Starting phenix.real_space_refine on Sat Aug 23 14:00:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v29_42902/08_2025/8v29_42902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v29_42902/08_2025/8v29_42902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v29_42902/08_2025/8v29_42902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v29_42902/08_2025/8v29_42902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v29_42902/08_2025/8v29_42902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v29_42902/08_2025/8v29_42902.map" } resolution = 3.99 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= -0.000 sd= 0.010 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 56 5.16 5 C 7901 2.51 5 N 2089 2.21 5 O 2411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12457 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1376 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 8, 'TRANS': 163} Chain breaks: 1 Chain: "B" Number of atoms: 4695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4695 Classifications: {'peptide': 586} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 551} Chain: "C" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6120 Classifications: {'peptide': 766} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 726} Chain breaks: 1 Chain: "D" 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: "E" 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: "F" 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: "G" 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: "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: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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 Time building chain proxies: 3.25, per 1000 atoms: 0.26 Number of scatterers: 12457 At special positions: 0 Unit cell: (137.6, 163.4, 229.62, 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 56 16.00 O 2411 8.00 N 2089 7.00 C 7901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 458 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 82 " - pdb=" SG CYS C 90 " distance=2.03 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 341 " - pdb=" SG CYS C 351 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 655 " - pdb=" SG CYS C 704 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 670 " distance=2.03 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 701 " - " ASN B 131 " " NAG B 702 " - " ASN B 390 " " NAG B 703 " - " ASN B 227 " " NAG B 704 " - " ASN B 383 " " NAG B 705 " - " ASN B 379 " " NAG B 706 " - " ASN B 83 " " NAG C 901 " - " ASN C 303 " " NAG C 902 " - " ASN C 489 " " NAG C 903 " - " ASN C 445 " " NAG D 1 " - " ASN A 100 " " NAG E 1 " - " ASN B 43 " " NAG F 1 " - " ASN C 407 " " NAG G 1 " - " ASN C 426 " " NAG H 1 " - " ASN C 243 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 609.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2892 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 30 sheets defined 14.0% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 51 through 63 removed outlier: 4.589A pdb=" N ASP A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) Proline residue: A 58 - end of helix Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 83 through 90 Processing helix chain 'A' and resid 92 through 117 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 158 Proline residue: A 141 - end of helix removed outlier: 3.903A pdb=" N ASP A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 212 removed outlier: 3.842A pdb=" N LYS A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 215 through 218 Processing helix chain 'B' and resid 247 through 251 removed outlier: 4.236A pdb=" N SER B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 543 through 548 removed outlier: 4.317A pdb=" N ASN B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 210 through 214 removed outlier: 3.642A pdb=" N ALA C 214 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.845A pdb=" N ARG C 365 " --> pdb=" O VAL C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 392 Processing helix chain 'C' and resid 560 through 565 Processing helix chain 'C' and resid 748 through 753 removed outlier: 3.826A pdb=" N ARG C 753 " --> pdb=" O VAL C 749 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.765A pdb=" N SER B 87 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 68 removed outlier: 4.009A pdb=" N TYR B 116 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 105 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASN B 114 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 181 through 183 removed outlier: 8.247A pdb=" N LYS B 221 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 136 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 171 removed outlier: 5.839A pdb=" N SER B 162 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP B 171 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU B 160 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B 201 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 205 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 168 through 171 removed outlier: 5.839A pdb=" N SER B 162 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP B 171 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU B 160 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B 201 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 212 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 226 through 231 removed outlier: 6.106A pdb=" N ASN B 227 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR B 245 " --> pdb=" O ASN B 227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 240 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 286 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 284 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.630A pdb=" N MET B 302 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 317 " --> pdb=" O PHE B 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 332 through 336 Processing sheet with id=AA9, first strand: chain 'B' and resid 377 through 382 removed outlier: 4.009A pdb=" N ASP B 365 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 428 through 434 removed outlier: 4.629A pdb=" N LEU B 430 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU B 442 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA B 432 " --> pdb=" O TRP B 440 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP B 440 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 480 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 469 through 474 removed outlier: 3.745A pdb=" N ASP B 469 " --> pdb=" O TRP B 457 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 471 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 458 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 525 through 530 removed outlier: 6.635A pdb=" N VAL B 536 " --> pdb=" O LYS B 528 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 535 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR B 577 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 566 through 571 removed outlier: 3.503A pdb=" N THR B 566 " --> pdb=" O TYR B 558 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR B 558 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 568 " --> pdb=" O ILE B 556 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN B 553 " --> pdb=" O TYR B 595 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR B 595 " --> pdb=" O ASN B 553 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 594 " --> pdb=" O LYS B 601 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 601 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 566 through 571 removed outlier: 3.503A pdb=" N THR B 566 " --> pdb=" O TYR B 558 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR B 558 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 568 " --> pdb=" O ILE B 556 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN B 553 " --> pdb=" O TYR B 595 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR B 595 " --> pdb=" O ASN B 553 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 97 through 101 removed outlier: 8.634A pdb=" N SER C 133 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N CYS C 55 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 78 through 79 removed outlier: 3.751A pdb=" N ASP C 78 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU C 109 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS C 82 " --> pdb=" O THR C 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 78 through 79 removed outlier: 3.751A pdb=" N ASP C 78 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 123 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 121 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 141 through 147 removed outlier: 7.234A pdb=" N ILE C 141 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASN C 158 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C 143 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP C 157 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 186 through 193 removed outlier: 3.556A pdb=" N LYS C 186 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS C 216 " --> pdb=" O ILE C 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 254 through 255 Processing sheet with id=AC3, first strand: chain 'C' and resid 260 through 262 removed outlier: 6.601A pdb=" N ILE C 261 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE C 327 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASN C 313 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE C 282 " --> pdb=" O ASN C 313 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL C 315 " --> pdb=" O ALA C 280 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA C 280 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR C 317 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA C 280 " --> pdb=" O CYS C 287 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 337 through 343 removed outlier: 4.337A pdb=" N LEU C 339 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N SER C 352 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N CYS C 341 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE C 350 " --> pdb=" O CYS C 341 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N THR C 343 " --> pdb=" O GLU C 348 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLU C 348 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 379 through 381 removed outlier: 3.567A pdb=" N THR C 409 " --> pdb=" O VAL C 372 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 437 through 445 removed outlier: 5.686A pdb=" N SER C 438 " --> pdb=" O HIS C 454 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS C 454 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE C 444 " --> pdb=" O ALA C 448 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 455 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER C 490 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY C 457 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU C 488 " --> pdb=" O GLY C 457 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 478 through 485 removed outlier: 3.976A pdb=" N ARG C 508 " --> pdb=" O GLU C 469 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 471 " --> pdb=" O THR C 506 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 541 through 545 removed outlier: 3.788A pdb=" N LEU C 552 " --> pdb=" O ILE C 596 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 596 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 584 through 588 removed outlier: 3.568A pdb=" N SER C 574 " --> pdb=" O SER C 606 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 607 " --> pdb=" O SER C 619 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER C 619 " --> pdb=" O VAL C 607 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 673 through 678 removed outlier: 3.554A pdb=" N ILE C 659 " --> pdb=" O ARG C 675 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASP C 656 " --> pdb=" O CYS C 704 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS C 704 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 658 " --> pdb=" O TYR C 702 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS C 662 " --> pdb=" O ASN C 698 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN C 698 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG C 713 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLY C 703 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU C 711 " --> pdb=" O GLY C 703 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLU C 634 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N TYR C 718 " --> pdb=" O GLU C 634 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C 636 " --> pdb=" O TYR C 718 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N GLN C 635 " --> pdb=" O THR C 646 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR C 646 " --> pdb=" O GLN C 635 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL C 637 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU C 644 " --> pdb=" O VAL C 637 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY C 642 " --> pdb=" O MET C 639 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 643 " --> pdb=" O ILE C 686 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 686 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 684 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 730 through 735 removed outlier: 3.526A pdb=" N GLU C 733 " --> pdb=" O LEU C 741 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU C 741 " --> pdb=" O GLU C 733 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE C 740 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE C 798 " --> pdb=" O ILE C 740 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 796 " --> pdb=" O VAL C 742 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 783 through 788 removed outlier: 3.651A pdb=" N PHE C 763 " --> pdb=" O LYS C 784 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 786 " --> pdb=" O PHE C 761 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 761 " --> pdb=" O LYS C 786 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY C 758 " --> pdb=" O TYR C 814 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR C 814 " --> pdb=" O GLY C 758 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 764 " --> pdb=" O HIS C 808 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N TYR C 807 " --> pdb=" O TYR C 826 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TYR C 826 " --> pdb=" O TYR C 807 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU C 809 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER C 824 " --> pdb=" O LEU C 809 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C 811 " --> pdb=" O GLU C 822 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU C 822 " --> pdb=" O LEU C 811 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA C 813 " --> pdb=" O GLY C 820 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 818 " --> pdb=" O THR C 815 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1131 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: 2.61 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3971 1.35 - 1.46: 3084 1.46 - 1.58: 5627 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 12758 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG C 901 " pdb=" O5 NAG C 901 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 ... (remaining 12753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 16786 1.16 - 2.32: 424 2.32 - 3.48: 123 3.48 - 4.64: 14 4.64 - 5.80: 2 Bond angle restraints: 17349 Sorted by residual: angle pdb=" N SER B 42 " pdb=" CA SER B 42 " pdb=" C SER B 42 " ideal model delta sigma weight residual 108.34 111.36 -3.02 1.31e+00 5.83e-01 5.30e+00 angle pdb=" C PHE B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 121.61 124.52 -2.91 1.39e+00 5.18e-01 4.38e+00 angle pdb=" C GLU C 391 " pdb=" N SER C 392 " pdb=" CA SER C 392 " ideal model delta sigma weight residual 120.82 123.93 -3.11 1.50e+00 4.44e-01 4.30e+00 angle pdb=" N GLU C 579 " pdb=" CA GLU C 579 " pdb=" C GLU C 579 " ideal model delta sigma weight residual 114.04 111.65 2.39 1.24e+00 6.50e-01 3.72e+00 angle pdb=" C PRO B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 121.54 125.19 -3.65 1.91e+00 2.74e-01 3.65e+00 ... (remaining 17344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 7468 21.45 - 42.89: 320 42.89 - 64.34: 76 64.34 - 85.79: 20 85.79 - 107.23: 50 Dihedral angle restraints: 7934 sinusoidal: 3463 harmonic: 4471 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 670 " pdb=" CB CYS C 670 " ideal model delta sinusoidal sigma weight residual 93.00 19.20 73.80 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS B 458 " pdb=" SG CYS B 458 " pdb=" SG CYS B 466 " pdb=" CB CYS B 466 " ideal model delta sinusoidal sigma weight residual 93.00 20.12 72.88 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual 93.00 37.20 55.80 1 1.00e+01 1.00e-02 4.20e+01 ... (remaining 7931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1698 0.055 - 0.110: 257 0.110 - 0.165: 34 0.165 - 0.220: 1 0.220 - 0.275: 1 Chirality restraints: 1991 Sorted by residual: chirality pdb=" C1 NAG C 901 " pdb=" ND2 ASN C 303 " pdb=" C2 NAG C 901 " pdb=" O5 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG B 704 " pdb=" ND2 ASN B 383 " pdb=" C2 NAG B 704 " pdb=" O5 NAG B 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" C1 NAG B 702 " pdb=" ND2 ASN B 390 " pdb=" C2 NAG B 702 " pdb=" O5 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 1988 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 414 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO C 415 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 415 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 415 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 587 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO C 588 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 588 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 588 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 387 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO C 388 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 388 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 388 " -0.017 5.00e-02 4.00e+02 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1643 2.76 - 3.30: 11035 3.30 - 3.83: 19852 3.83 - 4.37: 21762 4.37 - 4.90: 38463 Nonbonded interactions: 92755 Sorted by model distance: nonbonded pdb=" OG SER B 229 " pdb=" OG1 THR B 243 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR B 369 " pdb=" OG1 THR B 399 " model vdw 2.299 3.040 nonbonded pdb=" O HIS B 425 " pdb=" OH TYR B 500 " model vdw 2.300 3.040 nonbonded pdb=" O SER B 489 " pdb=" OG SER B 489 " model vdw 2.312 3.040 nonbonded pdb=" O TRP B 539 " pdb=" OG1 THR B 575 " model vdw 2.315 3.040 ... (remaining 92750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.180 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 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 : 0.002 0.037 12791 Z= 0.125 Angle : 0.481 8.791 17434 Z= 0.248 Chirality : 0.042 0.275 1991 Planarity : 0.003 0.041 2182 Dihedral : 15.961 107.235 5000 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -2.01 (0.19), residues: 1514 helix: -0.16 (0.41), residues: 166 sheet: -0.90 (0.19), residues: 622 loop : -1.98 (0.20), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.007 0.000 TYR C 807 PHE 0.005 0.000 PHE A 95 TRP 0.010 0.000 TRP A 212 HIS 0.001 0.000 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00247 (12758) covalent geometry : angle 0.46555 (17349) SS BOND : bond 0.00162 ( 14) SS BOND : angle 0.78152 ( 28) hydrogen bonds : bond 0.26579 ( 403) hydrogen bonds : angle 8.80117 ( 1131) link_BETA1-4 : bond 0.00316 ( 5) link_BETA1-4 : angle 1.59469 ( 15) link_NAG-ASN : bond 0.00458 ( 14) link_NAG-ASN : angle 2.27280 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.7270 (ttp) cc_final: 0.6979 (ttm) REVERT: B 302 MET cc_start: 0.8206 (ptm) cc_final: 0.7445 (ptt) REVERT: B 440 TRP cc_start: 0.7582 (m100) cc_final: 0.7316 (m100) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1533 time to fit residues: 29.4136 Evaluate side-chains 58 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 43 GLN A 137 GLN A 155 GLN A 186 GLN B 153 HIS B 167 HIS B 202 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 ASN B 541 GLN C 201 HIS ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN C 648 HIS C 729 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.120840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.104335 restraints weight = 85577.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.102848 restraints weight = 70784.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.103265 restraints weight = 57500.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.103192 restraints weight = 47313.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.103311 restraints weight = 46784.108| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12791 Z= 0.147 Angle : 0.638 9.223 17434 Z= 0.316 Chirality : 0.047 0.337 1991 Planarity : 0.004 0.045 2182 Dihedral : 12.644 81.435 2044 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.80 % Allowed : 10.08 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -1.18 (0.20), residues: 1514 helix: 0.96 (0.44), residues: 158 sheet: -0.42 (0.19), residues: 632 loop : -1.48 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 302 TYR 0.036 0.002 TYR B 453 PHE 0.023 0.002 PHE C 217 TRP 0.030 0.002 TRP B 146 HIS 0.004 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00324 (12758) covalent geometry : angle 0.62467 (17349) SS BOND : bond 0.00516 ( 14) SS BOND : angle 1.02460 ( 28) hydrogen bonds : bond 0.04514 ( 403) hydrogen bonds : angle 6.23349 ( 1131) link_BETA1-4 : bond 0.00688 ( 5) link_BETA1-4 : angle 1.62122 ( 15) link_NAG-ASN : bond 0.00457 ( 14) link_NAG-ASN : angle 2.48392 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.7250 (ttp) cc_final: 0.7016 (ttm) REVERT: B 146 TRP cc_start: 0.5988 (p90) cc_final: 0.5741 (p90) REVERT: B 302 MET cc_start: 0.7831 (ptm) cc_final: 0.7439 (ptt) REVERT: B 352 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7862 (mmtt) REVERT: B 592 MET cc_start: 0.4051 (tpp) cc_final: 0.3560 (tpt) REVERT: C 653 MET cc_start: 0.5307 (mmp) cc_final: 0.5053 (mmp) outliers start: 11 outliers final: 8 residues processed: 71 average time/residue: 0.1165 time to fit residues: 12.4411 Evaluate side-chains 53 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 555 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.116325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.097490 restraints weight = 83885.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.095961 restraints weight = 62908.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.095081 restraints weight = 67159.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.095177 restraints weight = 68019.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.095444 restraints weight = 51572.599| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 12791 Z= 0.237 Angle : 0.736 8.615 17434 Z= 0.373 Chirality : 0.049 0.281 1991 Planarity : 0.005 0.053 2182 Dihedral : 8.754 63.833 2044 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.39 % Allowed : 14.00 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -1.20 (0.20), residues: 1514 helix: 0.72 (0.43), residues: 151 sheet: -0.35 (0.19), residues: 640 loop : -1.51 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 54 TYR 0.022 0.002 TYR B 453 PHE 0.024 0.002 PHE C 217 TRP 0.037 0.003 TRP B 440 HIS 0.011 0.002 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00523 (12758) covalent geometry : angle 0.72075 (17349) SS BOND : bond 0.00647 ( 14) SS BOND : angle 1.41031 ( 28) hydrogen bonds : bond 0.06089 ( 403) hydrogen bonds : angle 6.25594 ( 1131) link_BETA1-4 : bond 0.00337 ( 5) link_BETA1-4 : angle 1.68696 ( 15) link_NAG-ASN : bond 0.00606 ( 14) link_NAG-ASN : angle 2.83581 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 53 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7476 (ttm) cc_final: 0.6767 (ttm) REVERT: B 55 MET cc_start: 0.3812 (tpp) cc_final: 0.3456 (tpt) REVERT: B 142 MET cc_start: 0.7523 (ttp) cc_final: 0.7307 (ttm) REVERT: B 202 ASN cc_start: 0.6270 (OUTLIER) cc_final: 0.5660 (p0) REVERT: B 592 MET cc_start: 0.3909 (tpp) cc_final: 0.3538 (tpp) REVERT: C 653 MET cc_start: 0.7558 (mmp) cc_final: 0.7349 (mmp) outliers start: 33 outliers final: 19 residues processed: 81 average time/residue: 0.0889 time to fit residues: 11.5038 Evaluate side-chains 59 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 76 optimal weight: 0.0050 chunk 46 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 19 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS B 226 HIS ** B 258 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 = 0.4481 r_free = 0.4481 target = 0.118347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.099779 restraints weight = 84540.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.098231 restraints weight = 61614.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.098074 restraints weight = 57563.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.098299 restraints weight = 50531.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.098392 restraints weight = 44449.493| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12791 Z= 0.109 Angle : 0.580 9.208 17434 Z= 0.285 Chirality : 0.045 0.311 1991 Planarity : 0.004 0.049 2182 Dihedral : 7.340 54.913 2044 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.03 % Allowed : 14.87 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.70 (0.21), residues: 1514 helix: 1.45 (0.45), residues: 151 sheet: -0.04 (0.19), residues: 633 loop : -1.25 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.018 0.001 TYR B 57 PHE 0.017 0.001 PHE B 58 TRP 0.029 0.001 TRP B 440 HIS 0.003 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00235 (12758) covalent geometry : angle 0.56271 (17349) SS BOND : bond 0.00457 ( 14) SS BOND : angle 0.99221 ( 28) hydrogen bonds : bond 0.04240 ( 403) hydrogen bonds : angle 5.60188 ( 1131) link_BETA1-4 : bond 0.00378 ( 5) link_BETA1-4 : angle 1.68127 ( 15) link_NAG-ASN : bond 0.00498 ( 14) link_NAG-ASN : angle 2.69952 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 52 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.3715 (tpp) cc_final: 0.3372 (tpt) REVERT: B 142 MET cc_start: 0.7256 (ttp) cc_final: 0.7007 (ttm) REVERT: B 202 ASN cc_start: 0.6374 (OUTLIER) cc_final: 0.5907 (p0) REVERT: B 440 TRP cc_start: 0.7869 (m100) cc_final: 0.7640 (m100) REVERT: B 455 LEU cc_start: 0.7158 (mt) cc_final: 0.6599 (tt) REVERT: B 592 MET cc_start: 0.4085 (tpp) cc_final: 0.3686 (tpp) REVERT: C 653 MET cc_start: 0.6557 (mmp) cc_final: 0.6239 (mmp) outliers start: 28 outliers final: 19 residues processed: 76 average time/residue: 0.1074 time to fit residues: 12.9092 Evaluate side-chains 65 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 805 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 65 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.115900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.097123 restraints weight = 84161.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.095382 restraints weight = 58357.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.095567 restraints weight = 50941.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.095547 restraints weight = 46521.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.095652 restraints weight = 42432.146| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12791 Z= 0.182 Angle : 0.649 9.900 17434 Z= 0.324 Chirality : 0.046 0.279 1991 Planarity : 0.004 0.057 2182 Dihedral : 6.921 55.543 2044 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.83 % Allowed : 16.17 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.83 (0.21), residues: 1514 helix: 0.99 (0.43), residues: 151 sheet: -0.15 (0.19), residues: 648 loop : -1.23 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 61 TYR 0.014 0.002 TYR B 344 PHE 0.020 0.002 PHE C 217 TRP 0.014 0.002 TRP B 440 HIS 0.007 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00404 (12758) covalent geometry : angle 0.63082 (17349) SS BOND : bond 0.00596 ( 14) SS BOND : angle 1.16205 ( 28) hydrogen bonds : bond 0.05005 ( 403) hydrogen bonds : angle 5.78295 ( 1131) link_BETA1-4 : bond 0.00265 ( 5) link_BETA1-4 : angle 1.65616 ( 15) link_NAG-ASN : bond 0.00581 ( 14) link_NAG-ASN : angle 2.96944 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 52 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: B 55 MET cc_start: 0.4068 (tpp) cc_final: 0.3677 (tpt) REVERT: B 142 MET cc_start: 0.7357 (ttp) cc_final: 0.7093 (ttm) REVERT: B 158 PHE cc_start: 0.5709 (m-80) cc_final: 0.5382 (m-80) REVERT: B 202 ASN cc_start: 0.6490 (OUTLIER) cc_final: 0.6027 (p0) REVERT: B 490 LYS cc_start: 0.7364 (mmtt) cc_final: 0.6918 (mmtt) REVERT: B 592 MET cc_start: 0.4223 (tpp) cc_final: 0.3779 (tpp) REVERT: C 653 MET cc_start: 0.6950 (mmp) cc_final: 0.6676 (mmp) outliers start: 39 outliers final: 26 residues processed: 87 average time/residue: 0.0918 time to fit residues: 13.2802 Evaluate side-chains 76 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 819 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.116787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.098044 restraints weight = 84016.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.096677 restraints weight = 56268.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.096802 restraints weight = 47990.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.096835 restraints weight = 45492.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.096755 restraints weight = 46253.754| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12791 Z= 0.116 Angle : 0.574 11.014 17434 Z= 0.282 Chirality : 0.044 0.296 1991 Planarity : 0.004 0.056 2182 Dihedral : 6.481 51.906 2044 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.61 % Allowed : 16.68 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.49 (0.21), residues: 1514 helix: 1.31 (0.44), residues: 156 sheet: 0.10 (0.20), residues: 629 loop : -1.04 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.010 0.001 TYR C 555 PHE 0.011 0.001 PHE C 217 TRP 0.039 0.001 TRP B 440 HIS 0.015 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00255 (12758) covalent geometry : angle 0.55518 (17349) SS BOND : bond 0.00451 ( 14) SS BOND : angle 1.04865 ( 28) hydrogen bonds : bond 0.04230 ( 403) hydrogen bonds : angle 5.51506 ( 1131) link_BETA1-4 : bond 0.00349 ( 5) link_BETA1-4 : angle 1.84177 ( 15) link_NAG-ASN : bond 0.00480 ( 14) link_NAG-ASN : angle 2.78140 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 50 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.3946 (tpp) cc_final: 0.3640 (tpt) REVERT: B 142 MET cc_start: 0.7306 (ttp) cc_final: 0.7071 (ttm) REVERT: B 202 ASN cc_start: 0.6378 (OUTLIER) cc_final: 0.5941 (p0) REVERT: B 592 MET cc_start: 0.4277 (tpp) cc_final: 0.3855 (tpp) REVERT: C 399 MET cc_start: 0.7213 (ptm) cc_final: 0.6836 (ptp) REVERT: C 653 MET cc_start: 0.6914 (mmp) cc_final: 0.6582 (mmp) outliers start: 36 outliers final: 28 residues processed: 84 average time/residue: 0.0916 time to fit residues: 12.9458 Evaluate side-chains 77 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 48 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 827 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 86 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 118 optimal weight: 0.0970 chunk 76 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.113778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.095136 restraints weight = 83364.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.093180 restraints weight = 57786.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.092775 restraints weight = 58727.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.092958 restraints weight = 50494.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.092999 restraints weight = 45549.218| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12791 Z= 0.253 Angle : 0.734 9.031 17434 Z= 0.373 Chirality : 0.048 0.251 1991 Planarity : 0.005 0.059 2182 Dihedral : 6.967 57.033 2044 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.34 % Allowed : 17.26 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.90 (0.21), residues: 1514 helix: 0.63 (0.42), residues: 156 sheet: -0.16 (0.20), residues: 651 loop : -1.25 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 479 TYR 0.022 0.002 TYR C 406 PHE 0.028 0.002 PHE C 217 TRP 0.067 0.003 TRP B 440 HIS 0.006 0.002 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00564 (12758) covalent geometry : angle 0.71573 (17349) SS BOND : bond 0.00701 ( 14) SS BOND : angle 1.23895 ( 28) hydrogen bonds : bond 0.05759 ( 403) hydrogen bonds : angle 6.24700 ( 1131) link_BETA1-4 : bond 0.00265 ( 5) link_BETA1-4 : angle 1.94975 ( 15) link_NAG-ASN : bond 0.00635 ( 14) link_NAG-ASN : angle 3.12733 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 53 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.4217 (tpp) cc_final: 0.4015 (tpt) REVERT: B 142 MET cc_start: 0.7544 (ttp) cc_final: 0.7257 (ttm) REVERT: B 202 ASN cc_start: 0.6966 (OUTLIER) cc_final: 0.6583 (p0) REVERT: B 352 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8107 (mmtt) REVERT: B 592 MET cc_start: 0.4342 (tpp) cc_final: 0.3888 (tpp) REVERT: C 399 MET cc_start: 0.8057 (ptm) cc_final: 0.7847 (ptm) REVERT: C 410 LEU cc_start: 0.7266 (tp) cc_final: 0.6829 (tt) REVERT: C 653 MET cc_start: 0.7502 (mmp) cc_final: 0.7257 (mmp) REVERT: C 743 LYS cc_start: 0.8676 (tptt) cc_final: 0.7946 (mmtt) outliers start: 46 outliers final: 34 residues processed: 94 average time/residue: 0.0861 time to fit residues: 13.0569 Evaluate side-chains 86 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 51 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 825 MET Chi-restraints excluded: chain C residue 827 VAL Chi-restraints excluded: chain C residue 829 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 137 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.114343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.095904 restraints weight = 83102.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.093977 restraints weight = 57492.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.094100 restraints weight = 54481.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.094159 restraints weight = 45220.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.094254 restraints weight = 41316.819| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12791 Z= 0.179 Angle : 0.659 10.020 17434 Z= 0.329 Chirality : 0.046 0.276 1991 Planarity : 0.004 0.061 2182 Dihedral : 6.582 52.455 2044 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.12 % Allowed : 18.06 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.79 (0.21), residues: 1514 helix: 1.12 (0.43), residues: 150 sheet: -0.22 (0.20), residues: 660 loop : -1.13 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 61 TYR 0.014 0.002 TYR C 826 PHE 0.018 0.002 PHE C 217 TRP 0.036 0.002 TRP B 440 HIS 0.005 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00400 (12758) covalent geometry : angle 0.64087 (17349) SS BOND : bond 0.00517 ( 14) SS BOND : angle 1.13640 ( 28) hydrogen bonds : bond 0.05053 ( 403) hydrogen bonds : angle 6.03421 ( 1131) link_BETA1-4 : bond 0.00177 ( 5) link_BETA1-4 : angle 2.02808 ( 15) link_NAG-ASN : bond 0.00506 ( 14) link_NAG-ASN : angle 2.91041 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 50 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7119 (ptp) cc_final: 0.6752 (ptp) REVERT: B 55 MET cc_start: 0.4271 (tpp) cc_final: 0.4013 (tpt) REVERT: B 142 MET cc_start: 0.7455 (ttp) cc_final: 0.7199 (ttm) REVERT: B 202 ASN cc_start: 0.6891 (OUTLIER) cc_final: 0.6518 (p0) REVERT: B 352 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8119 (mmtt) REVERT: B 592 MET cc_start: 0.4395 (tpp) cc_final: 0.3932 (tpp) REVERT: C 399 MET cc_start: 0.8055 (ptm) cc_final: 0.7831 (ptm) REVERT: C 653 MET cc_start: 0.7017 (mmp) cc_final: 0.6755 (mmp) outliers start: 43 outliers final: 32 residues processed: 86 average time/residue: 0.0788 time to fit residues: 11.4794 Evaluate side-chains 83 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 50 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 827 VAL Chi-restraints excluded: chain C residue 829 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 78 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN C 143 ASN C 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.115808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.097046 restraints weight = 83373.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.095614 restraints weight = 58895.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.095606 restraints weight = 51432.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.095703 restraints weight = 45991.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.095777 restraints weight = 41137.250| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12791 Z= 0.111 Angle : 0.587 10.191 17434 Z= 0.290 Chirality : 0.044 0.299 1991 Planarity : 0.004 0.057 2182 Dihedral : 6.048 52.156 2044 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.68 % Allowed : 18.27 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.44 (0.21), residues: 1514 helix: 1.83 (0.45), residues: 144 sheet: 0.01 (0.20), residues: 639 loop : -0.97 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 71 TYR 0.011 0.001 TYR C 223 PHE 0.009 0.001 PHE C 217 TRP 0.026 0.001 TRP B 440 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00241 (12758) covalent geometry : angle 0.56741 (17349) SS BOND : bond 0.00513 ( 14) SS BOND : angle 1.09007 ( 28) hydrogen bonds : bond 0.04250 ( 403) hydrogen bonds : angle 5.61508 ( 1131) link_BETA1-4 : bond 0.00394 ( 5) link_BETA1-4 : angle 2.19087 ( 15) link_NAG-ASN : bond 0.00529 ( 14) link_NAG-ASN : angle 2.72179 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 57 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.4221 (tpp) cc_final: 0.4002 (tpt) REVERT: B 142 MET cc_start: 0.7369 (ttp) cc_final: 0.7140 (ttm) REVERT: B 202 ASN cc_start: 0.6762 (OUTLIER) cc_final: 0.6452 (p0) REVERT: B 352 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7974 (mmtt) REVERT: B 438 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.5359 (ppp) REVERT: B 592 MET cc_start: 0.4333 (tpp) cc_final: 0.3865 (tpp) REVERT: C 399 MET cc_start: 0.7783 (ptm) cc_final: 0.7565 (ptm) REVERT: C 653 MET cc_start: 0.7104 (mmp) cc_final: 0.6830 (mmp) outliers start: 37 outliers final: 30 residues processed: 88 average time/residue: 0.0895 time to fit residues: 12.9008 Evaluate side-chains 84 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 616 SER Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 7 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.114175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.095159 restraints weight = 83455.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.093449 restraints weight = 53825.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.093467 restraints weight = 49650.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.093579 restraints weight = 45562.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.093583 restraints weight = 41848.209| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12791 Z= 0.174 Angle : 0.673 12.518 17434 Z= 0.335 Chirality : 0.046 0.278 1991 Planarity : 0.004 0.060 2182 Dihedral : 6.156 54.779 2044 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.90 % Allowed : 18.49 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.64 (0.21), residues: 1514 helix: 1.25 (0.44), residues: 151 sheet: -0.15 (0.19), residues: 661 loop : -1.00 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 510 TYR 0.015 0.002 TYR C 826 PHE 0.018 0.002 PHE C 217 TRP 0.016 0.002 TRP C 556 HIS 0.004 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00392 (12758) covalent geometry : angle 0.65378 (17349) SS BOND : bond 0.00533 ( 14) SS BOND : angle 1.73745 ( 28) hydrogen bonds : bond 0.04942 ( 403) hydrogen bonds : angle 5.82659 ( 1131) link_BETA1-4 : bond 0.00171 ( 5) link_BETA1-4 : angle 2.10444 ( 15) link_NAG-ASN : bond 0.00531 ( 14) link_NAG-ASN : angle 2.82393 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 51 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.4248 (tpp) cc_final: 0.3969 (tpt) REVERT: B 142 MET cc_start: 0.7480 (ttp) cc_final: 0.7250 (ttm) REVERT: B 202 ASN cc_start: 0.6937 (OUTLIER) cc_final: 0.6627 (p0) REVERT: B 352 LYS cc_start: 0.8374 (mmtt) cc_final: 0.8053 (mmtt) REVERT: B 592 MET cc_start: 0.4268 (tpp) cc_final: 0.3800 (tpp) REVERT: C 399 MET cc_start: 0.8015 (ptm) cc_final: 0.7783 (ptm) REVERT: C 653 MET cc_start: 0.7375 (mmp) cc_final: 0.7089 (mmp) outliers start: 40 outliers final: 34 residues processed: 87 average time/residue: 0.0856 time to fit residues: 12.3496 Evaluate side-chains 84 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 49 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 616 SER Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 120 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.114923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.095614 restraints weight = 83729.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.094079 restraints weight = 53886.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.094121 restraints weight = 47530.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.094132 restraints weight = 48331.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.094146 restraints weight = 40568.112| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12791 Z= 0.134 Angle : 0.629 12.202 17434 Z= 0.312 Chirality : 0.045 0.289 1991 Planarity : 0.004 0.059 2182 Dihedral : 5.948 53.007 2044 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.97 % Allowed : 18.49 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.57 (0.21), residues: 1514 helix: 1.41 (0.44), residues: 151 sheet: -0.08 (0.20), residues: 647 loop : -0.99 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 61 TYR 0.013 0.001 TYR C 826 PHE 0.013 0.001 PHE C 217 TRP 0.010 0.001 TRP C 517 HIS 0.005 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00300 (12758) covalent geometry : angle 0.60950 (17349) SS BOND : bond 0.00571 ( 14) SS BOND : angle 1.68322 ( 28) hydrogen bonds : bond 0.04553 ( 403) hydrogen bonds : angle 5.66363 ( 1131) link_BETA1-4 : bond 0.00279 ( 5) link_BETA1-4 : angle 2.21267 ( 15) link_NAG-ASN : bond 0.00512 ( 14) link_NAG-ASN : angle 2.70536 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2813.91 seconds wall clock time: 49 minutes 16.71 seconds (2956.71 seconds total)