Starting phenix.real_space_refine on Fri Jun 5 16:52:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9va2_64897/06_2026/9va2_64897_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9va2_64897/06_2026/9va2_64897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9va2_64897/06_2026/9va2_64897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9va2_64897/06_2026/9va2_64897.map" model { file = "/net/cci-nas-00/data/ceres_data/9va2_64897/06_2026/9va2_64897_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9va2_64897/06_2026/9va2_64897_neut.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.067 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 14340 2.51 5 N 3548 2.21 5 O 4078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22094 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6096 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Chain: "B" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain: "C" Number of atoms: 6096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6096 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Chain: "D" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.66, per 1000 atoms: 0.26 Number of scatterers: 22094 At special positions: 0 Unit cell: (118.845, 132.525, 183.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 4078 8.00 N 3548 7.00 C 14340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 383 " distance=2.02 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 383 " distance=2.02 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 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG N 1 " - " NAG N 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A 901 " - " ASN A 103 " " NAG A 902 " - " ASN A 546 " " NAG A 903 " - " ASN A 322 " " NAG B 701 " - " ASN B 182 " " NAG B 702 " - " ASN B 368 " " NAG B 703 " - " ASN B 354 " " NAG C 901 " - " ASN C 103 " " NAG C 902 " - " ASN C 546 " " NAG C 903 " - " ASN C 322 " " NAG D 701 " - " ASN D 182 " " NAG D 702 " - " ASN D 354 " " NAG D 703 " - " ASN D 368 " " NAG H 1 " - " ASN A 432 " " NAG J 1 " - " ASN A 690 " " NAG N 1 " - " ASN C 690 " " NAG S 1 " - " ASN C 432 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5088 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 10 sheets defined 65.4% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.224A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 109 through 130 removed outlier: 4.096A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 193 removed outlier: 5.030A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.827A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.862A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.888A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 305 through 318 removed outlier: 3.661A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.762A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.968A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.599A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.537A pdb=" N ILE A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.855A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.539A pdb=" N SER A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.526A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.938A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.754A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.608A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 658 removed outlier: 3.590A pdb=" N MET A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 696 through 714 removed outlier: 3.666A pdb=" N LYS A 702 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 767 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 37 through 48 removed outlier: 3.583A pdb=" N TYR B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 removed outlier: 3.838A pdb=" N TYR B 60 " --> pdb=" O TRP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 97 removed outlier: 5.373A pdb=" N ILE B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix removed outlier: 3.597A pdb=" N ARG B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 142 removed outlier: 4.242A pdb=" N GLY B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N MET B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE B 132 " --> pdb=" O TYR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 169 removed outlier: 3.590A pdb=" N SER B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.835A pdb=" N LEU B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N CYS B 200 " --> pdb=" O TRP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 227 removed outlier: 3.584A pdb=" N ALA B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 244 removed outlier: 4.097A pdb=" N THR B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 4.273A pdb=" N PHE B 255 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 279 removed outlier: 3.691A pdb=" N TRP B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 290 removed outlier: 4.384A pdb=" N ILE B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 349 removed outlier: 3.732A pdb=" N ASP B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 371 Processing helix chain 'B' and resid 371 through 378 removed outlier: 3.521A pdb=" N LEU B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 408 removed outlier: 3.751A pdb=" N GLU B 405 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 436 removed outlier: 3.541A pdb=" N TRP B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 432 " --> pdb=" O GLY B 428 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY B 434 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 445 removed outlier: 3.506A pdb=" N ASP B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 470 removed outlier: 3.892A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 removed outlier: 3.506A pdb=" N LEU B 475 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 490 removed outlier: 3.806A pdb=" N TYR B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 490 " --> pdb=" O ASP B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 508 removed outlier: 4.428A pdb=" N ALA B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 523 Processing helix chain 'B' and resid 527 through 536 removed outlier: 3.856A pdb=" N VAL B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 552 removed outlier: 3.827A pdb=" N PHE B 550 " --> pdb=" O PHE B 546 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 552 " --> pdb=" O PHE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 583 removed outlier: 3.565A pdb=" N TYR B 583 " --> pdb=" O ASN B 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 580 through 583' Processing helix chain 'B' and resid 584 through 591 Processing helix chain 'B' and resid 591 through 608 removed outlier: 4.595A pdb=" N ILE B 597 " --> pdb=" O PRO B 593 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 3.735A pdb=" N ALA B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 53 removed outlier: 3.816A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 109 through 130 removed outlier: 4.097A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 157 through 193 removed outlier: 5.030A pdb=" N LYS C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLN C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.829A pdb=" N VAL C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.862A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.887A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 293 through 300 Processing helix chain 'C' and resid 305 through 318 removed outlier: 3.660A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.763A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.967A pdb=" N ARG C 393 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 411 removed outlier: 3.599A pdb=" N VAL C 404 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.538A pdb=" N ILE C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 447 removed outlier: 3.855A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 464 Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 513 through 531 removed outlier: 3.526A pdb=" N ARG C 518 " --> pdb=" O ARG C 514 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN C 526 " --> pdb=" O GLN C 522 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 547 through 559 removed outlier: 3.938A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 removed outlier: 3.754A pdb=" N VAL C 573 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 588 through 599 Processing helix chain 'C' and resid 623 through 628 removed outlier: 3.609A pdb=" N ALA C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 658 removed outlier: 3.590A pdb=" N MET C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 696 through 714 removed outlier: 3.668A pdb=" N LYS C 702 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA C 714 " --> pdb=" O ARG C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 767 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 37 through 48 removed outlier: 3.584A pdb=" N TYR D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 65 removed outlier: 3.839A pdb=" N TYR D 60 " --> pdb=" O TRP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 97 removed outlier: 5.373A pdb=" N ILE D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix removed outlier: 3.597A pdb=" N ARG D 97 " --> pdb=" O GLY D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 142 removed outlier: 4.243A pdb=" N GLY D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N MET D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR D 128 " --> pdb=" O MET D 124 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 169 removed outlier: 3.591A pdb=" N SER D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 194 through 212 removed outlier: 3.836A pdb=" N LEU D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N CYS D 200 " --> pdb=" O TRP D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 227 removed outlier: 3.585A pdb=" N ALA D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 244 removed outlier: 4.097A pdb=" N THR D 235 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 4.273A pdb=" N PHE D 255 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 279 removed outlier: 3.690A pdb=" N TRP D 268 " --> pdb=" O GLN D 264 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE D 279 " --> pdb=" O VAL D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 290 removed outlier: 4.386A pdb=" N ILE D 287 " --> pdb=" O PHE D 283 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 349 removed outlier: 3.731A pdb=" N ASP D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 371 Processing helix chain 'D' and resid 371 through 378 removed outlier: 3.521A pdb=" N LEU D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 408 removed outlier: 3.750A pdb=" N GLU D 405 " --> pdb=" O ILE D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 436 removed outlier: 3.541A pdb=" N TRP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET D 432 " --> pdb=" O GLY D 428 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE D 433 " --> pdb=" O LEU D 429 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY D 434 " --> pdb=" O SER D 430 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 445 removed outlier: 3.507A pdb=" N ASP D 445 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 470 removed outlier: 3.892A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 475 removed outlier: 3.505A pdb=" N LEU D 475 " --> pdb=" O ILE D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 490 removed outlier: 3.806A pdb=" N TYR D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY D 490 " --> pdb=" O ASP D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 508 removed outlier: 4.429A pdb=" N ALA D 498 " --> pdb=" O LEU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 523 Processing helix chain 'D' and resid 527 through 536 removed outlier: 3.856A pdb=" N VAL D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 552 removed outlier: 3.826A pdb=" N PHE D 550 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL D 552 " --> pdb=" O PHE D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 583 removed outlier: 3.565A pdb=" N TYR D 583 " --> pdb=" O ASN D 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 580 through 583' Processing helix chain 'D' and resid 584 through 591 Processing helix chain 'D' and resid 591 through 608 removed outlier: 4.595A pdb=" N ILE D 597 " --> pdb=" O PRO D 593 " (cutoff:3.500A) Proline residue: D 598 - end of helix removed outlier: 3.736A pdb=" N ALA D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.008A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.839A pdb=" N LEU A 351 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 670 through 673 Processing sheet with id=AA5, first strand: chain 'B' and resid 559 through 562 Processing sheet with id=AA6, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.008A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 347 through 352 removed outlier: 3.839A pdb=" N LEU C 351 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 670 through 673 Processing sheet with id=AB1, first strand: chain 'D' and resid 559 through 562 1129 hydrogen bonds defined for protein. 3330 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: 4.18 Time building geometry restraints manager: 2.72 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: 6823 1.34 - 1.46: 4265 1.46 - 1.57: 11404 1.57 - 1.69: 0 1.69 - 1.81: 210 Bond restraints: 22702 Sorted by residual: bond pdb=" CA LYS C 470 " pdb=" C LYS C 470 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.41e-02 5.03e+03 1.57e+01 bond pdb=" CA LYS A 470 " pdb=" C LYS A 470 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.41e-02 5.03e+03 1.56e+01 bond pdb=" C ILE B 83 " pdb=" N PRO B 84 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.30e-02 5.92e+03 5.21e+00 bond pdb=" C ILE D 83 " pdb=" N PRO D 84 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.30e-02 5.92e+03 5.01e+00 bond pdb=" C1 NAG B 702 " pdb=" O5 NAG B 702 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.68e+00 ... (remaining 22697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 30165 2.27 - 4.54: 613 4.54 - 6.81: 107 6.81 - 9.08: 15 9.08 - 11.34: 2 Bond angle restraints: 30902 Sorted by residual: angle pdb=" N GLY B 434 " pdb=" CA GLY B 434 " pdb=" C GLY B 434 " ideal model delta sigma weight residual 112.73 107.01 5.72 1.20e+00 6.94e-01 2.27e+01 angle pdb=" N GLY D 434 " pdb=" CA GLY D 434 " pdb=" C GLY D 434 " ideal model delta sigma weight residual 112.73 107.07 5.66 1.20e+00 6.94e-01 2.22e+01 angle pdb=" C PRO A 737 " pdb=" N PRO A 738 " pdb=" CA PRO A 738 " ideal model delta sigma weight residual 120.47 115.53 4.94 1.07e+00 8.73e-01 2.13e+01 angle pdb=" C LEU B 281 " pdb=" N ALA B 282 " pdb=" CA ALA B 282 " ideal model delta sigma weight residual 123.24 116.29 6.95 1.54e+00 4.22e-01 2.03e+01 angle pdb=" C LEU D 281 " pdb=" N ALA D 282 " pdb=" CA ALA D 282 " ideal model delta sigma weight residual 123.24 116.32 6.92 1.54e+00 4.22e-01 2.02e+01 ... (remaining 30897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 11644 18.05 - 36.09: 1282 36.09 - 54.14: 486 54.14 - 72.18: 128 72.18 - 90.23: 28 Dihedral angle restraints: 13568 sinusoidal: 5658 harmonic: 7910 Sorted by residual: dihedral pdb=" CA PRO C 677 " pdb=" C PRO C 677 " pdb=" N ARG C 678 " pdb=" CA ARG C 678 " ideal model delta harmonic sigma weight residual 180.00 150.48 29.52 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA PRO A 677 " pdb=" C PRO A 677 " pdb=" N ARG A 678 " pdb=" CA ARG A 678 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ARG C 678 " pdb=" C ARG C 678 " pdb=" N ILE C 679 " pdb=" CA ILE C 679 " ideal model delta harmonic sigma weight residual 180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 13565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.323: 3424 0.323 - 0.646: 10 0.646 - 0.968: 1 0.968 - 1.291: 1 1.291 - 1.614: 2 Chirality restraints: 3438 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 432 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.79 -1.61 2.00e-01 2.50e+01 6.51e+01 chirality pdb=" C1 NAG D 702 " pdb=" ND2 ASN D 354 " pdb=" C2 NAG D 702 " pdb=" O5 NAG D 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.04 -1.36 2.00e-01 2.50e+01 4.60e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 690 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.16 -1.24 2.00e-01 2.50e+01 3.87e+01 ... (remaining 3435 not shown) Planarity restraints: 3912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 354 " 0.205 2.00e-02 2.50e+03 2.07e-01 5.34e+02 pdb=" CG ASN B 354 " -0.076 2.00e-02 2.50e+03 pdb=" OD1 ASN B 354 " -0.099 2.00e-02 2.50e+03 pdb=" ND2 ASN B 354 " -0.294 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " 0.264 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 690 " 0.115 2.00e-02 2.50e+03 1.62e-01 3.27e+02 pdb=" CG ASN A 690 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN A 690 " 0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN A 690 " -0.282 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 690 " -0.133 2.00e-02 2.50e+03 1.61e-01 3.24e+02 pdb=" CG ASN C 690 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN C 690 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN C 690 " 0.272 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " -0.184 2.00e-02 2.50e+03 ... (remaining 3909 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1238 2.71 - 3.26: 22894 3.26 - 3.81: 35982 3.81 - 4.35: 45294 4.35 - 4.90: 74384 Nonbonded interactions: 179792 Sorted by model distance: nonbonded pdb=" N ASP A 295 " pdb=" OD1 ASP A 295 " model vdw 2.168 3.120 nonbonded pdb=" N ASP C 295 " pdb=" OD1 ASP C 295 " model vdw 2.169 3.120 nonbonded pdb=" OD1 ASN A 53 " pdb=" NE2 GLN A 340 " model vdw 2.206 3.120 nonbonded pdb=" OD1 ASN C 53 " pdb=" NE2 GLN C 340 " model vdw 2.207 3.120 nonbonded pdb=" OG1 THR B 185 " pdb=" OD2 ASP B 189 " model vdw 2.211 3.040 ... (remaining 179787 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'N' selection = chain 'S' } 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.750 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 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 : 0.007 0.151 22732 Z= 0.306 Angle : 1.016 34.511 30982 Z= 0.508 Chirality : 0.072 1.614 3438 Planarity : 0.005 0.068 3896 Dihedral : 18.341 90.226 8450 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.48 % Favored : 92.48 % Rotamer: Outliers : 11.30 % Allowed : 14.98 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.14), residues: 2700 helix: -1.70 (0.11), residues: 1584 sheet: -1.61 (0.62), residues: 58 loop : -3.05 (0.17), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 710 TYR 0.020 0.002 TYR C 183 PHE 0.020 0.002 PHE B 70 TRP 0.019 0.002 TRP C 163 HIS 0.006 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.28 (22702) covalent geometry : angle 0.82334 / 0.47 (30902) SS BOND : bond 0.00388 / 0.28 ( 10) SS BOND : angle 1.07617 / 0.66 ( 20) hydrogen bonds : bond 0.14823 / 10.00 ( 1129) hydrogen bonds : angle 6.47377 / 4.58 ( 3330) link_BETA1-4 : bond 0.01228 / 0.52 ( 4) link_BETA1-4 : angle 2.82236 / 1.56 ( 12) link_NAG-ASN : bond 0.09751 / 5.72 ( 16) link_NAG-ASN : angle 15.08187 / 9.91 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 270 poor density : 335 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: C 190 MET cc_start: 0.7725 (tmm) cc_final: 0.7368 (ttp) REVERT: C 269 ASP cc_start: 0.8418 (p0) cc_final: 0.8192 (p0) REVERT: C 723 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8275 (mt-10) REVERT: D 464 LEU cc_start: 0.6525 (mp) cc_final: 0.6208 (mp) outliers start: 270 outliers final: 113 residues processed: 564 average time/residue: 0.4629 time to fit residues: 309.4129 Evaluate side-chains 361 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 246 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 538 SER Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 548 PHE Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 597 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 53 ASN A 89 GLN A 139 GLN A 277 ASN A 340 GLN A 345 HIS A 417 HIS A 493 HIS A 505 HIS B 40 GLN B 310 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 ASN C 42 GLN C 51 ASN C 53 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 96 GLN C 134 ASN C 277 ASN C 340 GLN C 417 HIS C 493 HIS C 505 HIS D 40 GLN D 54 ASN D 159 GLN D 310 ASN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.218729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142462 restraints weight = 27197.590| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.76 r_work: 0.3274 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22732 Z= 0.160 Angle : 0.743 16.370 30982 Z= 0.359 Chirality : 0.047 0.488 3438 Planarity : 0.005 0.058 3896 Dihedral : 9.709 77.606 3499 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.41 % Favored : 94.56 % Rotamer: Outliers : 6.36 % Allowed : 21.34 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.15), residues: 2700 helix: -0.42 (0.12), residues: 1630 sheet: -1.38 (0.61), residues: 58 loop : -2.59 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.021 0.002 TYR A 83 PHE 0.037 0.002 PHE A 72 TRP 0.013 0.001 TRP B 534 HIS 0.008 0.001 HIS D 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (22702) covalent geometry : angle 0.70806 / 0.35 (30902) SS BOND : bond 0.00177 / 0.10 ( 10) SS BOND : angle 0.73648 / 0.44 ( 20) hydrogen bonds : bond 0.05938 / 3.91 ( 1129) hydrogen bonds : angle 4.87778 / 3.47 ( 3330) link_BETA1-4 : bond 0.00601 / 0.31 ( 4) link_BETA1-4 : angle 2.81483 / 1.55 ( 12) link_NAG-ASN : bond 0.00686 / 0.40 ( 16) link_NAG-ASN : angle 5.62919 / 3.62 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 289 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7924 (mp10) REVERT: A 182 GLU cc_start: 0.8103 (tt0) cc_final: 0.7894 (mt-10) REVERT: A 580 ASN cc_start: 0.6938 (t0) cc_final: 0.6150 (m110) REVERT: A 659 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7983 (mttt) REVERT: B 70 PHE cc_start: 0.3756 (OUTLIER) cc_final: 0.2538 (t80) REVERT: B 365 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7294 (pp30) REVERT: B 377 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7891 (mm-40) REVERT: B 382 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7689 (p) REVERT: B 437 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6879 (tm-30) REVERT: B 558 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.5685 (pp) REVERT: B 576 ILE cc_start: 0.7234 (tt) cc_final: 0.6869 (pt) REVERT: C 134 ASN cc_start: 0.8456 (t0) cc_final: 0.7947 (t0) REVERT: C 171 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: C 192 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6427 (mtm110) REVERT: C 206 ASP cc_start: 0.8275 (t0) cc_final: 0.7819 (t0) REVERT: C 332 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7308 (tpp) REVERT: C 465 LYS cc_start: 0.8711 (ptpt) cc_final: 0.8326 (pttt) REVERT: C 660 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8333 (t0) REVERT: D 70 PHE cc_start: 0.4016 (OUTLIER) cc_final: 0.3003 (t80) REVERT: D 239 ILE cc_start: 0.6868 (pt) cc_final: 0.6465 (pp) REVERT: D 279 PHE cc_start: 0.8045 (m-10) cc_final: 0.7748 (m-80) REVERT: D 289 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7322 (m-10) outliers start: 152 outliers final: 66 residues processed: 409 average time/residue: 0.4540 time to fit residues: 220.5492 Evaluate side-chains 335 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 257 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 452 LYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 597 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 110 optimal weight: 5.9990 chunk 65 optimal weight: 0.2980 chunk 100 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 chunk 199 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 171 optimal weight: 0.0970 chunk 138 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 401 HIS A 417 HIS B 159 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.218017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.164538 restraints weight = 27015.144| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.41 r_work: 0.3283 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22732 Z= 0.179 Angle : 0.706 12.418 30982 Z= 0.346 Chirality : 0.047 0.415 3438 Planarity : 0.005 0.065 3896 Dihedral : 7.696 59.052 3409 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 6.07 % Allowed : 23.01 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.16), residues: 2700 helix: 0.03 (0.13), residues: 1620 sheet: -1.37 (0.62), residues: 58 loop : -2.30 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 710 TYR 0.022 0.002 TYR A 183 PHE 0.022 0.002 PHE B 549 TRP 0.014 0.001 TRP C 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (22702) covalent geometry : angle 0.67862 / 0.34 (30902) SS BOND : bond 0.00199 / 0.13 ( 10) SS BOND : angle 0.90141 / 0.52 ( 20) hydrogen bonds : bond 0.06038 / 3.95 ( 1129) hydrogen bonds : angle 4.67036 / 3.33 ( 3330) link_BETA1-4 : bond 0.00355 / 0.18 ( 4) link_BETA1-4 : angle 2.49079 / 1.40 ( 12) link_NAG-ASN : bond 0.00885 / 0.49 ( 16) link_NAG-ASN : angle 4.79254 / 3.01 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 274 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.7991 (t80) cc_final: 0.7688 (t80) REVERT: A 76 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8045 (mp10) REVERT: A 297 MET cc_start: 0.8241 (ttm) cc_final: 0.7778 (mtp) REVERT: A 659 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8340 (mttt) REVERT: B 83 ILE cc_start: 0.8713 (tp) cc_final: 0.8497 (mt) REVERT: B 437 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7593 (tm-30) REVERT: B 452 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6840 (tmmt) REVERT: B 530 TRP cc_start: 0.6384 (OUTLIER) cc_final: 0.6064 (m-90) REVERT: B 558 LEU cc_start: 0.5969 (OUTLIER) cc_final: 0.5499 (pp) REVERT: B 576 ILE cc_start: 0.7576 (tt) cc_final: 0.7165 (pt) REVERT: C 134 ASN cc_start: 0.8413 (t0) cc_final: 0.8178 (t0) REVERT: C 171 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: C 332 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7418 (tpp) REVERT: C 360 MET cc_start: 0.8042 (ptm) cc_final: 0.7784 (ptm) REVERT: C 518 ARG cc_start: 0.8281 (tmm160) cc_final: 0.8007 (ttt-90) REVERT: C 560 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8111 (mp) REVERT: C 660 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8301 (t0) REVERT: D 239 ILE cc_start: 0.6970 (pt) cc_final: 0.6526 (pp) REVERT: D 514 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8496 (t80) REVERT: D 583 TYR cc_start: 0.6138 (OUTLIER) cc_final: 0.5553 (t80) outliers start: 145 outliers final: 75 residues processed: 380 average time/residue: 0.4721 time to fit residues: 213.4329 Evaluate side-chains 343 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 257 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 452 LYS Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 625 LYS Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 597 ILE Chi-restraints excluded: chain D residue 606 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 230 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 256 optimal weight: 0.9980 chunk 131 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 HIS D 476 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.220125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.167630 restraints weight = 26993.307| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.38 r_work: 0.3328 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22732 Z= 0.133 Angle : 0.662 11.506 30982 Z= 0.320 Chirality : 0.044 0.389 3438 Planarity : 0.004 0.052 3896 Dihedral : 7.012 59.686 3393 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.27 % Allowed : 24.48 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.16), residues: 2700 helix: 0.36 (0.13), residues: 1648 sheet: -1.38 (0.60), residues: 58 loop : -2.19 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 652 TYR 0.017 0.001 TYR B 60 PHE 0.030 0.001 PHE C 746 TRP 0.022 0.001 TRP B 534 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (22702) covalent geometry : angle 0.63948 / 0.31 (30902) SS BOND : bond 0.00247 / 0.16 ( 10) SS BOND : angle 0.67418 / 0.37 ( 20) hydrogen bonds : bond 0.05077 / 3.33 ( 1129) hydrogen bonds : angle 4.50608 / 3.22 ( 3330) link_BETA1-4 : bond 0.00337 / 0.17 ( 4) link_BETA1-4 : angle 2.17765 / 1.23 ( 12) link_NAG-ASN : bond 0.00805 / 0.45 ( 16) link_NAG-ASN : angle 4.27641 / 2.62 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 284 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.7966 (t80) cc_final: 0.7766 (t80) REVERT: A 76 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: A 269 ASP cc_start: 0.8769 (p0) cc_final: 0.8471 (p0) REVERT: A 288 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7804 (ptpp) REVERT: A 297 MET cc_start: 0.8259 (ttm) cc_final: 0.7777 (mtp) REVERT: A 615 ASP cc_start: 0.8198 (p0) cc_final: 0.7833 (OUTLIER) REVERT: A 659 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8294 (mttt) REVERT: B 382 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7665 (p) REVERT: B 437 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7445 (tm-30) REVERT: B 452 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6838 (tmmt) REVERT: B 576 ILE cc_start: 0.7603 (tt) cc_final: 0.7109 (pt) REVERT: C 100 LEU cc_start: 0.8312 (mt) cc_final: 0.8101 (mp) REVERT: C 332 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7404 (tpp) REVERT: C 360 MET cc_start: 0.8024 (ptm) cc_final: 0.7726 (ptm) REVERT: C 560 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8106 (mp) REVERT: C 660 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8314 (t0) REVERT: D 514 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8481 (t80) REVERT: D 583 TYR cc_start: 0.6274 (OUTLIER) cc_final: 0.5657 (t80) outliers start: 126 outliers final: 64 residues processed: 367 average time/residue: 0.4342 time to fit residues: 190.9295 Evaluate side-chains 330 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 257 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 452 LYS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 534 TRP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 597 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 95 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 126 optimal weight: 0.6980 chunk 156 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 208 optimal weight: 30.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS A 552 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.219620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.166489 restraints weight = 26836.648| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.33 r_work: 0.3301 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22732 Z= 0.157 Angle : 0.697 12.458 30982 Z= 0.336 Chirality : 0.046 0.377 3438 Planarity : 0.005 0.064 3896 Dihedral : 6.733 59.855 3383 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.48 % Allowed : 24.39 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.16), residues: 2700 helix: 0.48 (0.13), residues: 1624 sheet: -1.37 (0.61), residues: 58 loop : -2.06 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 710 TYR 0.020 0.001 TYR A 183 PHE 0.029 0.001 PHE D 520 TRP 0.028 0.001 TRP B 534 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (22702) covalent geometry : angle 0.67618 / 0.33 (30902) SS BOND : bond 0.00224 / 0.14 ( 10) SS BOND : angle 0.79605 / 0.45 ( 20) hydrogen bonds : bond 0.05478 / 3.58 ( 1129) hydrogen bonds : angle 4.46456 / 3.19 ( 3330) link_BETA1-4 : bond 0.00324 / 0.16 ( 4) link_BETA1-4 : angle 2.16336 / 1.22 ( 12) link_NAG-ASN : bond 0.00858 / 0.48 ( 16) link_NAG-ASN : angle 4.19637 / 2.57 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 271 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: A 91 LEU cc_start: 0.3670 (OUTLIER) cc_final: 0.3467 (mm) REVERT: A 269 ASP cc_start: 0.8794 (p0) cc_final: 0.8494 (p0) REVERT: A 288 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7834 (ptpp) REVERT: A 297 MET cc_start: 0.8297 (ttm) cc_final: 0.7778 (mtp) REVERT: A 560 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7547 (mp) REVERT: A 615 ASP cc_start: 0.8223 (p0) cc_final: 0.7883 (OUTLIER) REVERT: A 659 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8429 (mttt) REVERT: B 224 TYR cc_start: 0.7331 (m-80) cc_final: 0.7025 (m-80) REVERT: B 382 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7694 (p) REVERT: B 437 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: B 452 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6855 (tmmt) REVERT: B 530 TRP cc_start: 0.6226 (m-90) cc_final: 0.5744 (m-90) REVERT: B 576 ILE cc_start: 0.7548 (tt) cc_final: 0.7086 (pt) REVERT: C 332 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7472 (tpp) REVERT: C 360 MET cc_start: 0.8052 (ptm) cc_final: 0.7765 (ptm) REVERT: C 560 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8125 (mp) REVERT: C 660 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8318 (t0) REVERT: D 514 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8489 (t80) REVERT: D 521 MET cc_start: 0.7431 (mmt) cc_final: 0.7168 (mmt) REVERT: D 583 TYR cc_start: 0.6308 (OUTLIER) cc_final: 0.5703 (t80) outliers start: 131 outliers final: 67 residues processed: 364 average time/residue: 0.4562 time to fit residues: 198.0103 Evaluate side-chains 338 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 259 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 452 LYS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 534 TRP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 597 ILE Chi-restraints excluded: chain D residue 606 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 101 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 246 optimal weight: 0.0050 chunk 3 optimal weight: 4.9990 chunk 192 optimal weight: 0.5980 chunk 71 optimal weight: 30.0000 chunk 165 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 30.0000 chunk 22 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS B 54 ASN B 159 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.219032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.164928 restraints weight = 27004.832| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.41 r_work: 0.3290 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22732 Z= 0.168 Angle : 0.698 11.553 30982 Z= 0.337 Chirality : 0.046 0.374 3438 Planarity : 0.005 0.065 3896 Dihedral : 6.512 59.949 3378 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.69 % Allowed : 25.23 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.16), residues: 2700 helix: 0.54 (0.13), residues: 1626 sheet: -1.23 (0.60), residues: 58 loop : -1.98 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 710 TYR 0.024 0.002 TYR C 215 PHE 0.036 0.001 PHE A 72 TRP 0.014 0.001 TRP B 534 HIS 0.006 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (22702) covalent geometry : angle 0.67787 / 0.33 (30902) SS BOND : bond 0.00226 / 0.14 ( 10) SS BOND : angle 0.86746 / 0.48 ( 20) hydrogen bonds : bond 0.05544 / 3.62 ( 1129) hydrogen bonds : angle 4.46567 / 3.20 ( 3330) link_BETA1-4 : bond 0.00445 / 0.21 ( 4) link_BETA1-4 : angle 2.18886 / 1.23 ( 12) link_NAG-ASN : bond 0.00864 / 0.49 ( 16) link_NAG-ASN : angle 4.12108 / 2.51 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 272 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.7950 (t80) cc_final: 0.7574 (t80) REVERT: A 76 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8081 (mp10) REVERT: A 269 ASP cc_start: 0.8824 (p0) cc_final: 0.8554 (p0) REVERT: A 288 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7987 (ptpp) REVERT: A 557 MET cc_start: 0.8238 (tmm) cc_final: 0.8024 (tmm) REVERT: A 615 ASP cc_start: 0.8296 (p0) cc_final: 0.7855 (OUTLIER) REVERT: A 659 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8476 (mttt) REVERT: B 211 CYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7250 (m) REVERT: B 270 ASP cc_start: 0.7836 (t0) cc_final: 0.7634 (t0) REVERT: B 382 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7702 (p) REVERT: B 435 ASN cc_start: 0.6824 (t0) cc_final: 0.6504 (t0) REVERT: B 437 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 452 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6905 (tmmt) REVERT: B 520 PHE cc_start: 0.7574 (t80) cc_final: 0.7316 (t80) REVERT: B 530 TRP cc_start: 0.6311 (m-90) cc_final: 0.5804 (m-90) REVERT: B 576 ILE cc_start: 0.7578 (tt) cc_final: 0.7035 (pt) REVERT: C 100 LEU cc_start: 0.8288 (mt) cc_final: 0.8069 (mp) REVERT: C 332 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7531 (tpp) REVERT: C 360 MET cc_start: 0.8098 (ptm) cc_final: 0.7813 (ptm) REVERT: C 560 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8137 (mp) REVERT: C 660 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8319 (t0) REVERT: D 34 LYS cc_start: 0.7295 (pptt) cc_final: 0.7043 (ptmm) REVERT: D 60 TYR cc_start: 0.6542 (t80) cc_final: 0.6302 (t80) REVERT: D 239 ILE cc_start: 0.7048 (pt) cc_final: 0.6619 (pp) REVERT: D 279 PHE cc_start: 0.8038 (m-10) cc_final: 0.7703 (m-80) REVERT: D 514 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8556 (t80) REVERT: D 583 TYR cc_start: 0.6205 (OUTLIER) cc_final: 0.5560 (t80) outliers start: 136 outliers final: 76 residues processed: 373 average time/residue: 0.4401 time to fit residues: 197.0427 Evaluate side-chains 346 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 260 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 452 LYS Chi-restraints excluded: chain B residue 534 TRP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 534 TRP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 597 ILE Chi-restraints excluded: chain D residue 606 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 120 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 20 optimal weight: 0.0870 chunk 56 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS B 159 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.219874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.166295 restraints weight = 26755.536| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.39 r_work: 0.3317 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22732 Z= 0.144 Angle : 0.697 16.186 30982 Z= 0.332 Chirality : 0.045 0.366 3438 Planarity : 0.005 0.053 3896 Dihedral : 6.348 59.472 3376 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.48 % Allowed : 26.61 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.16), residues: 2700 helix: 0.64 (0.13), residues: 1626 sheet: -1.09 (0.61), residues: 58 loop : -1.89 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.023 0.001 TYR C 215 PHE 0.027 0.001 PHE D 520 TRP 0.015 0.001 TRP B 534 HIS 0.005 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (22702) covalent geometry : angle 0.67903 / 0.33 (30902) SS BOND : bond 0.00231 / 0.14 ( 10) SS BOND : angle 0.80675 / 0.45 ( 20) hydrogen bonds : bond 0.05161 / 3.37 ( 1129) hydrogen bonds : angle 4.42528 / 3.17 ( 3330) link_BETA1-4 : bond 0.00351 / 0.17 ( 4) link_BETA1-4 : angle 2.01133 / 1.13 ( 12) link_NAG-ASN : bond 0.00830 / 0.46 ( 16) link_NAG-ASN : angle 3.97070 / 2.40 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 269 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.7948 (t80) cc_final: 0.7614 (t80) REVERT: A 76 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: A 269 ASP cc_start: 0.8776 (p0) cc_final: 0.8486 (p0) REVERT: A 288 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7970 (ptpp) REVERT: A 297 MET cc_start: 0.8407 (ttm) cc_final: 0.7835 (mtp) REVERT: A 557 MET cc_start: 0.8158 (tmm) cc_final: 0.7942 (tmm) REVERT: A 560 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7576 (mp) REVERT: A 615 ASP cc_start: 0.8260 (p0) cc_final: 0.7952 (OUTLIER) REVERT: A 659 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8462 (mttt) REVERT: B 211 CYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7342 (m) REVERT: B 382 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7700 (p) REVERT: B 437 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7233 (tm-30) REVERT: B 530 TRP cc_start: 0.6367 (OUTLIER) cc_final: 0.5831 (m-90) REVERT: B 576 ILE cc_start: 0.7552 (tt) cc_final: 0.7076 (pt) REVERT: C 100 LEU cc_start: 0.8306 (mt) cc_final: 0.8077 (mp) REVERT: C 332 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7470 (tpp) REVERT: C 360 MET cc_start: 0.8102 (ptm) cc_final: 0.7807 (ptm) REVERT: C 560 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8166 (mp) REVERT: C 660 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8296 (t0) REVERT: C 723 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8419 (mp0) REVERT: D 34 LYS cc_start: 0.7287 (pptt) cc_final: 0.7037 (ptmm) REVERT: D 514 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8558 (t80) REVERT: D 583 TYR cc_start: 0.6253 (OUTLIER) cc_final: 0.5611 (t80) outliers start: 107 outliers final: 69 residues processed: 353 average time/residue: 0.4432 time to fit residues: 187.5054 Evaluate side-chains 339 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 258 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 530 TRP Chi-restraints excluded: chain B residue 534 TRP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 534 TRP Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 597 ILE Chi-restraints excluded: chain D residue 606 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 232 optimal weight: 0.0870 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS B 159 GLN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.217280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.162132 restraints weight = 26688.082| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.44 r_work: 0.3258 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22732 Z= 0.222 Angle : 0.769 13.746 30982 Z= 0.374 Chirality : 0.049 0.374 3438 Planarity : 0.005 0.079 3896 Dihedral : 6.619 59.539 3376 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.27 % Allowed : 26.86 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 2700 helix: 0.37 (0.13), residues: 1638 sheet: -1.30 (0.73), residues: 44 loop : -1.87 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 366 TYR 0.029 0.002 TYR C 215 PHE 0.028 0.002 PHE D 549 TRP 0.016 0.002 TRP A 163 HIS 0.008 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 (22702) covalent geometry : angle 0.75032 / 0.37 (30902) SS BOND : bond 0.00249 / 0.16 ( 10) SS BOND : angle 1.09883 / 0.62 ( 20) hydrogen bonds : bond 0.06249 / 4.07 ( 1129) hydrogen bonds : angle 4.54808 / 3.27 ( 3330) link_BETA1-4 : bond 0.00581 / 0.26 ( 4) link_BETA1-4 : angle 2.44668 / 1.35 ( 12) link_NAG-ASN : bond 0.00940 / 0.54 ( 16) link_NAG-ASN : angle 4.17238 / 2.56 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 271 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 72 PHE cc_start: 0.7994 (t80) cc_final: 0.7665 (t80) REVERT: A 76 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8086 (mp10) REVERT: A 557 MET cc_start: 0.8270 (tmm) cc_final: 0.8032 (tmm) REVERT: A 659 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8588 (mttt) REVERT: B 71 MET cc_start: 0.4492 (OUTLIER) cc_final: 0.4140 (mmp) REVERT: B 211 CYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7376 (m) REVERT: B 382 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7753 (p) REVERT: B 437 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7327 (tm-30) REVERT: B 452 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6966 (tmmt) REVERT: C 100 LEU cc_start: 0.8313 (mt) cc_final: 0.8081 (mp) REVERT: C 171 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: C 332 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7422 (tpp) REVERT: C 560 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8167 (mp) REVERT: C 660 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8279 (t0) REVERT: C 723 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: D 34 LYS cc_start: 0.7270 (pptt) cc_final: 0.7023 (ptmm) REVERT: D 279 PHE cc_start: 0.8111 (m-10) cc_final: 0.7787 (m-80) REVERT: D 583 TYR cc_start: 0.6237 (OUTLIER) cc_final: 0.5514 (t80) outliers start: 126 outliers final: 76 residues processed: 366 average time/residue: 0.4374 time to fit residues: 192.3729 Evaluate side-chains 344 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 256 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 452 LYS Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 534 TRP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 597 ILE Chi-restraints excluded: chain D residue 606 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 86 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 263 optimal weight: 10.0000 chunk 171 optimal weight: 0.0370 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS B 159 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.220086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.165567 restraints weight = 26936.715| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.41 r_work: 0.3320 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22732 Z= 0.138 Angle : 0.708 13.788 30982 Z= 0.336 Chirality : 0.045 0.366 3438 Planarity : 0.004 0.052 3896 Dihedral : 6.195 59.260 3375 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.97 % Allowed : 27.99 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 2700 helix: 0.69 (0.13), residues: 1630 sheet: -1.02 (0.62), residues: 58 loop : -1.74 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 644 TYR 0.027 0.001 TYR D 60 PHE 0.031 0.001 PHE D 520 TRP 0.030 0.001 TRP B 534 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (22702) covalent geometry : angle 0.69067 / 0.33 (30902) SS BOND : bond 0.00204 / 0.13 ( 10) SS BOND : angle 0.68915 / 0.38 ( 20) hydrogen bonds : bond 0.05023 / 3.29 ( 1129) hydrogen bonds : angle 4.41141 / 3.16 ( 3330) link_BETA1-4 : bond 0.00407 / 0.21 ( 4) link_BETA1-4 : angle 1.95011 / 1.11 ( 12) link_NAG-ASN : bond 0.00812 / 0.45 ( 16) link_NAG-ASN : angle 3.86256 / 2.32 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 266 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 VAL cc_start: 0.7475 (OUTLIER) cc_final: 0.7240 (t) REVERT: A 72 PHE cc_start: 0.7998 (t80) cc_final: 0.7663 (t80) REVERT: A 76 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: A 269 ASP cc_start: 0.8738 (p0) cc_final: 0.8440 (p0) REVERT: A 297 MET cc_start: 0.8320 (ttm) cc_final: 0.7846 (mtp) REVERT: A 439 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8438 (mt) REVERT: A 615 ASP cc_start: 0.8200 (p0) cc_final: 0.7950 (OUTLIER) REVERT: A 659 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8505 (mttt) REVERT: B 211 CYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7364 (m) REVERT: B 255 PHE cc_start: 0.5214 (OUTLIER) cc_final: 0.4604 (m-80) REVERT: B 382 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7726 (p) REVERT: B 437 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7331 (tm-30) REVERT: B 452 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6971 (tmmt) REVERT: C 100 LEU cc_start: 0.8328 (mt) cc_final: 0.8095 (mp) REVERT: C 332 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7512 (tpp) REVERT: C 560 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8135 (mp) REVERT: C 585 LEU cc_start: 0.8124 (mm) cc_final: 0.7776 (mm) REVERT: C 660 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8263 (t0) REVERT: C 723 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: D 34 LYS cc_start: 0.7252 (pptt) cc_final: 0.7016 (ptmm) REVERT: D 583 TYR cc_start: 0.6212 (OUTLIER) cc_final: 0.5515 (t80) outliers start: 95 outliers final: 63 residues processed: 344 average time/residue: 0.4512 time to fit residues: 185.5390 Evaluate side-chains 334 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 259 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 452 LYS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 534 TRP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 597 ILE Chi-restraints excluded: chain D residue 606 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 65 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 135 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 251 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS B 159 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.218446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.163648 restraints weight = 26789.013| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.38 r_work: 0.3286 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22732 Z= 0.177 Angle : 0.742 13.436 30982 Z= 0.356 Chirality : 0.047 0.366 3438 Planarity : 0.005 0.072 3896 Dihedral : 6.256 59.974 3374 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.68 % Allowed : 28.28 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2700 helix: 0.63 (0.13), residues: 1628 sheet: -1.06 (0.63), residues: 58 loop : -1.72 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.022 0.002 TYR C 183 PHE 0.029 0.001 PHE B 549 TRP 0.021 0.001 TRP B 534 HIS 0.006 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (22702) covalent geometry : angle 0.72426 / 0.35 (30902) SS BOND : bond 0.00227 / 0.14 ( 10) SS BOND : angle 0.88177 / 0.50 ( 20) hydrogen bonds : bond 0.05623 / 3.67 ( 1129) hydrogen bonds : angle 4.48168 / 3.22 ( 3330) link_BETA1-4 : bond 0.00453 / 0.21 ( 4) link_BETA1-4 : angle 2.17292 / 1.22 ( 12) link_NAG-ASN : bond 0.00885 / 0.50 ( 16) link_NAG-ASN : angle 3.97911 / 2.42 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 264 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 59 VAL cc_start: 0.7497 (OUTLIER) cc_final: 0.7253 (t) REVERT: A 72 PHE cc_start: 0.7997 (t80) cc_final: 0.7668 (t80) REVERT: A 76 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: A 269 ASP cc_start: 0.8810 (p0) cc_final: 0.8562 (p0) REVERT: A 297 MET cc_start: 0.8341 (ttm) cc_final: 0.7891 (mtp) REVERT: A 615 ASP cc_start: 0.8164 (p0) cc_final: 0.7917 (OUTLIER) REVERT: A 659 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8550 (mttt) REVERT: B 382 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7749 (p) REVERT: B 436 MET cc_start: 0.8005 (tpp) cc_final: 0.7801 (tpt) REVERT: B 437 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7126 (tm-30) REVERT: B 452 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6983 (tmmt) REVERT: B 583 TYR cc_start: 0.5921 (OUTLIER) cc_final: 0.4874 (t80) REVERT: C 100 LEU cc_start: 0.8339 (mt) cc_final: 0.8100 (mp) REVERT: C 171 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: C 228 HIS cc_start: 0.7912 (t-90) cc_final: 0.7472 (m-70) REVERT: C 332 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7488 (tpp) REVERT: C 560 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8127 (mp) REVERT: C 660 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8275 (t0) REVERT: D 34 LYS cc_start: 0.7192 (pptt) cc_final: 0.6957 (ptmm) REVERT: D 239 ILE cc_start: 0.7049 (pt) cc_final: 0.6618 (pp) REVERT: D 279 PHE cc_start: 0.8019 (m-10) cc_final: 0.7711 (m-80) REVERT: D 583 TYR cc_start: 0.6236 (OUTLIER) cc_final: 0.5664 (t80) outliers start: 88 outliers final: 64 residues processed: 337 average time/residue: 0.4518 time to fit residues: 181.8098 Evaluate side-chains 333 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 259 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 452 LYS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 583 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 ASP Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 530 TRP Chi-restraints excluded: chain D residue 534 TRP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 597 ILE Chi-restraints excluded: chain D residue 606 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 239 optimal weight: 1.9990 chunk 135 optimal weight: 20.0000 chunk 101 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 226 optimal weight: 0.0970 chunk 33 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 202 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS B 159 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.221202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.159216 restraints weight = 27083.416| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.15 r_work: 0.3364 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22732 Z= 0.128 Angle : 0.704 13.459 30982 Z= 0.334 Chirality : 0.045 0.357 3438 Planarity : 0.004 0.052 3896 Dihedral : 5.877 59.556 3373 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.14 % Allowed : 28.66 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2700 helix: 0.79 (0.13), residues: 1642 sheet: -0.92 (0.75), residues: 44 loop : -1.67 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.015 0.001 TYR A 516 PHE 0.032 0.001 PHE D 520 TRP 0.035 0.001 TRP B 534 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (22702) covalent geometry : angle 0.68880 / 0.33 (30902) SS BOND : bond 0.00186 / 0.12 ( 10) SS BOND : angle 0.58603 / 0.32 ( 20) hydrogen bonds : bond 0.04623 / 3.02 ( 1129) hydrogen bonds : angle 4.37252 / 3.14 ( 3330) link_BETA1-4 : bond 0.00414 / 0.21 ( 4) link_BETA1-4 : angle 1.77995 / 1.02 ( 12) link_NAG-ASN : bond 0.00793 / 0.44 ( 16) link_NAG-ASN : angle 3.71087 / 2.22 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9995.53 seconds wall clock time: 170 minutes 21.63 seconds (10221.63 seconds total)