Starting phenix.real_space_refine on Thu Mar 5 01:33:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zbz_14597/03_2026/7zbz_14597.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zbz_14597/03_2026/7zbz_14597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zbz_14597/03_2026/7zbz_14597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zbz_14597/03_2026/7zbz_14597.map" model { file = "/net/cci-nas-00/data/ceres_data/7zbz_14597/03_2026/7zbz_14597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zbz_14597/03_2026/7zbz_14597.cif" } resolution = 3.1 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 101 5.16 5 C 11520 2.51 5 N 3118 2.21 5 O 3414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18156 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5846 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 707} Chain breaks: 4 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 8845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 8845 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 52, 'TRANS': 1088} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 33 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: "S" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1033 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1716 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 240} Link IDs: {'PTRANS': 13, 'TRANS': 300} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 803 Unresolved non-hydrogen angles: 1030 Unresolved non-hydrogen dihedrals: 648 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLU:plan': 13, 'GLN:plan1': 15, 'ASP:plan': 13, 'ASN:plan1': 14, 'HIS:plan': 10, 'ARG:plan': 12, 'PHE:plan': 11, 'TRP:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 408 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 14879 SG CYS R 42 133.680 56.736 48.066 1.00 79.00 S ATOM 14898 SG CYS R 45 136.275 55.032 50.601 1.00 81.82 S ATOM 15193 SG CYS R 83 133.385 56.988 51.863 1.00 68.21 S ATOM 15122 SG CYS R 75 125.646 64.042 40.976 1.00 50.84 S ATOM 15289 SG CYS R 94 129.020 64.738 42.879 1.00 59.13 S ATOM 14965 SG CYS R 53 132.122 54.091 54.272 1.00 89.56 S ATOM 14988 SG CYS R 56 132.048 52.494 57.739 1.00 92.42 S ATOM 15072 SG CYS R 68 129.797 51.170 54.779 1.00 81.95 S Time building chain proxies: 3.73, per 1000 atoms: 0.21 Number of scatterers: 18156 At special positions: 0 Unit cell: (148.109, 156.621, 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 101 16.00 O 3414 8.00 N 3118 7.00 C 11520 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: 1.56 Conformation dependent library (CDL) restraints added in 888.2 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 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " Number of angles added : 6 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4612 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 9 sheets defined 73.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'C' and resid 16 through 32 removed outlier: 3.907A pdb=" N ILE C 20 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP C 22 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASP C 23 " --> pdb=" O GLN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 55 removed outlier: 3.502A pdb=" N TYR C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 107 removed outlier: 3.710A pdb=" N LYS C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP C 106 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 137 removed outlier: 3.858A pdb=" N LEU C 116 " --> pdb=" O ASP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 143 removed outlier: 3.626A pdb=" N ASN C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 152 removed outlier: 3.505A pdb=" N GLY C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 171 through 193 removed outlier: 3.667A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS C 177 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLN C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 212 removed outlier: 3.770A pdb=" N GLY C 212 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 232 through 255 removed outlier: 3.645A pdb=" N GLN C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 279 removed outlier: 3.611A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.671A 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 Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 333 through 356 removed outlier: 4.036A pdb=" N CYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 362 through 385 Processing helix chain 'C' and resid 388 through 405 removed outlier: 3.753A pdb=" N ASN C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 3.572A 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: 3.627A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 454 removed outlier: 3.588A pdb=" N LYS C 454 " --> pdb=" O MET C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 477 removed outlier: 4.200A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 496 removed outlier: 3.677A pdb=" N GLU C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 528 removed outlier: 3.630A pdb=" N MET C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER C 528 " --> pdb=" O HIS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 558 No H-bonds generated for 'chain 'C' and resid 556 through 558' Processing helix chain 'C' and resid 559 through 574 Processing helix chain 'C' and resid 605 through 613 removed outlier: 3.575A pdb=" N GLN C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) 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: 4.336A pdb=" N GLN C 692 " --> pdb=" O MET C 688 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 739 removed outlier: 3.663A pdb=" N LEU C 730 " --> pdb=" O LYS C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 759 Processing helix chain 'D' and resid 6 through 15 Processing helix chain 'D' and resid 19 through 36 Processing helix chain 'D' and resid 43 through 57 removed outlier: 3.966A pdb=" N ARG D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 79 removed outlier: 4.002A pdb=" N GLY D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Proline residue: D 74 - end of helix removed outlier: 4.471A pdb=" N SER D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS D 78 " --> pdb=" O PRO D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.877A pdb=" N VAL D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR D 86 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 96 " --> pdb=" O CYS D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 116 Processing helix chain 'D' and resid 128 through 144 removed outlier: 3.681A pdb=" N LYS D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 164 removed outlier: 3.874A pdb=" N GLN D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 171 removed outlier: 4.008A pdb=" N LEU D 168 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 169 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL D 170 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASN D 171 " --> pdb=" O LEU D 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 165 through 171' Processing helix chain 'D' and resid 172 through 181 removed outlier: 3.551A pdb=" N CYS D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.728A pdb=" N THR D 185 " --> pdb=" O PRO D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 205 removed outlier: 3.566A pdb=" N ARG D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 224 removed outlier: 3.752A pdb=" N PHE D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.623A pdb=" N ARG D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 251 removed outlier: 4.508A 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: 3.835A pdb=" N ASN D 265 " --> pdb=" O VAL D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 286 removed outlier: 3.601A pdb=" N ARG D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 346 through 364 removed outlier: 4.000A pdb=" N ARG D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 382 removed outlier: 4.940A 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: 3.579A 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: 3.794A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 465 removed outlier: 3.692A 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: 6.177A pdb=" N GLN D 511 " --> pdb=" O HIS D 508 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS D 514 " --> pdb=" O GLN D 511 " (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: 3.640A pdb=" N GLY D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 551 removed outlier: 3.612A pdb=" N GLN D 545 " --> pdb=" O LEU D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 577 removed outlier: 3.576A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LYS D 566 " --> pdb=" O THR D 562 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP D 567 " --> pdb=" O PRO D 563 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 568 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS D 574 " --> pdb=" O THR D 570 " (cutoff:3.500A) removed outlier: 4.043A 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 621 removed outlier: 4.551A pdb=" N ASN D 610 " --> pdb=" O SER D 606 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS D 620 " --> pdb=" O LEU D 616 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN D 621 " --> pdb=" O GLU D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 644 through 658 removed outlier: 3.505A pdb=" N GLY D 649 " --> pdb=" O ARG D 645 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) Proline residue: D 653 - end of helix Processing helix chain 'D' and resid 659 through 661 No H-bonds generated for 'chain 'D' and resid 659 through 661' Processing helix chain 'D' and resid 663 through 681 Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.625A pdb=" N SER D 709 " --> pdb=" O ASP D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 731 removed outlier: 4.325A pdb=" N SER D 728 " --> pdb=" O SER D 725 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER D 731 " --> pdb=" O SER D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.660A pdb=" N ASN D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 766 removed outlier: 3.832A pdb=" N VAL D 764 " --> pdb=" O GLN D 760 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) removed outlier: 4.276A 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: 4.137A pdb=" N TYR D 797 " --> pdb=" O LYS D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 827 Processing helix chain 'D' and resid 831 through 849 removed outlier: 4.381A pdb=" N HIS D 848 " --> pdb=" O GLU D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 866 removed outlier: 4.070A pdb=" N SER D 866 " --> pdb=" O LEU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 887 Processing helix chain 'D' and resid 887 through 902 Proline residue: D 893 - end of helix removed outlier: 3.838A pdb=" N THR D 900 " --> pdb=" O LEU D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 919 removed outlier: 3.624A pdb=" N LEU D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 926 Processing helix chain 'D' and resid 928 through 940 Processing helix chain 'D' and resid 947 through 960 removed outlier: 3.724A pdb=" N LEU D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 976 removed outlier: 3.925A pdb=" N LEU D 966 " --> pdb=" O ASP D 962 " (cutoff:3.500A) Proline residue: D 968 - end of helix removed outlier: 3.735A pdb=" N TYR D 973 " --> pdb=" O ARG D 969 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU D 974 " --> pdb=" O LEU D 970 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE D 975 " --> pdb=" O LYS D 971 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER D 976 " --> pdb=" O GLY D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 990 removed outlier: 3.666A pdb=" N ARG D 982 " --> pdb=" O SER D 978 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 983 " --> pdb=" O SER D 979 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS D 990 " --> pdb=" O VAL D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 993 No H-bonds generated for 'chain 'D' and resid 991 through 993' Processing helix chain 'D' and resid 1000 through 1013 removed outlier: 5.084A pdb=" N GLY D1009 " --> pdb=" O LYS D1005 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP D1010 " --> pdb=" O ASN D1006 " (cutoff:3.500A) removed outlier: 3.626A 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: 3.706A pdb=" N ARG D1023 " --> pdb=" O ASP D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1041 Processing helix chain 'D' and resid 1044 through 1055 Proline residue: D1050 - end of helix removed outlier: 3.554A pdb=" N GLU D1055 " --> pdb=" O HIS D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1059 through 1063 Processing helix chain 'D' and resid 1078 through 1096 Processing helix chain 'D' and resid 1101 through 1113 removed outlier: 3.723A pdb=" N PHE D1105 " --> pdb=" O ASP D1101 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1133 removed outlier: 3.993A pdb=" N THR D1132 " --> pdb=" O VAL D1128 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D1133 " --> pdb=" O ARG D1129 " (cutoff:3.500A) Processing helix chain 'D' and resid 1134 through 1141 removed outlier: 4.250A pdb=" N VAL D1138 " --> pdb=" O CYS D1134 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1146 through 1154 Processing helix chain 'D' and resid 1162 through 1185 removed outlier: 3.754A pdb=" N PHE D1166 " --> pdb=" O VAL D1162 " (cutoff:3.500A) Processing helix chain 'D' and resid 1194 through 1205 Processing helix chain 'D' and resid 1205 through 1216 Processing helix chain 'R' and resid 53 through 59 Processing helix chain 'R' and resid 62 through 67 removed outlier: 3.761A 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 'S' and resid 18 through 22 Processing helix chain 'S' and resid 24 through 33 Processing helix chain 'S' and resid 51 through 65 removed outlier: 3.538A pdb=" N LYS S 57 " --> pdb=" O ALA S 53 " (cutoff:3.500A) 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 128 Processing helix chain 'S' and resid 131 through 140 removed outlier: 3.624A pdb=" N ILE S 135 " --> pdb=" O THR S 131 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 156 removed outlier: 3.754A pdb=" N GLU S 156 " --> pdb=" O GLN S 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 100 Processing helix chain 'F' and resid 101 through 110 removed outlier: 3.663A pdb=" N LEU F 105 " --> pdb=" O PRO F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 121 Processing helix chain 'F' and resid 124 through 132 removed outlier: 3.697A pdb=" N SER F 132 " --> pdb=" O TYR F 128 " (cutoff:3.500A) 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: 3.521A pdb=" N LEU F 334 " --> pdb=" O GLU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 359 removed outlier: 3.539A pdb=" N LEU F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 383 removed outlier: 3.878A pdb=" N LEU F 378 " --> pdb=" O GLY F 374 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 541 removed outlier: 7.559A pdb=" N PHE R 22 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEU C 590 " --> pdb=" O PHE R 22 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N VAL R 24 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N GLY C 588 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 11.523A pdb=" N LYS R 26 " --> pdb=" O SER C 586 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N SER C 586 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 11.391A pdb=" N ASN R 28 " --> pdb=" O GLN C 584 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLN C 584 " --> pdb=" O ASN R 28 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL R 30 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 3.525A 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 725 Processing sheet with id=AA4, first strand: chain 'R' and resid 79 through 80 removed outlier: 6.667A pdb=" N TRP R 72 " --> pdb=" O GLN R 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 13 through 17 removed outlier: 9.331A pdb=" N VAL S 45 " --> pdb=" O SER S 3 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS S 5 " --> pdb=" O VAL S 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 139 through 141 removed outlier: 3.906A pdb=" N MET F 186 " --> pdb=" O ASN F 210 " (cutoff:3.500A) removed outlier: 3.517A 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 1148 hydrogen bonds defined for protein. 3369 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: 3.31 Time building geometry restraints manager: 1.98 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: 5985 1.34 - 1.46: 2337 1.46 - 1.58: 9968 1.58 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 18437 Sorted by residual: bond pdb=" CG1 ILE D 241 " pdb=" CD1 ILE D 241 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.36e+00 bond pdb=" C SER F 179 " pdb=" N PRO F 180 " ideal model delta sigma weight residual 1.331 1.345 -0.013 1.27e-02 6.20e+03 1.12e+00 bond pdb=" N MET D 15 " pdb=" CA MET D 15 " ideal model delta sigma weight residual 1.458 1.472 -0.014 1.42e-02 4.96e+03 1.00e+00 bond pdb=" C LEU D 888 " pdb=" N PRO D 889 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.38e-02 5.25e+03 9.51e-01 bond pdb=" CG LEU D 181 " pdb=" CD1 LEU D 181 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 9.11e-01 ... (remaining 18432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 24719 2.04 - 4.09: 221 4.09 - 6.13: 52 6.13 - 8.18: 4 8.18 - 10.22: 2 Bond angle restraints: 24998 Sorted by residual: angle pdb=" N GLU D1171 " pdb=" CA GLU D1171 " pdb=" CB GLU D1171 " ideal model delta sigma weight residual 110.28 115.65 -5.37 1.55e+00 4.16e-01 1.20e+01 angle pdb=" N GLU C 705 " pdb=" CA GLU C 705 " pdb=" CB GLU C 705 " ideal model delta sigma weight residual 110.16 115.24 -5.08 1.48e+00 4.57e-01 1.18e+01 angle pdb=" C LYS D 661 " pdb=" N ASN D 662 " pdb=" CA ASN D 662 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.46e+00 angle pdb=" CA LYS D 793 " pdb=" CB LYS D 793 " pdb=" CG LYS D 793 " ideal model delta sigma weight residual 114.10 119.94 -5.84 2.00e+00 2.50e-01 8.54e+00 angle pdb=" CA LEU D 177 " pdb=" CB LEU D 177 " pdb=" CG LEU D 177 " ideal model delta sigma weight residual 116.30 126.52 -10.22 3.50e+00 8.16e-02 8.53e+00 ... (remaining 24993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10220 17.97 - 35.95: 890 35.95 - 53.92: 159 53.92 - 71.89: 18 71.89 - 89.87: 9 Dihedral angle restraints: 11296 sinusoidal: 4240 harmonic: 7056 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 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLU D 221 " pdb=" C GLU D 221 " pdb=" N LEU D 222 " pdb=" CA LEU D 222 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA TYR C 32 " pdb=" C TYR C 32 " pdb=" N THR C 33 " pdb=" CA THR C 33 " ideal model delta harmonic sigma weight residual 180.00 163.23 16.77 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 11293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2205 0.040 - 0.079: 601 0.079 - 0.119: 164 0.119 - 0.159: 12 0.159 - 0.198: 2 Chirality restraints: 2984 Sorted by residual: chirality pdb=" CA LEU D 181 " pdb=" N LEU D 181 " pdb=" C LEU D 181 " pdb=" CB LEU D 181 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CA GLU D 221 " pdb=" N GLU D 221 " pdb=" C GLU D 221 " pdb=" CB GLU D 221 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.48e-01 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 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 2981 not shown) Planarity restraints: 3186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 888 " -0.064 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO D 889 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 889 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 889 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 181 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO D 182 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 182 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 182 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 555 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO C 556 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 556 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 556 " -0.026 5.00e-02 4.00e+02 ... (remaining 3183 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 79 2.57 - 3.15: 14324 3.15 - 3.74: 27623 3.74 - 4.32: 35083 4.32 - 4.90: 61547 Nonbonded interactions: 138656 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.989 2.230 nonbonded pdb=" OD1 ASP D 691 " pdb=" NZ LYS D 729 " model vdw 2.251 3.120 nonbonded pdb=" OH TYR D 372 " pdb=" OG1 THR D 405 " model vdw 2.256 3.040 nonbonded pdb=" OE1 GLU D 617 " pdb=" NH1 ARG D 618 " model vdw 2.270 3.120 nonbonded pdb=" O PRO S 86 " pdb=" N ASP S 89 " model vdw 2.288 3.120 ... (remaining 138651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.640 Find NCS groups from input model: 0.090 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 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 0.271 18448 Z= 0.136 Angle : 0.524 10.221 25004 Z= 0.274 Chirality : 0.039 0.198 2984 Planarity : 0.004 0.095 3186 Dihedral : 13.596 89.868 6684 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 2360 helix: 2.22 (0.14), residues: 1548 sheet: -2.54 (0.54), residues: 81 loop : -0.88 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 764 TYR 0.019 0.001 TYR C 50 PHE 0.020 0.001 PHE C 402 TRP 0.010 0.001 TRP R 33 HIS 0.003 0.001 HIS C 727 Details of bonding type rmsd covalent geometry : bond 0.00258 (18437) covalent geometry : angle 0.51857 (24998) hydrogen bonds : bond 0.15138 ( 1148) hydrogen bonds : angle 4.70165 ( 3369) metal coordination : bond 0.08417 ( 11) metal coordination : angle 4.70347 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 146 ARG cc_start: 0.7374 (tmm160) cc_final: 0.7171 (ttp80) REVERT: C 375 LYS cc_start: 0.8228 (ttmt) cc_final: 0.8007 (ttpp) REVERT: C 510 ASP cc_start: 0.8121 (m-30) cc_final: 0.7710 (m-30) REVERT: C 519 GLU cc_start: 0.7134 (tp30) cc_final: 0.6908 (tp30) REVERT: C 578 LYS cc_start: 0.8303 (ptmt) cc_final: 0.8072 (ptmm) REVERT: C 641 GLN cc_start: 0.7472 (tm-30) cc_final: 0.6797 (tm-30) REVERT: C 642 ILE cc_start: 0.8487 (mm) cc_final: 0.8284 (mm) REVERT: C 645 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7156 (mmtt) REVERT: D 51 LYS cc_start: 0.7366 (mtmt) cc_final: 0.6930 (mtmt) REVERT: D 52 MET cc_start: 0.6959 (tpp) cc_final: 0.6601 (tpp) REVERT: D 104 ASP cc_start: 0.7593 (p0) cc_final: 0.7147 (p0) REVERT: D 216 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6475 (mm-30) REVERT: D 705 ASP cc_start: 0.6961 (t70) cc_final: 0.6704 (t0) REVERT: D 863 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7134 (tm-30) REVERT: D 962 ASP cc_start: 0.7062 (t0) cc_final: 0.6827 (t0) REVERT: D 1003 LEU cc_start: 0.8205 (mt) cc_final: 0.7789 (mp) REVERT: D 1007 CYS cc_start: 0.7623 (p) cc_final: 0.7259 (p) REVERT: D 1171 GLU cc_start: 0.6917 (mp0) cc_final: 0.6362 (mp0) REVERT: R 50 MET cc_start: 0.6854 (mtm) cc_final: 0.6613 (mtm) REVERT: S 105 LEU cc_start: 0.8093 (mm) cc_final: 0.7890 (mt) REVERT: F 116 GLU cc_start: 0.7044 (mp0) cc_final: 0.6719 (mp0) REVERT: F 126 ARG cc_start: 0.7675 (ttt-90) cc_final: 0.7340 (ttt180) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.1472 time to fit residues: 97.2925 Evaluate side-chains 410 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.0370 chunk 227 optimal weight: 30.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS C 641 GLN D 277 GLN D 939 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107868 restraints weight = 25955.231| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.86 r_work: 0.3206 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18448 Z= 0.135 Angle : 0.516 8.219 25004 Z= 0.268 Chirality : 0.039 0.147 2984 Planarity : 0.004 0.061 3186 Dihedral : 3.503 20.595 2539 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.06 % Allowed : 9.41 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.18), residues: 2360 helix: 2.33 (0.13), residues: 1570 sheet: -1.91 (0.63), residues: 71 loop : -0.62 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 147 TYR 0.020 0.001 TYR C 563 PHE 0.024 0.001 PHE D 211 TRP 0.011 0.001 TRP R 33 HIS 0.004 0.001 HIS D 939 Details of bonding type rmsd covalent geometry : bond 0.00308 (18437) covalent geometry : angle 0.51519 (24998) hydrogen bonds : bond 0.04897 ( 1148) hydrogen bonds : angle 3.88499 ( 3369) metal coordination : bond 0.00338 ( 11) metal coordination : angle 1.57144 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 417 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 519 GLU cc_start: 0.8115 (tp30) cc_final: 0.7571 (tp30) REVERT: C 620 TYR cc_start: 0.7205 (m-80) cc_final: 0.6479 (m-80) REVERT: C 641 GLN cc_start: 0.7863 (tm130) cc_final: 0.6954 (tm-30) REVERT: C 642 ILE cc_start: 0.8459 (mm) cc_final: 0.8249 (mm) REVERT: C 645 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7000 (mmtt) REVERT: C 705 GLU cc_start: 0.7420 (mp0) cc_final: 0.6752 (mp0) REVERT: D 51 LYS cc_start: 0.7890 (mtmt) cc_final: 0.7469 (mtmt) REVERT: D 52 MET cc_start: 0.7908 (tpp) cc_final: 0.7477 (tpp) REVERT: D 104 ASP cc_start: 0.7928 (p0) cc_final: 0.7498 (p0) REVERT: D 216 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7425 (mm-30) REVERT: D 398 TYR cc_start: 0.8770 (t80) cc_final: 0.8286 (t80) REVERT: D 705 ASP cc_start: 0.7535 (t70) cc_final: 0.7233 (t0) REVERT: D 863 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7766 (tm-30) REVERT: D 962 ASP cc_start: 0.7713 (t0) cc_final: 0.7410 (t0) REVERT: D 1003 LEU cc_start: 0.8243 (mt) cc_final: 0.7838 (mp) REVERT: D 1005 LYS cc_start: 0.8773 (tptp) cc_final: 0.8518 (tptt) REVERT: D 1007 CYS cc_start: 0.8226 (p) cc_final: 0.7797 (p) REVERT: D 1059 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7725 (mtp85) REVERT: D 1171 GLU cc_start: 0.7660 (mp0) cc_final: 0.6850 (mp0) REVERT: R 50 MET cc_start: 0.7672 (mtm) cc_final: 0.7269 (mtm) REVERT: F 116 GLU cc_start: 0.7543 (mp0) cc_final: 0.7225 (mp0) outliers start: 20 outliers final: 11 residues processed: 424 average time/residue: 0.1505 time to fit residues: 93.1258 Evaluate side-chains 418 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 407 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 14 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 183 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS D 277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107419 restraints weight = 26091.413| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.88 r_work: 0.3198 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 18448 Z= 0.131 Angle : 0.492 8.405 25004 Z= 0.255 Chirality : 0.039 0.136 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.487 20.420 2539 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.32 % Allowed : 11.89 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.18), residues: 2360 helix: 2.40 (0.13), residues: 1567 sheet: -1.56 (0.69), residues: 61 loop : -0.63 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 764 TYR 0.018 0.001 TYR C 563 PHE 0.021 0.001 PHE C 402 TRP 0.011 0.001 TRP R 33 HIS 0.005 0.001 HIS D 707 Details of bonding type rmsd covalent geometry : bond 0.00308 (18437) covalent geometry : angle 0.49152 (24998) hydrogen bonds : bond 0.04780 ( 1148) hydrogen bonds : angle 3.74094 ( 3369) metal coordination : bond 0.00219 ( 11) metal coordination : angle 1.73835 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 417 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 519 GLU cc_start: 0.8115 (tp30) cc_final: 0.7588 (tp30) REVERT: C 589 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7063 (mm-30) REVERT: C 620 TYR cc_start: 0.7189 (m-80) cc_final: 0.6471 (m-80) REVERT: C 641 GLN cc_start: 0.7889 (tm130) cc_final: 0.7005 (tm-30) REVERT: C 642 ILE cc_start: 0.8528 (mm) cc_final: 0.8258 (mm) REVERT: C 645 LYS cc_start: 0.7944 (mmtt) cc_final: 0.6999 (mmtt) REVERT: D 52 MET cc_start: 0.7845 (tpp) cc_final: 0.7282 (tpp) REVERT: D 81 GLU cc_start: 0.7314 (tm-30) cc_final: 0.7084 (tm-30) REVERT: D 104 ASP cc_start: 0.7908 (p0) cc_final: 0.7509 (p0) REVERT: D 216 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7457 (mm-30) REVERT: D 705 ASP cc_start: 0.7577 (t70) cc_final: 0.7280 (t0) REVERT: D 863 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7721 (tm-30) REVERT: D 962 ASP cc_start: 0.7706 (t0) cc_final: 0.7409 (t0) REVERT: D 1003 LEU cc_start: 0.8303 (mt) cc_final: 0.7873 (mp) REVERT: D 1007 CYS cc_start: 0.8236 (p) cc_final: 0.7829 (p) REVERT: D 1059 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7743 (mtp85) REVERT: D 1171 GLU cc_start: 0.7653 (mp0) cc_final: 0.7088 (mp0) REVERT: R 50 MET cc_start: 0.7674 (mtm) cc_final: 0.7267 (mtm) REVERT: S 32 GLU cc_start: 0.7886 (tt0) cc_final: 0.7673 (mt-10) REVERT: S 55 LEU cc_start: 0.8697 (tp) cc_final: 0.8421 (tt) REVERT: F 116 GLU cc_start: 0.7651 (mp0) cc_final: 0.7364 (mp0) outliers start: 25 outliers final: 15 residues processed: 425 average time/residue: 0.1420 time to fit residues: 88.1861 Evaluate side-chains 423 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 408 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 0.0270 chunk 194 optimal weight: 0.0770 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 223 optimal weight: 50.0000 chunk 215 optimal weight: 30.0000 chunk 197 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS C 641 GLN D 277 GLN D1169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.107657 restraints weight = 26093.972| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.89 r_work: 0.3209 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 18448 Z= 0.116 Angle : 0.479 8.418 25004 Z= 0.248 Chirality : 0.038 0.135 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.437 19.848 2539 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.64 % Allowed : 13.05 % Favored : 85.31 % 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: 2.16 (0.18), residues: 2360 helix: 2.46 (0.13), residues: 1566 sheet: -1.40 (0.70), residues: 61 loop : -0.64 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1141 TYR 0.017 0.001 TYR C 563 PHE 0.020 0.001 PHE C 402 TRP 0.011 0.001 TRP R 33 HIS 0.004 0.001 HIS D 707 Details of bonding type rmsd covalent geometry : bond 0.00267 (18437) covalent geometry : angle 0.47869 (24998) hydrogen bonds : bond 0.04326 ( 1148) hydrogen bonds : angle 3.65429 ( 3369) metal coordination : bond 0.00200 ( 11) metal coordination : angle 1.53924 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 409 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 375 LYS cc_start: 0.8715 (ttmt) cc_final: 0.8513 (ttpp) REVERT: C 519 GLU cc_start: 0.8117 (tp30) cc_final: 0.7590 (tp30) REVERT: C 589 GLU cc_start: 0.7566 (mm-30) cc_final: 0.6939 (mm-30) REVERT: C 620 TYR cc_start: 0.7213 (m-80) cc_final: 0.6474 (m-80) REVERT: C 641 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7003 (tm-30) REVERT: C 642 ILE cc_start: 0.8512 (mm) cc_final: 0.8249 (mm) REVERT: C 645 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7020 (mmtt) REVERT: D 51 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7494 (mtmt) REVERT: D 52 MET cc_start: 0.7810 (tpp) cc_final: 0.7555 (tpp) REVERT: D 104 ASP cc_start: 0.7936 (p0) cc_final: 0.7504 (p0) REVERT: D 216 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7424 (mm-30) REVERT: D 221 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: D 705 ASP cc_start: 0.7566 (t70) cc_final: 0.7294 (t0) REVERT: D 823 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8264 (mp10) REVERT: D 962 ASP cc_start: 0.7711 (t0) cc_final: 0.7328 (t0) REVERT: D 965 THR cc_start: 0.8693 (t) cc_final: 0.8216 (t) REVERT: D 1003 LEU cc_start: 0.8321 (mt) cc_final: 0.7878 (mp) REVERT: D 1007 CYS cc_start: 0.8215 (p) cc_final: 0.7804 (p) REVERT: D 1059 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7765 (mtp85) REVERT: D 1131 SER cc_start: 0.8193 (m) cc_final: 0.7823 (t) REVERT: D 1171 GLU cc_start: 0.7666 (mp0) cc_final: 0.7111 (mp0) REVERT: D 1212 PHE cc_start: 0.7981 (t80) cc_final: 0.7673 (t80) REVERT: R 50 MET cc_start: 0.7727 (mtm) cc_final: 0.7320 (mtm) REVERT: S 32 GLU cc_start: 0.7880 (tt0) cc_final: 0.7680 (mt-10) REVERT: S 55 LEU cc_start: 0.8687 (tp) cc_final: 0.8404 (tt) REVERT: S 102 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: S 103 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7789 (tt) REVERT: S 135 ILE cc_start: 0.5487 (OUTLIER) cc_final: 0.4997 (mt) REVERT: F 116 GLU cc_start: 0.7691 (mp0) cc_final: 0.7397 (mp0) outliers start: 31 outliers final: 20 residues processed: 421 average time/residue: 0.1479 time to fit residues: 90.8566 Evaluate side-chains 427 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 403 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 824 ASP Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 135 ILE Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 35 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 236 optimal weight: 40.0000 chunk 112 optimal weight: 0.1980 chunk 17 optimal weight: 0.0170 chunk 46 optimal weight: 1.9990 chunk 209 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 201 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1107 ASN D1140 GLN D1169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.134623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108573 restraints weight = 25959.095| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.87 r_work: 0.3219 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 18448 Z= 0.110 Angle : 0.473 9.314 25004 Z= 0.244 Chirality : 0.038 0.138 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.379 19.593 2539 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.74 % Allowed : 13.27 % Favored : 84.99 % 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: 2.22 (0.18), residues: 2360 helix: 2.50 (0.14), residues: 1569 sheet: -1.27 (0.71), residues: 61 loop : -0.61 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1141 TYR 0.016 0.001 TYR C 563 PHE 0.019 0.001 PHE C 402 TRP 0.011 0.001 TRP R 33 HIS 0.004 0.001 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.00249 (18437) covalent geometry : angle 0.47233 (24998) hydrogen bonds : bond 0.04105 ( 1148) hydrogen bonds : angle 3.58808 ( 3369) metal coordination : bond 0.00199 ( 11) metal coordination : angle 1.44351 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 406 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 468 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8610 (mmmt) REVERT: C 519 GLU cc_start: 0.8121 (tp30) cc_final: 0.7625 (tp30) REVERT: C 589 GLU cc_start: 0.7557 (mm-30) cc_final: 0.6952 (mm-30) REVERT: C 610 ILE cc_start: 0.8624 (pt) cc_final: 0.8395 (mt) REVERT: C 620 TYR cc_start: 0.7171 (m-80) cc_final: 0.6389 (m-80) REVERT: C 641 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7032 (tm-30) REVERT: C 642 ILE cc_start: 0.8502 (mm) cc_final: 0.8248 (mm) REVERT: C 645 LYS cc_start: 0.7943 (mmtt) cc_final: 0.7017 (mmtt) REVERT: D 104 ASP cc_start: 0.7908 (p0) cc_final: 0.7468 (p0) REVERT: D 216 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7473 (mm-30) REVERT: D 221 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: D 705 ASP cc_start: 0.7546 (t70) cc_final: 0.7282 (t0) REVERT: D 823 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8250 (mp10) REVERT: D 962 ASP cc_start: 0.7674 (t0) cc_final: 0.7281 (t0) REVERT: D 965 THR cc_start: 0.8691 (t) cc_final: 0.8216 (t) REVERT: D 1003 LEU cc_start: 0.8330 (mt) cc_final: 0.7886 (mp) REVERT: D 1007 CYS cc_start: 0.8186 (p) cc_final: 0.7773 (p) REVERT: D 1059 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7755 (mtp85) REVERT: D 1107 ASN cc_start: 0.7954 (m-40) cc_final: 0.7640 (m110) REVERT: D 1131 SER cc_start: 0.8176 (m) cc_final: 0.7813 (t) REVERT: D 1133 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7681 (pp) REVERT: D 1141 ARG cc_start: 0.8265 (mtp180) cc_final: 0.8019 (mtp180) REVERT: D 1170 ASP cc_start: 0.7919 (m-30) cc_final: 0.7693 (m-30) REVERT: D 1171 GLU cc_start: 0.7671 (mp0) cc_final: 0.7156 (mp0) REVERT: D 1212 PHE cc_start: 0.7986 (t80) cc_final: 0.7692 (t80) REVERT: R 50 MET cc_start: 0.7711 (mtm) cc_final: 0.7303 (mtm) REVERT: S 32 GLU cc_start: 0.7884 (tt0) cc_final: 0.7651 (mt-10) REVERT: S 55 LEU cc_start: 0.8659 (tp) cc_final: 0.8388 (tt) REVERT: S 103 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7767 (tt) REVERT: F 116 GLU cc_start: 0.7687 (mp0) cc_final: 0.7483 (mp0) outliers start: 33 outliers final: 22 residues processed: 422 average time/residue: 0.1547 time to fit residues: 94.8344 Evaluate side-chains 431 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 406 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1133 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 50.0000 chunk 125 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 221 optimal weight: 30.0000 chunk 167 optimal weight: 0.9990 chunk 205 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1140 GLN D1169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.133986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107910 restraints weight = 25763.453| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.87 r_work: 0.3204 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18448 Z= 0.118 Angle : 0.482 8.818 25004 Z= 0.248 Chirality : 0.038 0.142 2984 Planarity : 0.004 0.047 3186 Dihedral : 3.376 19.559 2539 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.96 % Allowed : 13.95 % Favored : 84.09 % 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: 2.22 (0.18), residues: 2360 helix: 2.50 (0.14), residues: 1565 sheet: -1.27 (0.71), residues: 61 loop : -0.60 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1141 TYR 0.021 0.001 TYR C 563 PHE 0.020 0.001 PHE C 402 TRP 0.011 0.001 TRP R 33 HIS 0.004 0.001 HIS D 707 Details of bonding type rmsd covalent geometry : bond 0.00272 (18437) covalent geometry : angle 0.48144 (24998) hydrogen bonds : bond 0.04292 ( 1148) hydrogen bonds : angle 3.58781 ( 3369) metal coordination : bond 0.00199 ( 11) metal coordination : angle 1.49255 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 413 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 468 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8592 (mmmt) REVERT: C 519 GLU cc_start: 0.8118 (tp30) cc_final: 0.7612 (tp30) REVERT: C 589 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6925 (mm-30) REVERT: C 620 TYR cc_start: 0.7195 (m-80) cc_final: 0.6370 (m-80) REVERT: C 641 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7015 (tm-30) REVERT: C 642 ILE cc_start: 0.8525 (mm) cc_final: 0.8265 (mm) REVERT: C 645 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7015 (mmtt) REVERT: D 14 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7965 (ttmm) REVERT: D 52 MET cc_start: 0.7937 (tpp) cc_final: 0.7557 (tpp) REVERT: D 104 ASP cc_start: 0.7889 (p0) cc_final: 0.7481 (p0) REVERT: D 156 ASP cc_start: 0.7888 (t70) cc_final: 0.7512 (t70) REVERT: D 216 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7466 (mm-30) REVERT: D 221 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: D 705 ASP cc_start: 0.7572 (t70) cc_final: 0.7316 (t0) REVERT: D 823 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8247 (mp10) REVERT: D 902 GLN cc_start: 0.8142 (mt0) cc_final: 0.7926 (mt0) REVERT: D 962 ASP cc_start: 0.7659 (t0) cc_final: 0.7280 (t0) REVERT: D 965 THR cc_start: 0.8680 (t) cc_final: 0.8206 (t) REVERT: D 1003 LEU cc_start: 0.8319 (mt) cc_final: 0.7858 (mp) REVERT: D 1007 CYS cc_start: 0.8167 (p) cc_final: 0.7747 (p) REVERT: D 1059 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7745 (mtp85) REVERT: D 1131 SER cc_start: 0.8191 (m) cc_final: 0.7814 (t) REVERT: D 1170 ASP cc_start: 0.7928 (m-30) cc_final: 0.7688 (m-30) REVERT: D 1171 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7092 (mp0) REVERT: D 1212 PHE cc_start: 0.7964 (t80) cc_final: 0.7678 (t80) REVERT: R 50 MET cc_start: 0.7676 (mtm) cc_final: 0.7276 (mtm) REVERT: S 32 GLU cc_start: 0.7872 (tt0) cc_final: 0.7643 (mt-10) REVERT: S 55 LEU cc_start: 0.8638 (tp) cc_final: 0.8354 (tt) REVERT: S 103 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7749 (tt) outliers start: 37 outliers final: 27 residues processed: 430 average time/residue: 0.1527 time to fit residues: 96.5009 Evaluate side-chains 437 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 408 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 199 optimal weight: 1.9990 chunk 191 optimal weight: 0.0980 chunk 212 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 213 optimal weight: 6.9990 chunk 104 optimal weight: 0.0370 chunk 15 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1107 ASN D1140 GLN D1169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108125 restraints weight = 26031.904| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.88 r_work: 0.3200 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18448 Z= 0.115 Angle : 0.488 10.713 25004 Z= 0.251 Chirality : 0.038 0.142 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.366 19.556 2539 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.22 % Allowed : 14.11 % Favored : 83.67 % 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: 2.23 (0.18), residues: 2360 helix: 2.51 (0.14), residues: 1564 sheet: -1.30 (0.70), residues: 61 loop : -0.57 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1141 TYR 0.024 0.001 TYR C 50 PHE 0.020 0.001 PHE C 402 TRP 0.011 0.001 TRP R 33 HIS 0.008 0.001 HIS C 524 Details of bonding type rmsd covalent geometry : bond 0.00264 (18437) covalent geometry : angle 0.48785 (24998) hydrogen bonds : bond 0.04175 ( 1148) hydrogen bonds : angle 3.57543 ( 3369) metal coordination : bond 0.00216 ( 11) metal coordination : angle 1.44196 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 402 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 MET cc_start: 0.8403 (ttp) cc_final: 0.8195 (ttp) REVERT: C 468 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8593 (mmmt) REVERT: C 519 GLU cc_start: 0.8123 (tp30) cc_final: 0.7627 (tp30) REVERT: C 589 GLU cc_start: 0.7561 (mm-30) cc_final: 0.6947 (mm-30) REVERT: C 610 ILE cc_start: 0.8587 (pt) cc_final: 0.8364 (mt) REVERT: C 620 TYR cc_start: 0.7148 (m-80) cc_final: 0.6493 (m-80) REVERT: C 641 GLN cc_start: 0.7905 (tm-30) cc_final: 0.6997 (tm-30) REVERT: C 642 ILE cc_start: 0.8538 (mm) cc_final: 0.8255 (mm) REVERT: C 645 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7032 (mmtt) REVERT: D 14 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7944 (ttmm) REVERT: D 104 ASP cc_start: 0.7882 (p0) cc_final: 0.7456 (p0) REVERT: D 216 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7471 (mm-30) REVERT: D 221 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: D 587 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7658 (mp0) REVERT: D 705 ASP cc_start: 0.7567 (t70) cc_final: 0.7306 (t0) REVERT: D 823 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8241 (mp10) REVERT: D 863 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7662 (tm-30) REVERT: D 871 GLU cc_start: 0.7306 (mp0) cc_final: 0.7079 (mp0) REVERT: D 962 ASP cc_start: 0.7667 (t0) cc_final: 0.7287 (t0) REVERT: D 965 THR cc_start: 0.8674 (t) cc_final: 0.8204 (t) REVERT: D 1003 LEU cc_start: 0.8332 (mt) cc_final: 0.7869 (mp) REVERT: D 1007 CYS cc_start: 0.8146 (p) cc_final: 0.7732 (p) REVERT: D 1059 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7752 (mtp85) REVERT: D 1131 SER cc_start: 0.8176 (m) cc_final: 0.7796 (t) REVERT: D 1133 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7686 (pp) REVERT: D 1170 ASP cc_start: 0.7939 (m-30) cc_final: 0.7717 (m-30) REVERT: D 1171 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7139 (mp0) REVERT: D 1212 PHE cc_start: 0.7957 (t80) cc_final: 0.7667 (t80) REVERT: R 50 MET cc_start: 0.7673 (mtm) cc_final: 0.7272 (mtm) REVERT: S 32 GLU cc_start: 0.7891 (tt0) cc_final: 0.7641 (mt-10) REVERT: S 55 LEU cc_start: 0.8650 (tp) cc_final: 0.8387 (tt) REVERT: F 116 GLU cc_start: 0.7718 (mp0) cc_final: 0.7379 (mp0) REVERT: F 117 LEU cc_start: 0.8545 (pt) cc_final: 0.8297 (pt) outliers start: 42 outliers final: 30 residues processed: 423 average time/residue: 0.1456 time to fit residues: 90.0931 Evaluate side-chains 429 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 397 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 738 LEU Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1133 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 198 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 203 optimal weight: 0.9990 chunk 112 optimal weight: 0.0070 chunk 232 optimal weight: 4.9990 chunk 228 optimal weight: 40.0000 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1140 GLN D1169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.133610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107564 restraints weight = 25816.815| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.86 r_work: 0.3192 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18448 Z= 0.125 Angle : 0.499 9.380 25004 Z= 0.256 Chirality : 0.038 0.138 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.382 19.583 2539 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.01 % Allowed : 14.80 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.18), residues: 2360 helix: 2.43 (0.13), residues: 1577 sheet: -1.16 (0.71), residues: 61 loop : -0.67 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1150 TYR 0.027 0.001 TYR C 50 PHE 0.021 0.001 PHE C 402 TRP 0.010 0.001 TRP R 33 HIS 0.007 0.001 HIS C 524 Details of bonding type rmsd covalent geometry : bond 0.00295 (18437) covalent geometry : angle 0.49872 (24998) hydrogen bonds : bond 0.04408 ( 1148) hydrogen bonds : angle 3.60418 ( 3369) metal coordination : bond 0.00192 ( 11) metal coordination : angle 1.55089 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 405 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 468 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8591 (mmmt) REVERT: C 519 GLU cc_start: 0.8120 (tp30) cc_final: 0.7617 (tp30) REVERT: C 589 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6980 (mm-30) REVERT: C 610 ILE cc_start: 0.8602 (pt) cc_final: 0.8375 (mt) REVERT: C 620 TYR cc_start: 0.7157 (m-80) cc_final: 0.6475 (m-80) REVERT: C 641 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7046 (tm-30) REVERT: C 642 ILE cc_start: 0.8538 (mm) cc_final: 0.8254 (mm) REVERT: C 645 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7148 (mmtt) REVERT: D 14 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7974 (ttmm) REVERT: D 104 ASP cc_start: 0.7860 (p0) cc_final: 0.7444 (p0) REVERT: D 216 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7545 (mm-30) REVERT: D 221 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: D 705 ASP cc_start: 0.7566 (t70) cc_final: 0.7305 (t0) REVERT: D 823 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8271 (mp10) REVERT: D 865 PHE cc_start: 0.8285 (m-80) cc_final: 0.7802 (t80) REVERT: D 962 ASP cc_start: 0.7674 (t0) cc_final: 0.7284 (t0) REVERT: D 965 THR cc_start: 0.8663 (t) cc_final: 0.8138 (t) REVERT: D 1003 LEU cc_start: 0.8348 (mt) cc_final: 0.7881 (mp) REVERT: D 1007 CYS cc_start: 0.8148 (p) cc_final: 0.7741 (p) REVERT: D 1059 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7726 (mtp85) REVERT: D 1131 SER cc_start: 0.8202 (m) cc_final: 0.7994 (m) REVERT: D 1133 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7657 (pp) REVERT: D 1170 ASP cc_start: 0.7937 (m-30) cc_final: 0.7694 (m-30) REVERT: D 1212 PHE cc_start: 0.7941 (t80) cc_final: 0.7640 (t80) REVERT: R 50 MET cc_start: 0.7647 (mtm) cc_final: 0.7242 (mtm) REVERT: S 14 PHE cc_start: 0.8317 (m-80) cc_final: 0.8003 (m-80) REVERT: S 32 GLU cc_start: 0.7900 (tt0) cc_final: 0.7650 (mt-10) REVERT: S 55 LEU cc_start: 0.8650 (tp) cc_final: 0.8384 (tt) REVERT: S 103 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7786 (tt) outliers start: 38 outliers final: 31 residues processed: 421 average time/residue: 0.1459 time to fit residues: 90.3502 Evaluate side-chains 435 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 401 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 403 LYS Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 738 LEU Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1133 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 157 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 52 optimal weight: 1.9990 chunk 146 optimal weight: 0.0070 chunk 153 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 237 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1140 GLN D1169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107129 restraints weight = 25707.966| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.86 r_work: 0.3194 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18448 Z= 0.128 Angle : 0.511 11.716 25004 Z= 0.262 Chirality : 0.038 0.137 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.416 21.055 2539 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.06 % Allowed : 15.06 % Favored : 82.88 % 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: 2.14 (0.18), residues: 2360 helix: 2.42 (0.13), residues: 1576 sheet: -1.10 (0.71), residues: 61 loop : -0.65 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1141 TYR 0.026 0.001 TYR C 50 PHE 0.021 0.001 PHE C 402 TRP 0.010 0.001 TRP R 33 HIS 0.007 0.001 HIS C 524 Details of bonding type rmsd covalent geometry : bond 0.00303 (18437) covalent geometry : angle 0.51064 (24998) hydrogen bonds : bond 0.04466 ( 1148) hydrogen bonds : angle 3.61759 ( 3369) metal coordination : bond 0.00198 ( 11) metal coordination : angle 1.58396 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 415 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 468 LYS cc_start: 0.8825 (mmmt) cc_final: 0.8613 (mmmt) REVERT: C 519 GLU cc_start: 0.8135 (tp30) cc_final: 0.7625 (tp30) REVERT: C 522 LYS cc_start: 0.7792 (tppp) cc_final: 0.7451 (tppt) REVERT: C 589 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6988 (mm-30) REVERT: C 610 ILE cc_start: 0.8598 (pt) cc_final: 0.8355 (mt) REVERT: C 620 TYR cc_start: 0.7153 (m-80) cc_final: 0.6462 (m-80) REVERT: C 641 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7046 (tm-30) REVERT: C 642 ILE cc_start: 0.8550 (mm) cc_final: 0.8267 (mm) REVERT: C 645 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7187 (mmtt) REVERT: C 706 ASP cc_start: 0.7843 (m-30) cc_final: 0.7462 (m-30) REVERT: D 14 LYS cc_start: 0.8285 (mtpt) cc_final: 0.8007 (ttmm) REVERT: D 52 MET cc_start: 0.7864 (tpp) cc_final: 0.7494 (tpp) REVERT: D 104 ASP cc_start: 0.7899 (p0) cc_final: 0.7476 (p0) REVERT: D 177 LEU cc_start: 0.8738 (tp) cc_final: 0.8529 (tt) REVERT: D 216 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7588 (mm-30) REVERT: D 221 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: D 457 MET cc_start: 0.8155 (ttp) cc_final: 0.7936 (ttm) REVERT: D 587 GLU cc_start: 0.7953 (mp0) cc_final: 0.7700 (mp0) REVERT: D 705 ASP cc_start: 0.7573 (t70) cc_final: 0.7312 (t0) REVERT: D 823 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8294 (mp10) REVERT: D 863 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7643 (tm-30) REVERT: D 865 PHE cc_start: 0.8304 (m-80) cc_final: 0.7749 (t80) REVERT: D 962 ASP cc_start: 0.7678 (t0) cc_final: 0.7293 (t0) REVERT: D 965 THR cc_start: 0.8671 (t) cc_final: 0.8144 (t) REVERT: D 1003 LEU cc_start: 0.8375 (mt) cc_final: 0.7896 (mp) REVERT: D 1007 CYS cc_start: 0.8148 (p) cc_final: 0.7742 (p) REVERT: D 1059 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7786 (mtp85) REVERT: D 1131 SER cc_start: 0.8209 (m) cc_final: 0.8009 (m) REVERT: D 1133 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7671 (pp) REVERT: D 1170 ASP cc_start: 0.7953 (m-30) cc_final: 0.7710 (m-30) REVERT: D 1212 PHE cc_start: 0.7972 (t80) cc_final: 0.7667 (t80) REVERT: R 50 MET cc_start: 0.7659 (mtm) cc_final: 0.7261 (mtm) REVERT: S 32 GLU cc_start: 0.7899 (tt0) cc_final: 0.7654 (mt-10) REVERT: S 55 LEU cc_start: 0.8672 (tp) cc_final: 0.8408 (tt) REVERT: S 103 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7796 (tt) outliers start: 39 outliers final: 33 residues processed: 433 average time/residue: 0.1388 time to fit residues: 88.4198 Evaluate side-chains 445 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 409 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 403 LYS Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 738 LEU Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1133 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 157 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.7980 chunk 210 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 79 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107231 restraints weight = 25913.894| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.87 r_work: 0.3193 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18448 Z= 0.129 Angle : 0.522 14.283 25004 Z= 0.266 Chirality : 0.039 0.148 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.450 22.344 2539 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.80 % Allowed : 15.38 % Favored : 82.82 % 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: 2.14 (0.18), residues: 2360 helix: 2.40 (0.13), residues: 1576 sheet: -1.10 (0.70), residues: 61 loop : -0.62 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1141 TYR 0.028 0.001 TYR C 50 PHE 0.021 0.001 PHE C 402 TRP 0.010 0.001 TRP R 33 HIS 0.007 0.001 HIS C 524 Details of bonding type rmsd covalent geometry : bond 0.00306 (18437) covalent geometry : angle 0.52106 (24998) hydrogen bonds : bond 0.04472 ( 1148) hydrogen bonds : angle 3.62630 ( 3369) metal coordination : bond 0.00200 ( 11) metal coordination : angle 1.59671 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 405 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 468 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8617 (mmmt) REVERT: C 519 GLU cc_start: 0.8149 (tp30) cc_final: 0.7641 (tp30) REVERT: C 522 LYS cc_start: 0.7796 (tppp) cc_final: 0.7449 (tppt) REVERT: C 589 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6998 (mm-30) REVERT: C 610 ILE cc_start: 0.8603 (pt) cc_final: 0.8361 (mt) REVERT: C 620 TYR cc_start: 0.7149 (m-80) cc_final: 0.6454 (m-80) REVERT: C 641 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7038 (tm-30) REVERT: C 642 ILE cc_start: 0.8546 (mm) cc_final: 0.8254 (mm) REVERT: C 645 LYS cc_start: 0.8011 (mmtt) cc_final: 0.7177 (mmtt) REVERT: C 706 ASP cc_start: 0.7833 (m-30) cc_final: 0.7450 (m-30) REVERT: D 14 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7804 (ttmm) REVERT: D 52 MET cc_start: 0.7844 (tpp) cc_final: 0.7496 (tpp) REVERT: D 104 ASP cc_start: 0.7913 (p0) cc_final: 0.7492 (p0) REVERT: D 177 LEU cc_start: 0.8744 (tp) cc_final: 0.8532 (tt) REVERT: D 216 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7595 (mm-30) REVERT: D 221 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: D 457 MET cc_start: 0.8143 (ttp) cc_final: 0.7938 (ttm) REVERT: D 587 GLU cc_start: 0.7963 (mp0) cc_final: 0.7659 (mp0) REVERT: D 705 ASP cc_start: 0.7578 (t70) cc_final: 0.7319 (t0) REVERT: D 823 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8306 (mp10) REVERT: D 863 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7648 (tm-30) REVERT: D 865 PHE cc_start: 0.8284 (m-80) cc_final: 0.7780 (t80) REVERT: D 962 ASP cc_start: 0.7671 (t0) cc_final: 0.7289 (t0) REVERT: D 965 THR cc_start: 0.8667 (t) cc_final: 0.8140 (t) REVERT: D 1003 LEU cc_start: 0.8380 (mt) cc_final: 0.7904 (mp) REVERT: D 1007 CYS cc_start: 0.8157 (p) cc_final: 0.7756 (p) REVERT: D 1059 ARG cc_start: 0.8030 (mtp85) cc_final: 0.7788 (mtp85) REVERT: D 1131 SER cc_start: 0.8226 (m) cc_final: 0.8022 (m) REVERT: D 1133 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7682 (pp) REVERT: D 1165 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7094 (mm-30) REVERT: D 1170 ASP cc_start: 0.7961 (m-30) cc_final: 0.7731 (m-30) REVERT: D 1171 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7186 (mp0) REVERT: D 1212 PHE cc_start: 0.7965 (t80) cc_final: 0.7654 (t80) REVERT: R 50 MET cc_start: 0.7659 (mtm) cc_final: 0.7262 (mtm) REVERT: S 32 GLU cc_start: 0.7911 (tt0) cc_final: 0.7660 (mt-10) REVERT: S 103 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7793 (tt) REVERT: F 116 GLU cc_start: 0.7650 (mp0) cc_final: 0.7186 (mp0) outliers start: 34 outliers final: 30 residues processed: 420 average time/residue: 0.1434 time to fit residues: 88.2617 Evaluate side-chains 436 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 403 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 403 LYS Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 738 LEU Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1133 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 157 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 162 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 233 optimal weight: 9.9990 chunk 26 optimal weight: 0.3980 chunk 51 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 211 optimal weight: 0.0570 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN D 277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.134430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108478 restraints weight = 26089.818| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.88 r_work: 0.3215 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18448 Z= 0.112 Angle : 0.504 9.103 25004 Z= 0.258 Chirality : 0.038 0.214 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.405 21.900 2539 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.90 % Allowed : 15.59 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.18), residues: 2360 helix: 2.46 (0.14), residues: 1571 sheet: -1.52 (0.64), residues: 71 loop : -0.56 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1141 TYR 0.027 0.001 TYR C 50 PHE 0.019 0.001 PHE S 14 TRP 0.012 0.001 TRP R 33 HIS 0.007 0.001 HIS C 524 Details of bonding type rmsd covalent geometry : bond 0.00256 (18437) covalent geometry : angle 0.50374 (24998) hydrogen bonds : bond 0.03967 ( 1148) hydrogen bonds : angle 3.56614 ( 3369) metal coordination : bond 0.00241 ( 11) metal coordination : angle 1.35493 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5411.42 seconds wall clock time: 93 minutes 10.78 seconds (5590.78 seconds total)