Starting phenix.real_space_refine on Sat Sep 28 03:42:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbz_14597/09_2024/7zbz_14597.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbz_14597/09_2024/7zbz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbz_14597/09_2024/7zbz_14597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbz_14597/09_2024/7zbz_14597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbz_14597/09_2024/7zbz_14597.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbz_14597/09_2024/7zbz_14597.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLN:plan1': 15, 'ASP:plan': 13, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 10, 'PHE:plan': 11, 'GLU:plan': 13, 'ARG:plan': 12} 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: 9.67, per 1000 atoms: 0.53 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: 4.21 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.97 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: 5.94 Time building geometry restraints manager: 4.93 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: 2.070 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: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 41.230 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.380 ------------------------------------------------------------------------------- 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 0.045 18437 Z= 0.168 Angle : 0.519 10.221 24998 Z= 0.273 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP R 33 HIS 0.003 0.001 HIS C 727 PHE 0.020 0.001 PHE C 402 TYR 0.019 0.001 TYR C 50 ARG 0.009 0.000 ARG C 764 *********************** 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 fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 1.841 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: 0.6600 (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: 0.6916 (mp0) cc_final: 0.6362 (mp0) REVERT: R 50 MET cc_start: 0.6854 (mtm) cc_final: 0.6614 (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: 0.3377 time to fit residues: 223.1306 Evaluate side-chains 410 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 216 optimal weight: 20.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN D 939 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18437 Z= 0.298 Angle : 0.553 8.655 24998 Z= 0.289 Chirality : 0.042 0.151 2984 Planarity : 0.005 0.063 3186 Dihedral : 3.622 21.074 2539 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.16 % Allowed : 9.41 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.18), residues: 2360 helix: 2.21 (0.13), residues: 1568 sheet: -2.21 (0.58), residues: 81 loop : -0.65 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 33 HIS 0.007 0.001 HIS D 707 PHE 0.024 0.002 PHE C 402 TYR 0.019 0.002 TYR C 563 ARG 0.006 0.000 ARG C 147 *********************** 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 447 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 425 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 519 GLU cc_start: 0.7192 (tp30) cc_final: 0.6940 (tp30) REVERT: C 578 LYS cc_start: 0.8295 (ptmt) cc_final: 0.8094 (ptmm) REVERT: C 620 TYR cc_start: 0.6927 (m-80) cc_final: 0.6371 (m-80) REVERT: C 641 GLN cc_start: 0.7577 (tm-30) cc_final: 0.6768 (tm-30) REVERT: C 642 ILE cc_start: 0.8460 (mm) cc_final: 0.8232 (mm) REVERT: C 645 LYS cc_start: 0.7821 (mmtt) cc_final: 0.6773 (mmtt) REVERT: D 51 LYS cc_start: 0.7483 (mtmt) cc_final: 0.7039 (mtmt) REVERT: D 104 ASP cc_start: 0.7569 (p0) cc_final: 0.7134 (p0) REVERT: D 216 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6771 (mm-30) REVERT: D 304 TYR cc_start: 0.8396 (m-80) cc_final: 0.8082 (m-80) REVERT: D 398 TYR cc_start: 0.8550 (t80) cc_final: 0.7955 (t80) REVERT: D 705 ASP cc_start: 0.7138 (t70) cc_final: 0.6860 (t0) REVERT: D 863 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7136 (tm-30) REVERT: D 962 ASP cc_start: 0.7087 (t0) cc_final: 0.6823 (t0) REVERT: D 1003 LEU cc_start: 0.8365 (mt) cc_final: 0.7810 (mp) REVERT: D 1007 CYS cc_start: 0.7680 (p) cc_final: 0.7230 (p) REVERT: D 1059 ARG cc_start: 0.7514 (mtp85) cc_final: 0.7257 (mtp85) REVERT: D 1171 GLU cc_start: 0.6975 (mp0) cc_final: 0.6153 (mp0) REVERT: R 50 MET cc_start: 0.6863 (mtm) cc_final: 0.6647 (mtm) REVERT: S 103 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7681 (tt) REVERT: F 116 GLU cc_start: 0.7182 (mp0) cc_final: 0.6890 (mp0) outliers start: 22 outliers final: 13 residues processed: 431 average time/residue: 0.3377 time to fit residues: 211.7334 Evaluate side-chains 428 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 414 time to evaluate : 2.013 ------------------------------------------------------------------------------- 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 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 S residue 103 LEU 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 120 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 179 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 216 optimal weight: 20.0000 chunk 233 optimal weight: 0.6980 chunk 192 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS D 277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18437 Z= 0.194 Angle : 0.497 9.028 24998 Z= 0.258 Chirality : 0.039 0.136 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.558 21.005 2539 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.16 % Allowed : 12.21 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.18), residues: 2360 helix: 2.34 (0.13), residues: 1567 sheet: -1.60 (0.69), residues: 61 loop : -0.67 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 33 HIS 0.004 0.001 HIS D 707 PHE 0.021 0.001 PHE C 402 TYR 0.019 0.001 TYR C 563 ARG 0.003 0.000 ARG C 764 *********************** 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 438 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 416 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 519 GLU cc_start: 0.7194 (tp30) cc_final: 0.6874 (tp30) REVERT: C 578 LYS cc_start: 0.8295 (ptmt) cc_final: 0.8085 (ptmm) REVERT: C 589 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6460 (mm-30) REVERT: C 620 TYR cc_start: 0.6939 (m-80) cc_final: 0.6374 (m-80) REVERT: C 641 GLN cc_start: 0.7568 (tm-30) cc_final: 0.6752 (tm-30) REVERT: C 642 ILE cc_start: 0.8485 (mm) cc_final: 0.8220 (mm) REVERT: C 645 LYS cc_start: 0.7768 (mmtt) cc_final: 0.6725 (mmtt) REVERT: D 52 MET cc_start: 0.7076 (tpp) cc_final: 0.6738 (tpp) REVERT: D 104 ASP cc_start: 0.7562 (p0) cc_final: 0.7118 (p0) REVERT: D 216 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6779 (mm-30) REVERT: D 221 GLU cc_start: 0.7170 (mp0) cc_final: 0.6630 (mp0) REVERT: D 705 ASP cc_start: 0.7148 (t70) cc_final: 0.6867 (t0) REVERT: D 863 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7113 (tm-30) REVERT: D 962 ASP cc_start: 0.7066 (t0) cc_final: 0.6739 (t0) REVERT: D 965 THR cc_start: 0.8671 (t) cc_final: 0.8117 (t) REVERT: D 1003 LEU cc_start: 0.8384 (mt) cc_final: 0.7817 (mp) REVERT: D 1007 CYS cc_start: 0.7647 (p) cc_final: 0.7208 (p) REVERT: D 1059 ARG cc_start: 0.7481 (mtp85) cc_final: 0.7260 (mtp85) REVERT: D 1171 GLU cc_start: 0.6937 (mp0) cc_final: 0.6368 (mp0) REVERT: R 50 MET cc_start: 0.6842 (mtm) cc_final: 0.6624 (mtm) REVERT: S 55 LEU cc_start: 0.8605 (tp) cc_final: 0.8325 (tt) REVERT: F 116 GLU cc_start: 0.7282 (mp0) cc_final: 0.7020 (mp0) outliers start: 22 outliers final: 15 residues processed: 423 average time/residue: 0.3335 time to fit residues: 205.1983 Evaluate side-chains 420 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 405 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 522 LYS Chi-restraints excluded: chain C residue 612 LEU 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 824 ASP Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain S residue 50 VAL 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 213 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 217 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 18437 Z= 0.319 Angle : 0.547 9.455 24998 Z= 0.284 Chirality : 0.042 0.145 2984 Planarity : 0.004 0.049 3186 Dihedral : 3.704 20.632 2539 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.22 % Allowed : 12.74 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.18), residues: 2360 helix: 2.19 (0.13), residues: 1567 sheet: -1.48 (0.70), residues: 61 loop : -0.76 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 33 HIS 0.009 0.001 HIS D 707 PHE 0.025 0.002 PHE C 402 TYR 0.020 0.002 TYR C 278 ARG 0.004 0.000 ARG D1141 *********************** 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 474 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 432 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 519 GLU cc_start: 0.7187 (tp30) cc_final: 0.6909 (tp30) REVERT: C 578 LYS cc_start: 0.8297 (ptmt) cc_final: 0.8078 (ptmm) REVERT: C 589 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6266 (mm-30) REVERT: C 620 TYR cc_start: 0.6979 (m-80) cc_final: 0.6396 (m-80) REVERT: C 641 GLN cc_start: 0.7616 (tm-30) cc_final: 0.7023 (tm-30) REVERT: C 642 ILE cc_start: 0.8558 (mm) cc_final: 0.8268 (mm) REVERT: C 705 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6440 (mt-10) REVERT: D 51 LYS cc_start: 0.7528 (mtmt) cc_final: 0.7126 (mtmt) REVERT: D 104 ASP cc_start: 0.7588 (p0) cc_final: 0.7161 (p0) REVERT: D 216 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6867 (mm-30) REVERT: D 221 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: D 304 TYR cc_start: 0.8432 (m-80) cc_final: 0.8151 (m-80) REVERT: D 393 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.6837 (m-30) REVERT: D 696 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: D 705 ASP cc_start: 0.7192 (t70) cc_final: 0.6918 (t0) REVERT: D 863 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7155 (tm-30) REVERT: D 962 ASP cc_start: 0.7091 (t0) cc_final: 0.6770 (t0) REVERT: D 965 THR cc_start: 0.8662 (t) cc_final: 0.8110 (t) REVERT: D 1003 LEU cc_start: 0.8485 (mt) cc_final: 0.7902 (mp) REVERT: D 1007 CYS cc_start: 0.7636 (p) cc_final: 0.7188 (p) REVERT: D 1059 ARG cc_start: 0.7497 (mtp85) cc_final: 0.7281 (mtp85) REVERT: D 1171 GLU cc_start: 0.6983 (mp0) cc_final: 0.6423 (mp0) REVERT: D 1178 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7712 (mtm-85) REVERT: D 1212 PHE cc_start: 0.8122 (t80) cc_final: 0.7794 (t80) REVERT: R 50 MET cc_start: 0.6868 (mtm) cc_final: 0.6661 (mtm) REVERT: S 32 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6649 (mt-10) REVERT: S 55 LEU cc_start: 0.8632 (tp) cc_final: 0.8345 (tt) REVERT: S 102 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6220 (mp0) REVERT: S 103 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7695 (tt) REVERT: F 116 GLU cc_start: 0.7339 (mp0) cc_final: 0.7049 (mp0) outliers start: 42 outliers final: 26 residues processed: 449 average time/residue: 0.3471 time to fit residues: 226.7289 Evaluate side-chains 453 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 421 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 114 SER 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 522 LYS Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 221 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 393 ASP Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 403 LYS 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 1093 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 S residue 126 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 0.0770 chunk 130 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 171 optimal weight: 0.0270 chunk 94 optimal weight: 0.8980 chunk 196 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1107 ASN D1169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18437 Z= 0.165 Angle : 0.486 8.940 24998 Z= 0.253 Chirality : 0.038 0.134 2984 Planarity : 0.004 0.049 3186 Dihedral : 3.528 21.059 2539 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.64 % Allowed : 14.48 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.18), residues: 2360 helix: 2.36 (0.13), residues: 1569 sheet: -1.36 (0.71), residues: 61 loop : -0.65 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 33 HIS 0.004 0.001 HIS D1108 PHE 0.019 0.001 PHE C 402 TYR 0.017 0.001 TYR C 563 ARG 0.004 0.000 ARG C 741 *********************** 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 fitting. rotamer outliers: 31 poor density : 408 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 519 GLU cc_start: 0.7187 (tp30) cc_final: 0.6930 (tp30) REVERT: C 578 LYS cc_start: 0.8292 (ptmt) cc_final: 0.8076 (ptmm) REVERT: C 589 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6279 (mm-30) REVERT: C 610 ILE cc_start: 0.8430 (pt) cc_final: 0.8156 (mt) REVERT: C 620 TYR cc_start: 0.6846 (m-80) cc_final: 0.6335 (m-80) REVERT: C 641 GLN cc_start: 0.7570 (tm-30) cc_final: 0.6738 (tm-30) REVERT: C 642 ILE cc_start: 0.8519 (mm) cc_final: 0.8206 (mm) REVERT: C 645 LYS cc_start: 0.7768 (mmtt) cc_final: 0.6754 (mmtt) REVERT: D 51 LYS cc_start: 0.7511 (mtmt) cc_final: 0.7105 (mtmt) REVERT: D 104 ASP cc_start: 0.7586 (p0) cc_final: 0.7165 (p0) REVERT: D 216 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6830 (mm-30) REVERT: D 221 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: D 705 ASP cc_start: 0.7183 (t70) cc_final: 0.6912 (t0) REVERT: D 823 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7960 (mp10) REVERT: D 962 ASP cc_start: 0.7031 (t0) cc_final: 0.6722 (t0) REVERT: D 965 THR cc_start: 0.8638 (t) cc_final: 0.8019 (t) REVERT: D 1003 LEU cc_start: 0.8441 (mt) cc_final: 0.7832 (mp) REVERT: D 1007 CYS cc_start: 0.7580 (p) cc_final: 0.7136 (p) REVERT: D 1171 GLU cc_start: 0.6904 (mp0) cc_final: 0.6363 (mp0) REVERT: D 1212 PHE cc_start: 0.8094 (t80) cc_final: 0.7792 (t80) REVERT: R 50 MET cc_start: 0.6855 (mtm) cc_final: 0.6628 (mtm) REVERT: S 32 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6618 (mt-10) REVERT: S 55 LEU cc_start: 0.8565 (tp) cc_final: 0.8286 (tt) outliers start: 31 outliers final: 21 residues processed: 418 average time/residue: 0.3456 time to fit residues: 210.8424 Evaluate side-chains 419 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 397 time to evaluate : 2.160 ------------------------------------------------------------------------------- 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 612 LEU 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 D residue 221 GLU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 403 LYS 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 824 ASP Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 1093 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 F residue 120 VAL Chi-restraints excluded: chain F residue 121 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 0.0170 chunk 207 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 135 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 230 optimal weight: 20.0000 chunk 191 optimal weight: 0.0970 chunk 106 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 18437 Z= 0.150 Angle : 0.486 8.890 24998 Z= 0.249 Chirality : 0.037 0.137 2984 Planarity : 0.004 0.049 3186 Dihedral : 3.429 18.728 2539 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.11 % Allowed : 14.59 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.18), residues: 2360 helix: 2.42 (0.13), residues: 1569 sheet: -1.35 (0.70), residues: 61 loop : -0.62 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 33 HIS 0.005 0.001 HIS D1108 PHE 0.017 0.001 PHE C 402 TYR 0.024 0.001 TYR C 50 ARG 0.005 0.000 ARG D1141 *********************** 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 452 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 412 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 322 MET cc_start: 0.8380 (ttm) cc_final: 0.8119 (ttt) REVERT: C 519 GLU cc_start: 0.7196 (tp30) cc_final: 0.6935 (tp30) REVERT: C 578 LYS cc_start: 0.8287 (ptmt) cc_final: 0.8069 (ptmm) REVERT: C 589 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6272 (mm-30) REVERT: C 620 TYR cc_start: 0.6883 (m-80) cc_final: 0.6336 (m-80) REVERT: C 641 GLN cc_start: 0.7581 (tm-30) cc_final: 0.6744 (tm-30) REVERT: C 642 ILE cc_start: 0.8536 (mm) cc_final: 0.8205 (mm) REVERT: C 645 LYS cc_start: 0.7777 (mmtt) cc_final: 0.6776 (mmtt) REVERT: C 706 ASP cc_start: 0.7042 (m-30) cc_final: 0.6682 (m-30) REVERT: D 104 ASP cc_start: 0.7585 (p0) cc_final: 0.7148 (p0) REVERT: D 216 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6785 (mm-30) REVERT: D 221 GLU cc_start: 0.7209 (mp0) cc_final: 0.6824 (mp0) REVERT: D 705 ASP cc_start: 0.7164 (t70) cc_final: 0.6908 (t0) REVERT: D 823 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7946 (mp10) REVERT: D 898 GLU cc_start: 0.7575 (tp30) cc_final: 0.7319 (mm-30) REVERT: D 962 ASP cc_start: 0.7028 (t0) cc_final: 0.6711 (t0) REVERT: D 965 THR cc_start: 0.8628 (t) cc_final: 0.8021 (t) REVERT: D 1003 LEU cc_start: 0.8418 (mt) cc_final: 0.7747 (mp) REVERT: D 1007 CYS cc_start: 0.7580 (p) cc_final: 0.7147 (p) REVERT: D 1131 SER cc_start: 0.7988 (m) cc_final: 0.7633 (t) REVERT: D 1133 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7560 (pp) REVERT: D 1212 PHE cc_start: 0.8082 (t80) cc_final: 0.7775 (t80) REVERT: R 50 MET cc_start: 0.6866 (mtm) cc_final: 0.6634 (mtm) REVERT: S 32 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6614 (mt-10) REVERT: S 55 LEU cc_start: 0.8555 (tp) cc_final: 0.8281 (tt) REVERT: F 116 GLU cc_start: 0.7297 (mp0) cc_final: 0.6966 (mp0) outliers start: 40 outliers final: 27 residues processed: 431 average time/residue: 0.3381 time to fit residues: 212.3827 Evaluate side-chains 432 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 404 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 286 GLU 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 116 GLU Chi-restraints excluded: chain D residue 156 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 696 GLU 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 1040 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1133 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 F residue 120 VAL Chi-restraints excluded: chain F residue 121 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 128 optimal weight: 0.5980 chunk 229 optimal weight: 50.0000 chunk 143 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18437 Z= 0.199 Angle : 0.506 10.985 24998 Z= 0.259 Chirality : 0.039 0.149 2984 Planarity : 0.004 0.049 3186 Dihedral : 3.454 20.958 2539 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.01 % Allowed : 15.43 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.18), residues: 2360 helix: 2.38 (0.13), residues: 1569 sheet: -1.32 (0.70), residues: 61 loop : -0.64 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 33 HIS 0.005 0.001 HIS D 707 PHE 0.021 0.001 PHE C 402 TYR 0.026 0.002 TYR C 50 ARG 0.004 0.000 ARG D1144 *********************** 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 443 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 405 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 519 GLU cc_start: 0.7208 (tp30) cc_final: 0.6876 (tp30) REVERT: C 578 LYS cc_start: 0.8281 (ptmt) cc_final: 0.8051 (ptmm) REVERT: C 589 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6307 (mm-30) REVERT: C 620 TYR cc_start: 0.6849 (m-80) cc_final: 0.6333 (m-80) REVERT: C 641 GLN cc_start: 0.7595 (tm-30) cc_final: 0.6737 (tm-30) REVERT: C 642 ILE cc_start: 0.8531 (mm) cc_final: 0.8205 (mm) REVERT: C 645 LYS cc_start: 0.7821 (mmtt) cc_final: 0.6810 (mmtt) REVERT: C 706 ASP cc_start: 0.7069 (m-30) cc_final: 0.6727 (m-30) REVERT: D 14 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7720 (ttmm) REVERT: D 104 ASP cc_start: 0.7530 (p0) cc_final: 0.7114 (p0) REVERT: D 216 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6836 (mm-30) REVERT: D 221 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: D 705 ASP cc_start: 0.7170 (t70) cc_final: 0.6905 (t0) REVERT: D 863 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6982 (tm-30) REVERT: D 898 GLU cc_start: 0.7597 (tp30) cc_final: 0.7380 (tp30) REVERT: D 902 GLN cc_start: 0.7880 (mt0) cc_final: 0.7616 (mt0) REVERT: D 962 ASP cc_start: 0.7042 (t0) cc_final: 0.6721 (t0) REVERT: D 965 THR cc_start: 0.8637 (t) cc_final: 0.8033 (t) REVERT: D 1003 LEU cc_start: 0.8478 (mt) cc_final: 0.7893 (mp) REVERT: D 1007 CYS cc_start: 0.7589 (p) cc_final: 0.7160 (p) REVERT: D 1133 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7549 (pp) REVERT: R 50 MET cc_start: 0.6851 (mtm) cc_final: 0.6616 (mtm) REVERT: S 32 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6630 (mt-10) REVERT: S 55 LEU cc_start: 0.8561 (tp) cc_final: 0.8279 (tt) REVERT: F 116 GLU cc_start: 0.7256 (mp0) cc_final: 0.6880 (mp0) outliers start: 38 outliers final: 31 residues processed: 424 average time/residue: 0.3313 time to fit residues: 205.0531 Evaluate side-chains 434 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 401 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 522 LYS Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 705 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 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 549 VAL 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 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 F residue 120 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 140 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 137 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18437 Z= 0.176 Angle : 0.498 10.583 24998 Z= 0.257 Chirality : 0.038 0.209 2984 Planarity : 0.004 0.049 3186 Dihedral : 3.423 20.153 2539 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.11 % Allowed : 15.80 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.18), residues: 2360 helix: 2.39 (0.13), residues: 1576 sheet: -1.29 (0.70), residues: 61 loop : -0.74 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 33 HIS 0.005 0.001 HIS D1108 PHE 0.019 0.001 PHE C 402 TYR 0.026 0.001 TYR C 50 ARG 0.006 0.000 ARG D1141 *********************** 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 449 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 409 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 519 GLU cc_start: 0.7211 (tp30) cc_final: 0.6882 (tp30) REVERT: C 589 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6302 (mm-30) REVERT: C 610 ILE cc_start: 0.8443 (pt) cc_final: 0.8183 (mt) REVERT: C 620 TYR cc_start: 0.6813 (m-80) cc_final: 0.6289 (m-80) REVERT: C 641 GLN cc_start: 0.7590 (tm-30) cc_final: 0.6771 (tm-30) REVERT: C 642 ILE cc_start: 0.8532 (mm) cc_final: 0.8173 (mm) REVERT: C 645 LYS cc_start: 0.7817 (mmtt) cc_final: 0.6936 (mmtt) REVERT: C 706 ASP cc_start: 0.7051 (m-30) cc_final: 0.6687 (m-30) REVERT: D 52 MET cc_start: 0.7083 (tpp) cc_final: 0.6448 (tpp) REVERT: D 104 ASP cc_start: 0.7540 (p0) cc_final: 0.7111 (p0) REVERT: D 216 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6842 (mm-30) REVERT: D 221 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: D 705 ASP cc_start: 0.7174 (t70) cc_final: 0.6898 (t0) REVERT: D 863 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6982 (tm-30) REVERT: D 898 GLU cc_start: 0.7579 (tp30) cc_final: 0.7134 (mm-30) REVERT: D 902 GLN cc_start: 0.7877 (mt0) cc_final: 0.7417 (mt0) REVERT: D 962 ASP cc_start: 0.7048 (t0) cc_final: 0.6715 (t0) REVERT: D 965 THR cc_start: 0.8629 (t) cc_final: 0.8026 (t) REVERT: D 1003 LEU cc_start: 0.8439 (mt) cc_final: 0.7764 (mp) REVERT: D 1007 CYS cc_start: 0.7571 (p) cc_final: 0.7141 (p) REVERT: D 1133 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7558 (pp) REVERT: D 1141 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7809 (mtp180) REVERT: R 50 MET cc_start: 0.6843 (mtm) cc_final: 0.6608 (mtm) REVERT: S 14 PHE cc_start: 0.8115 (m-80) cc_final: 0.7627 (m-80) REVERT: S 32 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6678 (mt-10) REVERT: S 55 LEU cc_start: 0.8558 (tp) cc_final: 0.8277 (tt) outliers start: 40 outliers final: 32 residues processed: 429 average time/residue: 0.3373 time to fit residues: 210.7877 Evaluate side-chains 435 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 401 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 SER 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 690 THR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 224 LYS 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 549 VAL 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 F residue 120 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 140 LEU 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 208 optimal weight: 0.7980 chunk 219 optimal weight: 9.9990 chunk 200 optimal weight: 0.9980 chunk 213 optimal weight: 10.0000 chunk 128 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18437 Z= 0.209 Angle : 0.516 10.949 24998 Z= 0.266 Chirality : 0.039 0.217 2984 Planarity : 0.004 0.049 3186 Dihedral : 3.478 20.954 2539 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.90 % Allowed : 15.96 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.18), residues: 2360 helix: 2.37 (0.13), residues: 1574 sheet: -1.20 (0.71), residues: 61 loop : -0.69 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 33 HIS 0.004 0.001 HIS D 707 PHE 0.022 0.001 PHE C 402 TYR 0.027 0.002 TYR C 50 ARG 0.007 0.000 ARG D1141 *********************** 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 442 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 406 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 519 GLU cc_start: 0.7217 (tp30) cc_final: 0.6877 (tp30) REVERT: C 589 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6306 (mm-30) REVERT: C 610 ILE cc_start: 0.8444 (pt) cc_final: 0.8178 (mt) REVERT: C 620 TYR cc_start: 0.6827 (m-80) cc_final: 0.6308 (m-80) REVERT: C 641 GLN cc_start: 0.7597 (tm-30) cc_final: 0.6769 (tm-30) REVERT: C 642 ILE cc_start: 0.8548 (mm) cc_final: 0.8190 (mm) REVERT: C 645 LYS cc_start: 0.7835 (mmtt) cc_final: 0.6937 (mmtt) REVERT: C 706 ASP cc_start: 0.7064 (m-30) cc_final: 0.6718 (m-30) REVERT: D 52 MET cc_start: 0.7061 (tpp) cc_final: 0.5982 (tpp) REVERT: D 55 LYS cc_start: 0.8202 (ttpp) cc_final: 0.7332 (pttm) REVERT: D 104 ASP cc_start: 0.7544 (p0) cc_final: 0.7119 (p0) REVERT: D 216 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6881 (mm-30) REVERT: D 221 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: D 705 ASP cc_start: 0.7175 (t70) cc_final: 0.6896 (t0) REVERT: D 863 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6997 (tm-30) REVERT: D 898 GLU cc_start: 0.7581 (tp30) cc_final: 0.7092 (mm-30) REVERT: D 902 GLN cc_start: 0.7927 (mt0) cc_final: 0.7431 (mt0) REVERT: D 962 ASP cc_start: 0.7060 (t0) cc_final: 0.6729 (t0) REVERT: D 965 THR cc_start: 0.8638 (t) cc_final: 0.8041 (t) REVERT: D 1003 LEU cc_start: 0.8486 (mt) cc_final: 0.7893 (mp) REVERT: D 1007 CYS cc_start: 0.7586 (p) cc_final: 0.7158 (p) REVERT: D 1133 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7521 (pp) REVERT: D 1141 ARG cc_start: 0.8147 (mtp180) cc_final: 0.7843 (mtp180) REVERT: R 50 MET cc_start: 0.6852 (mtm) cc_final: 0.6617 (mtm) REVERT: S 32 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6686 (mt-10) REVERT: S 55 LEU cc_start: 0.8578 (tp) cc_final: 0.8312 (tt) outliers start: 36 outliers final: 33 residues processed: 423 average time/residue: 0.3337 time to fit residues: 205.5553 Evaluate side-chains 437 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 402 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 SER 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 690 THR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 286 CYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 549 VAL 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 F residue 120 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 140 LEU 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 226 optimal weight: 50.0000 chunk 137 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 218 optimal weight: 30.0000 chunk 188 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18437 Z= 0.230 Angle : 0.532 9.676 24998 Z= 0.274 Chirality : 0.040 0.221 2984 Planarity : 0.004 0.049 3186 Dihedral : 3.535 22.952 2539 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.85 % Allowed : 16.33 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.18), residues: 2360 helix: 2.30 (0.13), residues: 1578 sheet: -1.16 (0.71), residues: 61 loop : -0.68 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 33 HIS 0.005 0.001 HIS D 217 PHE 0.022 0.001 PHE C 402 TYR 0.027 0.002 TYR C 50 ARG 0.007 0.000 ARG D1141 ********************** 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 443 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 408 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 146 ARG cc_start: 0.7307 (tmm160) cc_final: 0.7099 (ttp80) REVERT: C 519 GLU cc_start: 0.7226 (tp30) cc_final: 0.6879 (tp30) REVERT: C 589 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6297 (mm-30) REVERT: C 610 ILE cc_start: 0.8438 (pt) cc_final: 0.8176 (mt) REVERT: C 620 TYR cc_start: 0.6822 (m-80) cc_final: 0.6294 (m-80) REVERT: C 641 GLN cc_start: 0.7602 (tm-30) cc_final: 0.6753 (tm-30) REVERT: C 642 ILE cc_start: 0.8539 (mm) cc_final: 0.8188 (mm) REVERT: C 645 LYS cc_start: 0.7847 (mmtt) cc_final: 0.6904 (mmtt) REVERT: C 706 ASP cc_start: 0.7070 (m-30) cc_final: 0.6756 (m-30) REVERT: D 52 MET cc_start: 0.7021 (tpp) cc_final: 0.6676 (tpp) REVERT: D 104 ASP cc_start: 0.7552 (p0) cc_final: 0.7125 (p0) REVERT: D 216 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6908 (mm-30) REVERT: D 221 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: D 481 ILE cc_start: 0.8453 (mm) cc_final: 0.8239 (mt) REVERT: D 705 ASP cc_start: 0.7186 (t70) cc_final: 0.6907 (t0) REVERT: D 729 LYS cc_start: 0.8476 (mtmm) cc_final: 0.8266 (mtmt) REVERT: D 863 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6947 (tm-30) REVERT: D 865 PHE cc_start: 0.8422 (m-80) cc_final: 0.8041 (t80) REVERT: D 898 GLU cc_start: 0.7565 (tp30) cc_final: 0.7037 (mm-30) REVERT: D 902 GLN cc_start: 0.7949 (mt0) cc_final: 0.7428 (mt0) REVERT: D 962 ASP cc_start: 0.7063 (t0) cc_final: 0.6732 (t0) REVERT: D 965 THR cc_start: 0.8637 (t) cc_final: 0.8043 (t) REVERT: D 1003 LEU cc_start: 0.8501 (mt) cc_final: 0.7901 (mp) REVERT: D 1007 CYS cc_start: 0.7588 (p) cc_final: 0.7158 (p) REVERT: D 1133 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7556 (pp) REVERT: D 1141 ARG cc_start: 0.8220 (mtp180) cc_final: 0.7961 (mtp180) REVERT: D 1178 ARG cc_start: 0.8044 (ttm170) cc_final: 0.7705 (mtm-85) REVERT: R 50 MET cc_start: 0.6853 (mtm) cc_final: 0.6625 (mtm) REVERT: S 32 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6706 (mt-10) REVERT: S 55 LEU cc_start: 0.8591 (tp) cc_final: 0.8319 (tt) outliers start: 35 outliers final: 32 residues processed: 424 average time/residue: 0.3344 time to fit residues: 206.1248 Evaluate side-chains 443 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 409 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 SER 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 690 THR 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 286 CYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 549 VAL 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 1016 GLU 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 F residue 120 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 140 LEU 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 201 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 174 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106366 restraints weight = 26023.621| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.87 r_work: 0.3183 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 18437 Z= 0.211 Angle : 0.528 9.893 24998 Z= 0.272 Chirality : 0.039 0.216 2984 Planarity : 0.004 0.049 3186 Dihedral : 3.523 22.739 2539 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.06 % Allowed : 16.33 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.18), residues: 2360 helix: 2.31 (0.13), residues: 1578 sheet: -1.54 (0.65), residues: 71 loop : -0.60 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 33 HIS 0.005 0.001 HIS D 217 PHE 0.021 0.001 PHE C 402 TYR 0.026 0.002 TYR C 50 ARG 0.007 0.000 ARG D1141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5015.30 seconds wall clock time: 89 minutes 52.22 seconds (5392.22 seconds total)