Starting phenix.real_space_refine on Wed Jul 30 15:56:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v29_42902/07_2025/8v29_42902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v29_42902/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v29_42902/07_2025/8v29_42902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v29_42902/07_2025/8v29_42902.map" model { file = "/net/cci-nas-00/data/ceres_data/8v29_42902/07_2025/8v29_42902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v29_42902/07_2025/8v29_42902.cif" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.24, per 1000 atoms: 0.74 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: 3.29 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.88 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: 5.65 Time building geometry restraints manager: 3.94 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: 5.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.730 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.060 ------------------------------------------------------------------------------- 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 : 5.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.19), 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 TRP 0.010 0.000 TRP A 212 HIS 0.001 0.000 HIS A 199 PHE 0.005 0.000 PHE A 95 TYR 0.007 0.000 TYR C 807 ARG 0.001 0.000 ARG A 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 14) link_NAG-ASN : angle 2.27280 ( 42) link_BETA1-4 : bond 0.00316 ( 5) link_BETA1-4 : angle 1.59469 ( 15) hydrogen bonds : bond 0.26579 ( 403) hydrogen bonds : angle 8.80117 ( 1131) SS BOND : bond 0.00162 ( 14) SS BOND : angle 0.78152 ( 28) covalent geometry : bond 0.00247 (12758) covalent geometry : angle 0.46555 (17349) *********************** 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 : 1.464 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: 0.3497 time to fit residues: 67.0959 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 : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 63 optimal weight: 0.0970 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 118 optimal weight: 0.0980 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- 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 = 0.4516 r_free = 0.4516 target = 0.120131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.102901 restraints weight = 84862.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.101146 restraints weight = 65825.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.101173 restraints weight = 58348.007| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12791 Z= 0.174 Angle : 0.660 9.254 17434 Z= 0.329 Chirality : 0.047 0.327 1991 Planarity : 0.004 0.047 2182 Dihedral : 12.868 81.048 2044 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.87 % Allowed : 10.59 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.20), residues: 1514 helix: 0.96 (0.43), residues: 158 sheet: -0.43 (0.19), residues: 629 loop : -1.57 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 146 HIS 0.004 0.001 HIS B 167 PHE 0.026 0.002 PHE C 217 TYR 0.036 0.002 TYR B 453 ARG 0.009 0.001 ARG C 666 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 14) link_NAG-ASN : angle 2.53250 ( 42) link_BETA1-4 : bond 0.00540 ( 5) link_BETA1-4 : angle 1.71675 ( 15) hydrogen bonds : bond 0.04568 ( 403) hydrogen bonds : angle 6.29823 ( 1131) SS BOND : bond 0.00569 ( 14) SS BOND : angle 1.08073 ( 28) covalent geometry : bond 0.00379 (12758) covalent geometry : angle 0.64589 (17349) *********************** 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 71 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.7078 (ttp) cc_final: 0.6792 (ttm) REVERT: B 146 TRP cc_start: 0.6204 (p90) cc_final: 0.5949 (p90) REVERT: B 202 ASN cc_start: 0.5881 (OUTLIER) cc_final: 0.5539 (p0) REVERT: B 302 MET cc_start: 0.7775 (ptm) cc_final: 0.7496 (ptm) REVERT: B 352 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7918 (mmtt) REVERT: B 592 MET cc_start: 0.3863 (tpp) cc_final: 0.3312 (tpt) REVERT: C 653 MET cc_start: 0.6231 (mmp) cc_final: 0.6001 (mmp) outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 0.2691 time to fit residues: 28.2647 Evaluate side-chains 55 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET 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 414 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 THR 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 55 optimal weight: 0.0980 chunk 119 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 150 optimal weight: 0.0000 chunk 94 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 137 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.118804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.100475 restraints weight = 85001.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.098403 restraints weight = 65523.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.098520 restraints weight = 54630.619| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12791 Z= 0.155 Angle : 0.606 9.073 17434 Z= 0.299 Chirality : 0.045 0.308 1991 Planarity : 0.004 0.048 2182 Dihedral : 9.520 70.480 2044 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.38 % Allowed : 13.34 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.20), residues: 1514 helix: 1.28 (0.44), residues: 157 sheet: -0.23 (0.19), residues: 634 loop : -1.43 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 440 HIS 0.004 0.001 HIS A 199 PHE 0.015 0.001 PHE B 44 TYR 0.021 0.001 TYR B 453 ARG 0.013 0.001 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 14) link_NAG-ASN : angle 2.51464 ( 42) link_BETA1-4 : bond 0.00239 ( 5) link_BETA1-4 : angle 1.56608 ( 15) hydrogen bonds : bond 0.04703 ( 403) hydrogen bonds : angle 5.87271 ( 1131) SS BOND : bond 0.00485 ( 14) SS BOND : angle 1.06130 ( 28) covalent geometry : bond 0.00338 (12758) covalent geometry : angle 0.59191 (17349) *********************** 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 74 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.3462 (tpp) cc_final: 0.3185 (tpt) REVERT: B 57 TYR cc_start: 0.5064 (t80) cc_final: 0.4852 (t80) REVERT: B 142 MET cc_start: 0.7284 (ttp) cc_final: 0.7024 (ttm) REVERT: B 302 MET cc_start: 0.7804 (ptm) cc_final: 0.7596 (ptm) REVERT: B 592 MET cc_start: 0.3802 (tpp) cc_final: 0.3452 (tpp) REVERT: C 624 MET cc_start: -0.0697 (ptm) cc_final: -0.0968 (ppp) REVERT: C 653 MET cc_start: 0.6878 (mmp) cc_final: 0.6610 (mmp) outliers start: 19 outliers final: 10 residues processed: 68 average time/residue: 0.2644 time to fit residues: 29.2107 Evaluate side-chains 53 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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 414 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 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 Chi-restraints excluded: chain C residue 672 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 202 ASN B 258 ASN C 344 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.119017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.101092 restraints weight = 84413.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.099592 restraints weight = 63047.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.099659 restraints weight = 52564.749| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12791 Z= 0.113 Angle : 0.564 9.065 17434 Z= 0.276 Chirality : 0.045 0.314 1991 Planarity : 0.003 0.048 2182 Dihedral : 7.473 59.821 2044 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.60 % Allowed : 13.92 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1514 helix: 1.60 (0.44), residues: 158 sheet: -0.06 (0.19), residues: 644 loop : -1.22 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 440 HIS 0.003 0.001 HIS B 41 PHE 0.012 0.001 PHE B 44 TYR 0.013 0.001 TYR B 453 ARG 0.002 0.000 ARG C 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 14) link_NAG-ASN : angle 2.57979 ( 42) link_BETA1-4 : bond 0.00389 ( 5) link_BETA1-4 : angle 1.56411 ( 15) hydrogen bonds : bond 0.04034 ( 403) hydrogen bonds : angle 5.51134 ( 1131) SS BOND : bond 0.00324 ( 14) SS BOND : angle 0.94352 ( 28) covalent geometry : bond 0.00247 (12758) covalent geometry : angle 0.54785 (17349) *********************** 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 70 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.3763 (tpp) cc_final: 0.3368 (tpt) REVERT: B 352 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8030 (mmtt) REVERT: B 440 TRP cc_start: 0.7590 (m100) cc_final: 0.7320 (m100) REVERT: B 592 MET cc_start: 0.4077 (tpp) cc_final: 0.3695 (tpp) REVERT: C 624 MET cc_start: -0.0346 (ptm) cc_final: -0.0807 (ppp) REVERT: C 653 MET cc_start: 0.6115 (mmp) cc_final: 0.5767 (mmp) outliers start: 22 outliers final: 18 residues processed: 67 average time/residue: 0.4029 time to fit residues: 45.0157 Evaluate side-chains 59 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 1.818 ------------------------------------------------------------------------------- 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 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 546 VAL Chi-restraints excluded: chain B residue 560 THR 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 468 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 82 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 118 optimal weight: 0.3980 chunk 48 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.116844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.098284 restraints weight = 84012.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.096840 restraints weight = 55042.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.096927 restraints weight = 49661.401| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12791 Z= 0.171 Angle : 0.616 8.827 17434 Z= 0.309 Chirality : 0.045 0.288 1991 Planarity : 0.004 0.057 2182 Dihedral : 6.927 54.401 2044 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.25 % Allowed : 15.23 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.21), residues: 1514 helix: 1.50 (0.44), residues: 157 sheet: -0.07 (0.19), residues: 662 loop : -1.19 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 440 HIS 0.005 0.001 HIS A 196 PHE 0.017 0.002 PHE C 217 TYR 0.011 0.001 TYR B 344 ARG 0.004 0.000 ARG A 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 14) link_NAG-ASN : angle 2.84791 ( 42) link_BETA1-4 : bond 0.00207 ( 5) link_BETA1-4 : angle 1.56631 ( 15) hydrogen bonds : bond 0.04665 ( 403) hydrogen bonds : angle 5.63234 ( 1131) SS BOND : bond 0.00497 ( 14) SS BOND : angle 1.01500 ( 28) covalent geometry : bond 0.00378 (12758) covalent geometry : angle 0.59876 (17349) *********************** 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 78 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 47 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8947 (tt) REVERT: B 55 MET cc_start: 0.3861 (tpp) cc_final: 0.3503 (tpt) REVERT: B 202 ASN cc_start: 0.5371 (OUTLIER) cc_final: 0.4588 (t0) REVERT: B 302 MET cc_start: 0.7621 (ptm) cc_final: 0.6648 (ptm) REVERT: B 592 MET cc_start: 0.4071 (tpp) cc_final: 0.3652 (tpp) REVERT: C 410 LEU cc_start: 0.6926 (tp) cc_final: 0.6648 (tt) REVERT: C 624 MET cc_start: -0.0391 (ptm) cc_final: -0.0772 (ppp) REVERT: C 653 MET cc_start: 0.6622 (mmp) cc_final: 0.6325 (mmp) outliers start: 31 outliers final: 18 residues processed: 73 average time/residue: 0.2856 time to fit residues: 33.9284 Evaluate side-chains 63 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU 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 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 315 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 805 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 23 optimal weight: 7.9990 chunk 86 optimal weight: 0.4980 chunk 43 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 HIS ** C 202 HIS ** 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 = 0.4391 r_free = 0.4391 target = 0.114124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.095285 restraints weight = 83409.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.093198 restraints weight = 59764.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.093329 restraints weight = 60367.546| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12791 Z= 0.247 Angle : 0.751 12.301 17434 Z= 0.381 Chirality : 0.048 0.254 1991 Planarity : 0.005 0.058 2182 Dihedral : 7.189 55.528 2044 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.12 % Allowed : 15.74 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.21), residues: 1514 helix: 0.67 (0.41), residues: 162 sheet: -0.19 (0.20), residues: 638 loop : -1.32 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP B 440 HIS 0.008 0.002 HIS A 196 PHE 0.028 0.002 PHE C 217 TYR 0.028 0.002 TYR B 481 ARG 0.010 0.001 ARG B 483 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 14) link_NAG-ASN : angle 3.13091 ( 42) link_BETA1-4 : bond 0.00306 ( 5) link_BETA1-4 : angle 1.75133 ( 15) hydrogen bonds : bond 0.05884 ( 403) hydrogen bonds : angle 6.28088 ( 1131) SS BOND : bond 0.01254 ( 14) SS BOND : angle 1.37142 ( 28) covalent geometry : bond 0.00547 (12758) covalent geometry : angle 0.73326 (17349) *********************** 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 97 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 54 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7199 (mp10) REVERT: B 55 MET cc_start: 0.4179 (tpp) cc_final: 0.3811 (tpt) REVERT: B 302 MET cc_start: 0.7692 (ptm) cc_final: 0.7142 (ptt) REVERT: B 490 LYS cc_start: 0.7288 (mmtt) cc_final: 0.6802 (mmtt) REVERT: B 592 MET cc_start: 0.4296 (tpp) cc_final: 0.3862 (tpp) REVERT: C 624 MET cc_start: -0.0216 (ptm) cc_final: -0.0575 (ppp) REVERT: C 653 MET cc_start: 0.7361 (mmp) cc_final: 0.7118 (mmp) outliers start: 43 outliers final: 26 residues processed: 91 average time/residue: 0.2314 time to fit residues: 34.3309 Evaluate side-chains 76 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU 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 182 CYS Chi-restraints excluded: chain B residue 399 THR 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 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 315 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 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 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 127 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.115714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.096705 restraints weight = 83692.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.095211 restraints weight = 52662.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.095442 restraints weight = 45197.670| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.4956 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= 0.126 Angle : 0.609 9.031 17434 Z= 0.302 Chirality : 0.045 0.288 1991 Planarity : 0.004 0.052 2182 Dihedral : 6.553 52.111 2044 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.54 % Allowed : 16.32 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1514 helix: 1.27 (0.44), residues: 162 sheet: -0.15 (0.20), residues: 660 loop : -1.13 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 440 HIS 0.003 0.001 HIS B 41 PHE 0.012 0.001 PHE B 58 TYR 0.016 0.001 TYR C 393 ARG 0.003 0.000 ARG A 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 14) link_NAG-ASN : angle 2.80973 ( 42) link_BETA1-4 : bond 0.00364 ( 5) link_BETA1-4 : angle 1.96400 ( 15) hydrogen bonds : bond 0.04743 ( 403) hydrogen bonds : angle 5.79282 ( 1131) SS BOND : bond 0.00416 ( 14) SS BOND : angle 1.21330 ( 28) covalent geometry : bond 0.00275 (12758) covalent geometry : angle 0.58936 (17349) *********************** 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 86 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 51 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.4085 (tpp) cc_final: 0.3748 (tpt) REVERT: B 302 MET cc_start: 0.7334 (ptm) cc_final: 0.6911 (ptt) REVERT: B 490 LYS cc_start: 0.7166 (mmtt) cc_final: 0.6633 (mmtt) REVERT: B 592 MET cc_start: 0.4272 (tpp) cc_final: 0.3836 (tpp) REVERT: C 410 LEU cc_start: 0.6923 (tp) cc_final: 0.6642 (tt) REVERT: C 624 MET cc_start: -0.0211 (ptm) cc_final: -0.0569 (ppp) REVERT: C 653 MET cc_start: 0.7165 (mmp) cc_final: 0.6910 (mmp) REVERT: C 825 MET cc_start: 0.6540 (ppp) cc_final: 0.6340 (ppp) outliers start: 35 outliers final: 23 residues processed: 80 average time/residue: 0.2346 time to fit residues: 30.9906 Evaluate side-chains 71 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 399 THR Chi-restraints excluded: chain B residue 406 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 144 LEU 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 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 819 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 133 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 142 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 77 optimal weight: 0.0040 chunk 137 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.116929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.098461 restraints weight = 83982.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.097091 restraints weight = 60918.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.097020 restraints weight = 54440.238| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.4880 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= 0.102 Angle : 0.575 10.179 17434 Z= 0.281 Chirality : 0.044 0.309 1991 Planarity : 0.004 0.050 2182 Dihedral : 5.942 52.096 2044 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.32 % Allowed : 17.11 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1514 helix: 1.50 (0.44), residues: 156 sheet: 0.08 (0.20), residues: 654 loop : -0.92 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 440 HIS 0.002 0.001 HIS B 41 PHE 0.010 0.001 PHE B 58 TYR 0.010 0.001 TYR C 555 ARG 0.002 0.000 ARG C 666 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 14) link_NAG-ASN : angle 2.63072 ( 42) link_BETA1-4 : bond 0.00420 ( 5) link_BETA1-4 : angle 2.12213 ( 15) hydrogen bonds : bond 0.03972 ( 403) hydrogen bonds : angle 5.37903 ( 1131) SS BOND : bond 0.00309 ( 14) SS BOND : angle 1.06525 ( 28) covalent geometry : bond 0.00220 (12758) covalent geometry : angle 0.55688 (17349) *********************** 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 87 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.4095 (tpp) cc_final: 0.3726 (tpt) REVERT: B 302 MET cc_start: 0.7211 (ptm) cc_final: 0.6443 (ptm) REVERT: B 592 MET cc_start: 0.4337 (tpp) cc_final: 0.3877 (tpp) REVERT: C 234 GLU cc_start: 0.7719 (mp0) cc_final: 0.7413 (mp0) REVERT: C 653 MET cc_start: 0.6635 (mmp) cc_final: 0.6343 (mmp) outliers start: 32 outliers final: 25 residues processed: 80 average time/residue: 0.2060 time to fit residues: 26.5339 Evaluate side-chains 76 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 192 CYS 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 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 494 ILE Chi-restraints excluded: chain B residue 560 THR 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 399 MET 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 Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 819 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 71 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 36 optimal weight: 0.0020 chunk 122 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 155 GLN A 196 HIS B 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.117088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.098720 restraints weight = 84538.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.097057 restraints weight = 62168.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.097182 restraints weight = 53024.113| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12791 Z= 0.099 Angle : 0.557 9.946 17434 Z= 0.274 Chirality : 0.044 0.305 1991 Planarity : 0.004 0.050 2182 Dihedral : 5.698 52.506 2044 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.10 % Allowed : 17.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1514 helix: 1.50 (0.44), residues: 156 sheet: 0.19 (0.20), residues: 659 loop : -0.87 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 457 HIS 0.004 0.001 HIS A 196 PHE 0.010 0.001 PHE B 58 TYR 0.023 0.001 TYR A 151 ARG 0.002 0.000 ARG B 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 14) link_NAG-ASN : angle 2.60911 ( 42) link_BETA1-4 : bond 0.00372 ( 5) link_BETA1-4 : angle 2.10619 ( 15) hydrogen bonds : bond 0.03863 ( 403) hydrogen bonds : angle 5.24486 ( 1131) SS BOND : bond 0.00314 ( 14) SS BOND : angle 0.99188 ( 28) covalent geometry : bond 0.00215 (12758) covalent geometry : angle 0.53800 (17349) *********************** 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 79 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 50 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.4097 (tpp) cc_final: 0.3719 (tpt) REVERT: B 302 MET cc_start: 0.7179 (ptm) cc_final: 0.6381 (ptm) REVERT: B 592 MET cc_start: 0.4321 (tpp) cc_final: 0.3867 (tpp) REVERT: C 234 GLU cc_start: 0.7700 (mp0) cc_final: 0.7396 (mp0) REVERT: C 653 MET cc_start: 0.6552 (mmp) cc_final: 0.6248 (mmp) outliers start: 29 outliers final: 26 residues processed: 74 average time/residue: 0.3315 time to fit residues: 41.5356 Evaluate side-chains 74 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 399 THR 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 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 399 MET 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 819 VAL Chi-restraints excluded: chain C residue 829 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 88 optimal weight: 0.0170 chunk 22 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 138 optimal weight: 30.0000 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.116870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.098757 restraints weight = 83550.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.096889 restraints weight = 67714.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.096941 restraints weight = 57255.258| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12791 Z= 0.104 Angle : 0.559 10.657 17434 Z= 0.274 Chirality : 0.043 0.301 1991 Planarity : 0.004 0.051 2182 Dihedral : 5.535 53.467 2044 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.32 % Allowed : 17.04 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.22), residues: 1514 helix: 1.49 (0.44), residues: 157 sheet: 0.28 (0.20), residues: 651 loop : -0.86 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 440 HIS 0.003 0.001 HIS A 196 PHE 0.008 0.001 PHE B 58 TYR 0.015 0.001 TYR A 151 ARG 0.002 0.000 ARG C 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 14) link_NAG-ASN : angle 2.56650 ( 42) link_BETA1-4 : bond 0.00359 ( 5) link_BETA1-4 : angle 2.07767 ( 15) hydrogen bonds : bond 0.03867 ( 403) hydrogen bonds : angle 5.21189 ( 1131) SS BOND : bond 0.00335 ( 14) SS BOND : angle 0.99007 ( 28) covalent geometry : bond 0.00231 (12758) covalent geometry : angle 0.54076 (17349) ********************** 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 80 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 48 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.4133 (tpp) cc_final: 0.3904 (tpt) REVERT: B 302 MET cc_start: 0.7242 (ptm) cc_final: 0.6453 (ptm) REVERT: B 438 MET cc_start: 0.4942 (ppp) cc_final: 0.3841 (ppp) REVERT: B 592 MET cc_start: 0.4319 (tpp) cc_final: 0.3865 (tpp) REVERT: C 234 GLU cc_start: 0.7741 (mp0) cc_final: 0.7423 (mp0) REVERT: C 653 MET cc_start: 0.6777 (mmp) cc_final: 0.6474 (mmp) outliers start: 32 outliers final: 27 residues processed: 76 average time/residue: 0.2847 time to fit residues: 35.5569 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 : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 196 HIS 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 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 494 ILE Chi-restraints excluded: chain B residue 560 THR 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 315 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 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 819 VAL Chi-restraints excluded: chain C residue 829 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 76 optimal weight: 8.9990 chunk 35 optimal weight: 0.3980 chunk 110 optimal weight: 0.7980 chunk 139 optimal weight: 0.0770 chunk 96 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 73 HIS ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 ASN C 420 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.117541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.099732 restraints weight = 83839.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.098338 restraints weight = 62083.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.098287 restraints weight = 52371.023| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12791 Z= 0.096 Angle : 0.563 10.558 17434 Z= 0.275 Chirality : 0.044 0.305 1991 Planarity : 0.004 0.050 2182 Dihedral : 5.344 52.899 2044 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.03 % Allowed : 17.40 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.22), residues: 1514 helix: 1.54 (0.44), residues: 157 sheet: 0.37 (0.20), residues: 642 loop : -0.72 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 440 HIS 0.004 0.001 HIS C 344 PHE 0.009 0.001 PHE A 95 TYR 0.014 0.001 TYR A 151 ARG 0.002 0.000 ARG C 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 14) link_NAG-ASN : angle 2.51624 ( 42) link_BETA1-4 : bond 0.00412 ( 5) link_BETA1-4 : angle 2.15505 ( 15) hydrogen bonds : bond 0.03650 ( 403) hydrogen bonds : angle 5.06630 ( 1131) SS BOND : bond 0.00429 ( 14) SS BOND : angle 0.91309 ( 28) covalent geometry : bond 0.00207 (12758) covalent geometry : angle 0.54572 (17349) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5549.17 seconds wall clock time: 103 minutes 43.20 seconds (6223.20 seconds total)