REVERT: D 429 GLN cc_start: 0.8235 (tp-100) cc_final: 0.7964 (mm-40) REVERT: D 748 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8169 (pt0) REVERT: D 890 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: D 1041 ILE cc_start: 0.8503 (pt) cc_final: 0.8290 (pp) REVERT: D 1065 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: D 1081 ILE cc_start: 0.8471 (mt) cc_final: 0.8244 (mm) REVERT: D 1171 GLU cc_start: 0.7759 (mp0) cc_final: 0.7107 (mp0) REVERT: F 127 TRP cc_start: 0.7876 (m-10) cc_final: 0.7622 (m-10) REVERT: S 88 TRP cc_start: 0.6071 (t60) cc_final: 0.4584 (t60) outliers start: 34 outliers final: 13 residues processed: 429 average time/residue: 0.6147 time to fit residues: 294.0499 Evaluate side-chains 419 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 402 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 723 LYS Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 748 GLN Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 1065 GLU Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 121 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 224 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 163 optimal weight: 0.0980 chunk 108 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 98 ASN C 206 GLN C 368 GLN C 448 GLN C 520 GLN C 615 ASN C 641 GLN D 66 ASN D 83 GLN D 931 ASN D1199 GLN R 28 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.138416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112975 restraints weight = 26004.926| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.75 r_work: 0.3354 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18614 Z= 0.130 Angle : 0.495 7.423 25240 Z= 0.262 Chirality : 0.039 0.171 3009 Planarity : 0.004 0.059 3221 Dihedral : 3.587 18.418 2566 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.25 % Allowed : 12.38 % Favored : 85.37 % 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: 1.69 (0.18), residues: 2391 helix: 2.15 (0.13), residues: 1573 sheet: -1.03 (0.64), residues: 78 loop : -0.92 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 573 TYR 0.020 0.001 TYR C 377 PHE 0.020 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 0.00299 (18603) covalent geometry : angle 0.49492 (25234) hydrogen bonds : bond 0.04895 ( 1118) hydrogen bonds : angle 3.79344 ( 3288) metal coordination : bond 0.00351 ( 11) metal coordination : angle 1.63334 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 406 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: C 175 LEU cc_start: 0.8067 (mt) cc_final: 0.7815 (mt) REVERT: C 241 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7807 (tp30) REVERT: C 331 ASP cc_start: 0.7850 (t0) cc_final: 0.7490 (t0) REVERT: C 478 ASN cc_start: 0.8291 (p0) cc_final: 0.8005 (p0) REVERT: D 165 GLN cc_start: 0.7113 (mp-120) cc_final: 0.6730 (mp-120) REVERT: D 429 GLN cc_start: 0.8230 (tp-100) cc_final: 0.7977 (mm-40) REVERT: D 617 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7607 (tm-30) REVERT: D 748 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8134 (pt0) REVERT: D 890 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: D 1041 ILE cc_start: 0.8505 (pt) cc_final: 0.8271 (pp) REVERT: D 1081 ILE cc_start: 0.8422 (mt) cc_final: 0.8200 (mm) REVERT: D 1171 GLU cc_start: 0.7778 (mp0) cc_final: 0.7390 (mp0) REVERT: F 127 TRP cc_start: 0.7942 (m-10) cc_final: 0.7696 (m-10) outliers start: 43 outliers final: 16 residues processed: 420 average time/residue: 0.6224 time to fit residues: 291.4143 Evaluate side-chains 421 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 402 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 748 GLN Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 944 GLU Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain F residue 134 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 95 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 53 optimal weight: 0.0070 chunk 203 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 128 optimal weight: 0.0050 chunk 230 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 214 optimal weight: 50.0000 chunk 60 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 overall best weight: 0.4412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN C 527 ASN C 615 ASN C 641 GLN D 66 ASN D 83 GLN D 823 GLN D 931 ASN R 48 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.139510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114005 restraints weight = 25992.373| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.76 r_work: 0.3372 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18614 Z= 0.110 Angle : 0.482 9.758 25240 Z= 0.251 Chirality : 0.038 0.138 3009 Planarity : 0.004 0.054 3221 Dihedral : 3.477 17.520 2566 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.15 % Allowed : 14.00 % Favored : 83.85 % 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: 2391 helix: 2.27 (0.14), residues: 1573 sheet: -1.05 (0.64), residues: 78 loop : -0.84 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 573 TYR 0.019 0.001 TYR C 377 PHE 0.018 0.001 PHE C 402 TRP 0.011 0.001 TRP R 33 HIS 0.005 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00242 (18603) covalent geometry : angle 0.48183 (25234) hydrogen bonds : bond 0.04259 ( 1118) hydrogen bonds : angle 3.67293 ( 3288) metal coordination : bond 0.00393 ( 11) metal coordination : angle 1.37213 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 419 time to evaluate : 0.697 Fit side-chains REVERT: C 175 LEU cc_start: 0.8023 (mt) cc_final: 0.7787 (mt) REVERT: C 241 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7809 (tp30) REVERT: C 331 ASP cc_start: 0.7825 (t0) cc_final: 0.7468 (t0) REVERT: C 478 ASN cc_start: 0.8241 (p0) cc_final: 0.7981 (p0) REVERT: D 96 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8572 (mp) REVERT: D 111 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8472 (mttm) REVERT: D 165 GLN cc_start: 0.7083 (mp-120) cc_final: 0.6749 (mp-120) REVERT: D 429 GLN cc_start: 0.8213 (tp-100) cc_final: 0.7946 (mm-40) REVERT: D 890 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: D 955 LEU cc_start: 0.8897 (tp) cc_final: 0.8694 (mt) REVERT: D 1041 ILE cc_start: 0.8489 (pt) cc_final: 0.8241 (pp) REVERT: D 1171 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: F 127 TRP cc_start: 0.7937 (m-10) cc_final: 0.7725 (m-10) REVERT: S 88 TRP cc_start: 0.6082 (t60) cc_final: 0.4380 (t60) outliers start: 41 outliers final: 20 residues processed: 429 average time/residue: 0.6190 time to fit residues: 296.1878 Evaluate side-chains 428 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 404 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 944 GLU Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1171 GLU Chi-restraints excluded: chain D residue 1199 GLN Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 179 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 220 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 221 optimal weight: 30.0000 chunk 152 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 196 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 HIS C 98 ASN C 102 ASN C 206 GLN C 387 ASN C 448 GLN C 520 GLN C 615 ASN D 83 GLN D 518 GLN D 931 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111120 restraints weight = 25812.172| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.74 r_work: 0.3317 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18614 Z= 0.185 Angle : 0.542 9.380 25240 Z= 0.282 Chirality : 0.042 0.231 3009 Planarity : 0.004 0.052 3221 Dihedral : 3.607 18.172 2566 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.10 % Allowed : 15.15 % Favored : 82.75 % 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: 1.68 (0.18), residues: 2391 helix: 2.12 (0.13), residues: 1573 sheet: -0.99 (0.63), residues: 80 loop : -0.87 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 573 TYR 0.023 0.002 TYR C 377 PHE 0.020 0.002 PHE C 402 TRP 0.012 0.001 TRP R 33 HIS 0.005 0.001 HIS D1116 Details of bonding type rmsd covalent geometry : bond 0.00457 (18603) covalent geometry : angle 0.54114 (25234) hydrogen bonds : bond 0.05781 ( 1118) hydrogen bonds : angle 3.80536 ( 3288) metal coordination : bond 0.00399 ( 11) metal coordination : angle 2.20529 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 409 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: C 331 ASP cc_start: 0.7822 (t0) cc_final: 0.7496 (t0) REVERT: C 478 ASN cc_start: 0.8307 (p0) cc_final: 0.8014 (p0) REVERT: D 165 GLN cc_start: 0.7152 (mp-120) cc_final: 0.6799 (mp-120) REVERT: D 351 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8161 (ttm-80) REVERT: D 429 GLN cc_start: 0.8297 (tp-100) cc_final: 0.8023 (mm-40) REVERT: D 457 MET cc_start: 0.8580 (ttm) cc_final: 0.8377 (ttp) REVERT: D 691 ASP cc_start: 0.7375 (p0) cc_final: 0.7096 (p0) REVERT: D 748 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8110 (pt0) REVERT: D 890 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: D 1041 ILE cc_start: 0.8512 (pt) cc_final: 0.8291 (pp) REVERT: D 1171 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: F 127 TRP cc_start: 0.8001 (m-10) cc_final: 0.7795 (m-10) REVERT: S 88 TRP cc_start: 0.6102 (t60) cc_final: 0.4556 (t60) outliers start: 40 outliers final: 21 residues processed: 420 average time/residue: 0.6415 time to fit residues: 300.3329 Evaluate side-chains 425 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 400 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 351 ARG Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 748 GLN Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1171 GLU Chi-restraints excluded: chain D residue 1204 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 179 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 224 optimal weight: 50.0000 chunk 1 optimal weight: 3.9990 chunk 189 optimal weight: 0.0970 chunk 169 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.0030 chunk 100 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 ASN C 448 GLN C 520 GLN C 527 ASN C 615 ASN D 66 ASN D 83 GLN D 244 GLN D 823 GLN D 931 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.140293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.114981 restraints weight = 25758.797| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.74 r_work: 0.3367 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18614 Z= 0.111 Angle : 0.486 7.939 25240 Z= 0.254 Chirality : 0.038 0.186 3009 Planarity : 0.004 0.050 3221 Dihedral : 3.476 17.544 2566 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.15 % Allowed : 15.31 % Favored : 82.54 % 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: 1.92 (0.18), residues: 2391 helix: 2.31 (0.14), residues: 1574 sheet: -1.04 (0.64), residues: 79 loop : -0.77 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 743 TYR 0.019 0.001 TYR C 377 PHE 0.017 0.001 PHE C 569 TRP 0.012 0.001 TRP R 33 HIS 0.005 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00243 (18603) covalent geometry : angle 0.48585 (25234) hydrogen bonds : bond 0.04188 ( 1118) hydrogen bonds : angle 3.60913 ( 3288) metal coordination : bond 0.00463 ( 11) metal coordination : angle 1.44275 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 413 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: C 241 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7793 (tp30) REVERT: C 331 ASP cc_start: 0.7809 (t0) cc_final: 0.7466 (t0) REVERT: C 478 ASN cc_start: 0.8222 (p0) cc_final: 0.7967 (p0) REVERT: D 111 LYS cc_start: 0.8710 (ttmt) cc_final: 0.8492 (mttm) REVERT: D 165 GLN cc_start: 0.7107 (mp-120) cc_final: 0.6807 (mp-120) REVERT: D 351 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8074 (ttm-80) REVERT: D 429 GLN cc_start: 0.8248 (tp-100) cc_final: 0.7962 (mm-40) REVERT: D 748 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8109 (pt0) REVERT: D 890 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: D 1041 ILE cc_start: 0.8469 (pt) cc_final: 0.8226 (pp) REVERT: D 1171 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: F 127 TRP cc_start: 0.7965 (m-10) cc_final: 0.7748 (m100) REVERT: S 88 TRP cc_start: 0.6078 (t60) cc_final: 0.4433 (t60) outliers start: 41 outliers final: 20 residues processed: 426 average time/residue: 0.6247 time to fit residues: 297.2434 Evaluate side-chains 429 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 404 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 351 ARG Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 748 GLN Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 944 GLU Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1171 GLU Chi-restraints excluded: chain D residue 1204 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 179 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 154 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 229 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN C 102 ASN C 448 GLN C 520 GLN C 527 ASN C 615 ASN C 641 GLN D 83 GLN D 823 GLN D 931 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.138194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.112821 restraints weight = 25851.367| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.74 r_work: 0.3337 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18614 Z= 0.147 Angle : 0.522 11.828 25240 Z= 0.271 Chirality : 0.040 0.205 3009 Planarity : 0.004 0.048 3221 Dihedral : 3.515 17.417 2566 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.25 % Allowed : 15.89 % Favored : 81.86 % 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: 1.86 (0.18), residues: 2391 helix: 2.26 (0.13), residues: 1573 sheet: -1.10 (0.63), residues: 79 loop : -0.79 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 565 TYR 0.023 0.002 TYR S 109 PHE 0.020 0.002 PHE C 569 TRP 0.011 0.001 TRP R 33 HIS 0.004 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00354 (18603) covalent geometry : angle 0.52156 (25234) hydrogen bonds : bond 0.05084 ( 1118) hydrogen bonds : angle 3.68323 ( 3288) metal coordination : bond 0.00384 ( 11) metal coordination : angle 1.88608 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 412 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: C 274 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7830 (mtt90) REVERT: C 331 ASP cc_start: 0.7822 (t0) cc_final: 0.7501 (t0) REVERT: C 478 ASN cc_start: 0.8276 (p0) cc_final: 0.7983 (p0) REVERT: C 750 LYS cc_start: 0.8023 (mttp) cc_final: 0.7811 (mttp) REVERT: D 111 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8506 (mttm) REVERT: D 165 GLN cc_start: 0.7114 (mp-120) cc_final: 0.6813 (mp-120) REVERT: D 351 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8121 (ttm-80) REVERT: D 429 GLN cc_start: 0.8307 (tp-100) cc_final: 0.8030 (mm-40) REVERT: D 748 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8143 (pt0) REVERT: D 890 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: D 1041 ILE cc_start: 0.8474 (pt) cc_final: 0.8235 (pp) REVERT: D 1171 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: F 127 TRP cc_start: 0.7994 (m-10) cc_final: 0.7786 (m100) REVERT: S 88 TRP cc_start: 0.6095 (t60) cc_final: 0.4454 (t60) outliers start: 43 outliers final: 29 residues processed: 426 average time/residue: 0.6271 time to fit residues: 297.7342 Evaluate side-chains 443 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 410 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 351 ARG Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 748 GLN Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1171 GLU Chi-restraints excluded: chain D residue 1204 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain S residue 45 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 208 optimal weight: 30.0000 chunk 216 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 167 optimal weight: 0.0000 chunk 77 optimal weight: 0.0980 chunk 132 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 42 optimal weight: 0.5980 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN C 102 ASN C 448 GLN C 520 GLN C 527 ASN C 615 ASN C 641 GLN D 83 GLN D 931 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.139774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114574 restraints weight = 26009.869| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.75 r_work: 0.3380 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18614 Z= 0.104 Angle : 0.487 8.189 25240 Z= 0.253 Chirality : 0.038 0.161 3009 Planarity : 0.004 0.049 3221 Dihedral : 3.406 18.355 2566 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.15 % Allowed : 16.41 % Favored : 81.44 % 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: 2.02 (0.18), residues: 2391 helix: 2.38 (0.14), residues: 1576 sheet: -1.13 (0.62), residues: 79 loop : -0.71 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 743 TYR 0.018 0.001 TYR S 109 PHE 0.023 0.001 PHE C 569 TRP 0.012 0.001 TRP R 33 HIS 0.005 0.000 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00227 (18603) covalent geometry : angle 0.48666 (25234) hydrogen bonds : bond 0.03790 ( 1118) hydrogen bonds : angle 3.54398 ( 3288) metal coordination : bond 0.00431 ( 11) metal coordination : angle 1.27175 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 416 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: C 241 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7754 (tp30) REVERT: C 331 ASP cc_start: 0.7807 (t0) cc_final: 0.7476 (t0) REVERT: C 478 ASN cc_start: 0.8190 (p0) cc_final: 0.7957 (p0) REVERT: D 111 LYS cc_start: 0.8681 (ttmt) cc_final: 0.8467 (mttm) REVERT: D 165 GLN cc_start: 0.7039 (mp-120) cc_final: 0.6812 (mp-120) REVERT: D 429 GLN cc_start: 0.8268 (tp-100) cc_final: 0.7987 (mm-40) REVERT: D 748 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8125 (pt0) REVERT: D 890 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: D 1171 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7358 (mp0) outliers start: 41 outliers final: 23 residues processed: 432 average time/residue: 0.6061 time to fit residues: 292.2222 Evaluate side-chains 432 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 405 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 522 LYS Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 748 GLN Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1171 GLU Chi-restraints excluded: chain D residue 1204 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain S residue 45 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 105 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 219 optimal weight: 40.0000 chunk 119 optimal weight: 2.9990 chunk 93 optimal weight: 0.0980 chunk 154 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN C 102 ASN C 448 GLN C 520 GLN C 602 GLN C 615 ASN D 83 GLN D 823 GLN D 931 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110919 restraints weight = 25919.606| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.74 r_work: 0.3311 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18614 Z= 0.192 Angle : 0.566 10.618 25240 Z= 0.293 Chirality : 0.042 0.226 3009 Planarity : 0.004 0.047 3221 Dihedral : 3.597 17.680 2566 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.99 % Allowed : 17.20 % Favored : 80.81 % 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: 1.79 (0.18), residues: 2391 helix: 2.19 (0.13), residues: 1573 sheet: -1.04 (0.62), residues: 83 loop : -0.79 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 565 TYR 0.026 0.002 TYR S 109 PHE 0.024 0.002 PHE C 569 TRP 0.010 0.001 TRP R 33 HIS 0.005 0.001 HIS D1116 Details of bonding type rmsd covalent geometry : bond 0.00475 (18603) covalent geometry : angle 0.56457 (25234) hydrogen bonds : bond 0.05802 ( 1118) hydrogen bonds : angle 3.75565 ( 3288) metal coordination : bond 0.00394 ( 11) metal coordination : angle 2.28340 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 412 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: C 331 ASP cc_start: 0.7804 (t0) cc_final: 0.7483 (t0) REVERT: C 478 ASN cc_start: 0.8327 (p0) cc_final: 0.8023 (p0) REVERT: D 55 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8457 (ttpp) REVERT: D 111 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8541 (mttm) REVERT: D 165 GLN cc_start: 0.7086 (mp-120) cc_final: 0.6821 (mp-120) REVERT: D 351 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8145 (ttm-80) REVERT: D 429 GLN cc_start: 0.8356 (tp-100) cc_final: 0.8070 (mm-40) REVERT: D 748 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8140 (pt0) REVERT: D 890 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: D 1171 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: S 88 TRP cc_start: 0.6089 (t60) cc_final: 0.4472 (t60) outliers start: 38 outliers final: 27 residues processed: 427 average time/residue: 0.6331 time to fit residues: 300.9874 Evaluate side-chains 437 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 406 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 351 ARG Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 621 ASN Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 748 GLN Chi-restraints excluded: chain D residue 755 MET Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1136 SER Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1171 GLU Chi-restraints excluded: chain D residue 1194 LEU Chi-restraints excluded: chain D residue 1204 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain S residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 38 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 146 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 94 optimal weight: 0.3980 chunk 80 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 GLN C 520 GLN C 527 ASN C 602 GLN C 615 ASN C 641 GLN D 66 ASN D 83 GLN D 931 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.114111 restraints weight = 25832.116| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.74 r_work: 0.3360 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18614 Z= 0.117 Angle : 0.515 8.959 25240 Z= 0.268 Chirality : 0.039 0.163 3009 Planarity : 0.004 0.043 3221 Dihedral : 3.496 17.382 2566 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.84 % Allowed : 17.51 % Favored : 80.65 % 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: 1.87 (0.18), residues: 2391 helix: 2.27 (0.13), residues: 1585 sheet: -0.94 (0.64), residues: 78 loop : -0.87 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 743 TYR 0.021 0.001 TYR S 109 PHE 0.027 0.001 PHE C 569 TRP 0.013 0.001 TRP R 33 HIS 0.004 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00267 (18603) covalent geometry : angle 0.51477 (25234) hydrogen bonds : bond 0.04262 ( 1118) hydrogen bonds : angle 3.61938 ( 3288) metal coordination : bond 0.00412 ( 11) metal coordination : angle 1.51652 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 412 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 165 VAL cc_start: 0.8576 (t) cc_final: 0.8373 (m) REVERT: C 331 ASP cc_start: 0.7798 (t0) cc_final: 0.7473 (t0) REVERT: C 478 ASN cc_start: 0.8221 (p0) cc_final: 0.7978 (p0) REVERT: D 111 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8502 (mttm) REVERT: D 204 MET cc_start: 0.7857 (mmm) cc_final: 0.7576 (tpp) REVERT: D 429 GLN cc_start: 0.8327 (tp-100) cc_final: 0.8049 (mm-40) REVERT: D 748 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8132 (pt0) REVERT: D 890 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: D 1171 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: S 88 TRP cc_start: 0.6050 (t60) cc_final: 0.4372 (t60) outliers start: 35 outliers final: 25 residues processed: 425 average time/residue: 0.6194 time to fit residues: 293.9151 Evaluate side-chains 431 residues out of total 2183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 403 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 621 ASN Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 748 GLN Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1136 SER Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1171 GLU Chi-restraints excluded: chain D residue 1204 SER Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain S residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 158 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 211 optimal weight: 50.0000 chunk 149 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 227 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 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 98 ASN C 448 GLN C 505 GLN C 520 GLN C 602 GLN C 615 ASN C 641 GLN D 83 GLN D 823 GLN D 931 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.138219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112907 restraints weight = 25826.876| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.75 r_work: 0.3341 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18614 Z= 0.142 Angle : 0.537 8.723 25240 Z= 0.279 Chirality : 0.040 0.190 3009 Planarity : 0.004 0.045 3221 Dihedral : 3.516 17.800 2566 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.78 % Allowed : 17.67 % Favored : 80.55 % 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: 1.84 (0.18), residues: 2391 helix: 2.23 (0.13), residues: 1586 sheet: -0.99 (0.63), residues: 78 loop : -0.85 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 565 TYR 0.024 0.001 TYR S 109 PHE 0.029 0.002 PHE C 569 TRP 0.011 0.001 TRP R 33 HIS 0.004 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00338 (18603) covalent geometry : angle 0.53666 (25234) hydrogen bonds : bond 0.04850 ( 1118) hydrogen bonds : angle 3.67153 ( 3288) metal coordination : bond 0.00368 ( 11) metal coordination : angle 1.84968 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8805.27 seconds wall clock time: 149 minutes 56.47 seconds (8996.47 seconds total)