Starting phenix.real_space_refine on Sat Jan 18 16:57:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v29_42902/01_2025/8v29_42902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v29_42902/01_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_42902/01_2025/8v29_42902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v29_42902/01_2025/8v29_42902.map" model { file = "/net/cci-nas-00/data/ceres_data/8v29_42902/01_2025/8v29_42902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v29_42902/01_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-5571/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: 8.19, per 1000 atoms: 0.66 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: 2.81 Conformation dependent library (CDL) restraints added in 1.5 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: 1.52 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: 4.77 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3971 1.35 - 1.46: 3084 1.46 - 1.58: 5627 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 12758 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG C 901 " pdb=" O5 NAG C 901 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 ... (remaining 12753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 16786 1.16 - 2.32: 424 2.32 - 3.48: 123 3.48 - 4.64: 14 4.64 - 5.80: 2 Bond angle restraints: 17349 Sorted by residual: angle pdb=" N SER B 42 " pdb=" CA SER B 42 " pdb=" C SER B 42 " ideal model delta sigma weight residual 108.34 111.36 -3.02 1.31e+00 5.83e-01 5.30e+00 angle pdb=" C PHE B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 121.61 124.52 -2.91 1.39e+00 5.18e-01 4.38e+00 angle pdb=" C GLU C 391 " pdb=" N SER C 392 " pdb=" CA SER C 392 " ideal model delta sigma weight residual 120.82 123.93 -3.11 1.50e+00 4.44e-01 4.30e+00 angle pdb=" N GLU C 579 " pdb=" CA GLU C 579 " pdb=" C GLU C 579 " ideal model delta sigma weight residual 114.04 111.65 2.39 1.24e+00 6.50e-01 3.72e+00 angle pdb=" C PRO B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 121.54 125.19 -3.65 1.91e+00 2.74e-01 3.65e+00 ... (remaining 17344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 7468 21.45 - 42.89: 320 42.89 - 64.34: 76 64.34 - 85.79: 20 85.79 - 107.23: 50 Dihedral angle restraints: 7934 sinusoidal: 3463 harmonic: 4471 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 670 " pdb=" CB CYS C 670 " ideal model delta sinusoidal sigma weight residual 93.00 19.20 73.80 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS B 458 " pdb=" SG CYS B 458 " pdb=" SG CYS B 466 " pdb=" CB CYS B 466 " ideal model delta sinusoidal sigma weight residual 93.00 20.12 72.88 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual 93.00 37.20 55.80 1 1.00e+01 1.00e-02 4.20e+01 ... (remaining 7931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1698 0.055 - 0.110: 257 0.110 - 0.165: 34 0.165 - 0.220: 1 0.220 - 0.275: 1 Chirality restraints: 1991 Sorted by residual: chirality pdb=" C1 NAG C 901 " pdb=" ND2 ASN C 303 " pdb=" C2 NAG C 901 " pdb=" O5 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG B 704 " pdb=" ND2 ASN B 383 " pdb=" C2 NAG B 704 " pdb=" O5 NAG B 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" C1 NAG B 702 " pdb=" ND2 ASN B 390 " pdb=" C2 NAG B 702 " pdb=" O5 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 1988 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 414 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO C 415 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 415 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 415 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 587 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO C 588 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 588 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 588 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 387 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO C 388 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 388 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 388 " -0.017 5.00e-02 4.00e+02 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1643 2.76 - 3.30: 11035 3.30 - 3.83: 19852 3.83 - 4.37: 21762 4.37 - 4.90: 38463 Nonbonded interactions: 92755 Sorted by model distance: nonbonded pdb=" OG SER B 229 " pdb=" OG1 THR B 243 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR B 369 " pdb=" OG1 THR B 399 " model vdw 2.299 3.040 nonbonded pdb=" O HIS B 425 " pdb=" OH TYR B 500 " model vdw 2.300 3.040 nonbonded pdb=" O SER B 489 " pdb=" OG SER B 489 " model vdw 2.312 3.040 nonbonded pdb=" O TRP B 539 " pdb=" OG1 THR B 575 " model vdw 2.315 3.040 ... (remaining 92750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.430 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.650 ------------------------------------------------------------------------------- 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 12758 Z= 0.159 Angle : 0.466 5.798 17349 Z= 0.245 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 *********************** 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 : 1.082 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: 0.3475 time to fit residues: 67.3069 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 : 1.292 ------------------------------------------------------------------------------- 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: 0.0070 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.120356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.104087 restraints weight = 85161.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.102210 restraints weight = 72792.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.101905 restraints weight = 68997.553| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12758 Z= 0.237 Angle : 0.619 7.314 17349 Z= 0.313 Chirality : 0.047 0.330 1991 Planarity : 0.004 0.046 2182 Dihedral : 13.371 83.306 2044 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.87 % Allowed : 10.01 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.28 (0.20), residues: 1514 helix: 0.75 (0.43), residues: 164 sheet: -0.44 (0.19), residues: 628 loop : -1.57 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 146 HIS 0.003 0.001 HIS B 167 PHE 0.025 0.002 PHE B 58 TYR 0.040 0.002 TYR B 453 ARG 0.004 0.001 ARG B 298 *********************** 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 69 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.7238 (ttp) cc_final: 0.6991 (ttm) REVERT: B 146 TRP cc_start: 0.6276 (p90) cc_final: 0.6036 (p90) REVERT: B 202 ASN cc_start: 0.5999 (OUTLIER) cc_final: 0.5690 (p0) REVERT: B 302 MET cc_start: 0.7790 (ptm) cc_final: 0.7467 (ptm) REVERT: B 352 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7829 (mmtt) REVERT: B 592 MET cc_start: 0.3787 (tpp) cc_final: 0.3221 (tpt) REVERT: C 653 MET cc_start: 0.6059 (mmp) cc_final: 0.5845 (mmp) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.2458 time to fit residues: 25.0749 Evaluate side-chains 56 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 1.431 ------------------------------------------------------------------------------- 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: 4.9990 chunk 119 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 34 optimal weight: 0.0980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.119515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.100947 restraints weight = 85154.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.098992 restraints weight = 62946.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.099211 restraints weight = 61036.817| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12758 Z= 0.192 Angle : 0.577 7.466 17349 Z= 0.288 Chirality : 0.045 0.312 1991 Planarity : 0.004 0.046 2182 Dihedral : 9.527 70.956 2044 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.31 % Allowed : 13.13 % Favored : 85.57 % 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: -0.91 (0.21), residues: 1514 helix: 1.38 (0.44), residues: 158 sheet: -0.17 (0.19), residues: 635 loop : -1.44 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 440 HIS 0.003 0.001 HIS A 199 PHE 0.022 0.001 PHE B 58 TYR 0.021 0.001 TYR B 453 ARG 0.006 0.000 ARG A 54 *********************** 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 70 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.7106 (ttp) cc_final: 0.6817 (ttm) REVERT: B 146 TRP cc_start: 0.6663 (p90) cc_final: 0.6296 (p90) REVERT: B 302 MET cc_start: 0.7726 (ptm) cc_final: 0.7518 (ptm) REVERT: B 592 MET cc_start: 0.3768 (tpp) cc_final: 0.3265 (tpt) REVERT: B 596 THR cc_start: 0.4340 (OUTLIER) cc_final: 0.3942 (m) REVERT: C 653 MET cc_start: 0.7032 (mmp) cc_final: 0.6793 (mmp) outliers start: 18 outliers final: 10 residues processed: 64 average time/residue: 0.2296 time to fit residues: 23.4532 Evaluate side-chains 53 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 B residue 596 THR 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: 2.9990 chunk 7 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 51 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN C 344 HIS C 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.119784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.101975 restraints weight = 84354.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.100344 restraints weight = 65201.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.100525 restraints weight = 51962.121| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12758 Z= 0.142 Angle : 0.528 8.204 17349 Z= 0.262 Chirality : 0.044 0.316 1991 Planarity : 0.003 0.046 2182 Dihedral : 7.305 59.997 2044 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.16 % Allowed : 14.07 % Favored : 84.77 % 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: -0.54 (0.21), residues: 1514 helix: 1.89 (0.44), residues: 152 sheet: -0.01 (0.19), residues: 641 loop : -1.16 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 440 HIS 0.002 0.001 HIS C 166 PHE 0.010 0.001 PHE B 58 TYR 0.013 0.001 TYR B 309 ARG 0.002 0.000 ARG B 483 *********************** 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: 16 poor density : 54 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8689 (tt) REVERT: B 55 MET cc_start: 0.3645 (tpp) cc_final: 0.3278 (tpt) REVERT: B 142 MET cc_start: 0.7131 (ttp) cc_final: 0.6904 (ttm) REVERT: B 440 TRP cc_start: 0.7690 (m100) cc_final: 0.7304 (m100) REVERT: B 592 MET cc_start: 0.4051 (tpp) cc_final: 0.3654 (tpp) REVERT: B 596 THR cc_start: 0.3159 (OUTLIER) cc_final: 0.2715 (m) REVERT: C 653 MET cc_start: 0.6086 (mmp) cc_final: 0.5739 (mmp) outliers start: 16 outliers final: 11 residues processed: 66 average time/residue: 0.2424 time to fit residues: 24.9788 Evaluate side-chains 54 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU 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 B residue 445 THR Chi-restraints excluded: chain B residue 596 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 82 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.114801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.095760 restraints weight = 82647.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.094131 restraints weight = 56739.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.094122 restraints weight = 50350.620| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12758 Z= 0.391 Angle : 0.754 8.522 17349 Z= 0.391 Chirality : 0.049 0.262 1991 Planarity : 0.005 0.061 2182 Dihedral : 7.484 58.058 2044 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.83 % Allowed : 14.79 % Favored : 82.38 % 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: -1.05 (0.21), residues: 1514 helix: 0.65 (0.42), residues: 157 sheet: -0.20 (0.20), residues: 636 loop : -1.44 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 212 HIS 0.013 0.002 HIS A 196 PHE 0.032 0.002 PHE C 217 TYR 0.020 0.002 TYR B 344 ARG 0.008 0.001 ARG A 75 *********************** 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 86 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 47 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: B 55 MET cc_start: 0.4019 (tpp) cc_final: 0.3603 (tpt) REVERT: B 142 MET cc_start: 0.7470 (ttp) cc_final: 0.7166 (ttm) REVERT: B 202 ASN cc_start: 0.5663 (OUTLIER) cc_final: 0.5022 (t0) REVERT: B 302 MET cc_start: 0.7831 (ptm) cc_final: 0.7459 (ptt) REVERT: B 490 LYS cc_start: 0.7372 (mmtt) cc_final: 0.6952 (mmtt) REVERT: B 592 MET cc_start: 0.4133 (tpp) cc_final: 0.3695 (tpp) REVERT: C 653 MET cc_start: 0.7143 (mmp) cc_final: 0.6901 (mmp) outliers start: 39 outliers final: 21 residues processed: 83 average time/residue: 0.2034 time to fit residues: 27.8988 Evaluate side-chains 67 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 414 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain 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 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 607 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 732 VAL 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: 10.0000 chunk 86 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 94 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** A 196 HIS B 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.116744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.098302 restraints weight = 84631.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.097061 restraints weight = 57432.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.097108 restraints weight = 50751.182| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12758 Z= 0.168 Angle : 0.577 11.835 17349 Z= 0.289 Chirality : 0.045 0.293 1991 Planarity : 0.004 0.052 2182 Dihedral : 6.689 51.693 2044 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.10 % Allowed : 16.32 % Favored : 81.58 % 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: -0.61 (0.21), residues: 1514 helix: 1.15 (0.43), residues: 162 sheet: 0.03 (0.20), residues: 635 loop : -1.13 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 440 HIS 0.003 0.001 HIS A 196 PHE 0.031 0.001 PHE B 72 TYR 0.012 0.001 TYR C 393 ARG 0.002 0.000 ARG A 61 *********************** 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 80 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 51 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.3998 (tpp) cc_final: 0.3670 (tpt) REVERT: B 142 MET cc_start: 0.7340 (ttp) cc_final: 0.7102 (ttm) REVERT: B 158 PHE cc_start: 0.5792 (m-80) cc_final: 0.5386 (m-80) REVERT: B 302 MET cc_start: 0.7453 (ptm) cc_final: 0.6443 (ptm) REVERT: B 592 MET cc_start: 0.4045 (tpp) cc_final: 0.3625 (tpp) REVERT: C 410 LEU cc_start: 0.6812 (tp) cc_final: 0.6503 (tt) REVERT: C 653 MET cc_start: 0.6682 (mmp) cc_final: 0.6365 (mmp) REVERT: C 825 MET cc_start: 0.6156 (ppp) cc_final: 0.5896 (ppp) outliers start: 29 outliers final: 19 residues processed: 75 average time/residue: 0.2051 time to fit residues: 25.2963 Evaluate side-chains 63 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 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 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 272 VAL Chi-restraints excluded: chain C residue 322 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.116369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.097702 restraints weight = 83528.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.096265 restraints weight = 56406.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.096614 restraints weight = 48285.091| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12758 Z= 0.185 Angle : 0.578 10.151 17349 Z= 0.288 Chirality : 0.045 0.294 1991 Planarity : 0.004 0.051 2182 Dihedral : 6.361 52.339 2044 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.25 % Allowed : 16.61 % 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: -0.51 (0.21), residues: 1514 helix: 1.28 (0.43), residues: 162 sheet: 0.06 (0.20), residues: 631 loop : -1.05 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 440 HIS 0.016 0.001 HIS A 196 PHE 0.030 0.001 PHE B 72 TYR 0.013 0.001 TYR A 151 ARG 0.004 0.000 ARG A 61 *********************** 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 77 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 46 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8953 (tt) REVERT: B 55 MET cc_start: 0.3923 (tpp) cc_final: 0.3487 (tpt) REVERT: B 142 MET cc_start: 0.7353 (ttp) cc_final: 0.7098 (ttm) REVERT: B 302 MET cc_start: 0.7466 (ptm) cc_final: 0.6979 (ptt) REVERT: B 592 MET cc_start: 0.4270 (tpp) cc_final: 0.3819 (tpp) REVERT: C 410 LEU cc_start: 0.6915 (tp) cc_final: 0.6579 (tt) REVERT: C 653 MET cc_start: 0.6716 (mmp) cc_final: 0.6409 (mmp) outliers start: 31 outliers final: 25 residues processed: 73 average time/residue: 0.2036 time to fit residues: 24.2780 Evaluate side-chains 70 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 44 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 146 LEU 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 425 HIS 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 272 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 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 827 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 34 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 137 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** A 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.117082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.098435 restraints weight = 83789.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.096647 restraints weight = 60187.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.096872 restraints weight = 58842.518| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12758 Z= 0.149 Angle : 0.547 9.437 17349 Z= 0.272 Chirality : 0.044 0.300 1991 Planarity : 0.004 0.050 2182 Dihedral : 6.002 51.619 2044 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.10 % Allowed : 16.68 % Favored : 81.22 % 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: -0.35 (0.22), residues: 1514 helix: 1.65 (0.44), residues: 156 sheet: 0.18 (0.20), residues: 627 loop : -1.00 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 440 HIS 0.005 0.001 HIS A 196 PHE 0.024 0.001 PHE B 72 TYR 0.010 0.001 TYR C 555 ARG 0.002 0.000 ARG C 221 *********************** 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 79 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 50 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8866 (tt) REVERT: B 55 MET cc_start: 0.3716 (tpp) cc_final: 0.3378 (tpt) REVERT: B 142 MET cc_start: 0.7232 (ttp) cc_final: 0.6973 (ttm) REVERT: B 302 MET cc_start: 0.7341 (ptm) cc_final: 0.6910 (ptt) REVERT: B 592 MET cc_start: 0.4247 (tpp) cc_final: 0.3808 (tpp) REVERT: C 653 MET cc_start: 0.6957 (mmp) cc_final: 0.6660 (mmp) REVERT: C 825 MET cc_start: 0.6176 (ppp) cc_final: 0.5934 (ppp) outliers start: 29 outliers final: 23 residues processed: 74 average time/residue: 0.2045 time to fit residues: 24.7710 Evaluate side-chains 71 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 146 LEU 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 244 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 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 Chi-restraints excluded: chain C residue 827 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 71 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 36 optimal weight: 0.0670 chunk 122 optimal weight: 8.9990 chunk 5 optimal weight: 0.0980 chunk 98 optimal weight: 0.0010 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 148 ASN C 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.118120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.099604 restraints weight = 84581.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.097979 restraints weight = 62293.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.098013 restraints weight = 51477.999| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12758 Z= 0.131 Angle : 0.535 9.773 17349 Z= 0.265 Chirality : 0.044 0.311 1991 Planarity : 0.004 0.048 2182 Dihedral : 5.569 51.868 2044 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.74 % Allowed : 17.04 % Favored : 81.22 % 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: -0.07 (0.22), residues: 1514 helix: 1.90 (0.44), residues: 150 sheet: 0.37 (0.20), residues: 638 loop : -0.83 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 457 HIS 0.009 0.001 HIS A 196 PHE 0.019 0.001 PHE B 72 TYR 0.020 0.001 TYR C 555 ARG 0.003 0.000 ARG C 666 *********************** 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 77 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8845 (tt) REVERT: A 202 MET cc_start: 0.7821 (tmm) cc_final: 0.7561 (tmm) REVERT: B 55 MET cc_start: 0.3912 (tpp) cc_final: 0.3582 (tpt) REVERT: B 142 MET cc_start: 0.7261 (ttp) cc_final: 0.7003 (ttm) REVERT: B 302 MET cc_start: 0.7167 (ptm) cc_final: 0.6278 (ptm) REVERT: B 352 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7852 (mmtt) REVERT: B 592 MET cc_start: 0.4268 (tpp) cc_final: 0.3825 (tpp) REVERT: C 203 TRP cc_start: 0.5754 (t60) cc_final: 0.5478 (t-100) REVERT: C 556 TRP cc_start: 0.6341 (p90) cc_final: 0.5871 (p90) REVERT: C 653 MET cc_start: 0.6687 (mmp) cc_final: 0.6400 (mmp) REVERT: C 825 MET cc_start: 0.6035 (ppp) cc_final: 0.5793 (ppp) outliers start: 24 outliers final: 18 residues processed: 73 average time/residue: 0.2305 time to fit residues: 26.9857 Evaluate side-chains 69 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 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 454 ILE Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 827 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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** B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.117527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.099106 restraints weight = 83464.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.097706 restraints weight = 58353.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.097692 restraints weight = 52145.646| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12758 Z= 0.150 Angle : 0.546 10.181 17349 Z= 0.270 Chirality : 0.044 0.302 1991 Planarity : 0.004 0.049 2182 Dihedral : 5.389 53.711 2044 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.89 % Allowed : 17.11 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.47 (0.43), residues: 158 sheet: 0.43 (0.20), residues: 630 loop : -0.76 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 457 HIS 0.013 0.001 HIS A 196 PHE 0.019 0.001 PHE B 72 TYR 0.034 0.001 TYR C 393 ARG 0.002 0.000 ARG A 147 ********************** 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 78 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8820 (tt) REVERT: B 55 MET cc_start: 0.3909 (tpp) cc_final: 0.3646 (tpt) REVERT: B 142 MET cc_start: 0.7308 (ttp) cc_final: 0.7064 (ttm) REVERT: B 302 MET cc_start: 0.7245 (ptm) cc_final: 0.6415 (ptm) REVERT: B 352 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7908 (mmtt) REVERT: B 592 MET cc_start: 0.4311 (tpp) cc_final: 0.3853 (tpp) REVERT: C 203 TRP cc_start: 0.5757 (t60) cc_final: 0.5505 (t-100) REVERT: C 399 MET cc_start: 0.6919 (ptm) cc_final: 0.6330 (ptp) REVERT: C 556 TRP cc_start: 0.6420 (p90) cc_final: 0.5966 (p90) REVERT: C 653 MET cc_start: 0.6603 (mmp) cc_final: 0.6296 (mmp) REVERT: C 825 MET cc_start: 0.6127 (ppp) cc_final: 0.5887 (ppp) outliers start: 26 outliers final: 25 residues processed: 75 average time/residue: 0.2268 time to fit residues: 27.2248 Evaluate side-chains 77 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 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 454 ILE Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 827 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4464 r_free = 0.4464 target = 0.117520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.099389 restraints weight = 83590.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.098034 restraints weight = 63272.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.098224 restraints weight = 51530.791| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12758 Z= 0.144 Angle : 0.534 10.539 17349 Z= 0.265 Chirality : 0.044 0.302 1991 Planarity : 0.004 0.048 2182 Dihedral : 5.235 53.403 2044 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.03 % Allowed : 16.90 % Favored : 81.07 % 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: 1.74 (0.45), residues: 152 sheet: 0.49 (0.20), residues: 632 loop : -0.72 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 457 HIS 0.015 0.001 HIS A 196 PHE 0.019 0.001 PHE B 72 TYR 0.031 0.001 TYR C 393 ARG 0.002 0.000 ARG A 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4535.55 seconds wall clock time: 82 minutes 14.50 seconds (4934.50 seconds total)