Starting phenix.real_space_refine on Mon Dec 30 07:27:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v29_42902/12_2024/8v29_42902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v29_42902/12_2024/8v29_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_42902/12_2024/8v29_42902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v29_42902/12_2024/8v29_42902.map" model { file = "/net/cci-nas-00/data/ceres_data/8v29_42902/12_2024/8v29_42902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v29_42902/12_2024/8v29_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-5532/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: 8.07, per 1000 atoms: 0.65 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: 2.78 Conformation dependent library (CDL) restraints added in 1.6 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: 1.81 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: 4.73 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3971 1.35 - 1.46: 3084 1.46 - 1.58: 5627 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 12758 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG C 901 " pdb=" O5 NAG C 901 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 ... (remaining 12753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 16786 1.16 - 2.32: 424 2.32 - 3.48: 123 3.48 - 4.64: 14 4.64 - 5.80: 2 Bond angle restraints: 17349 Sorted by residual: angle pdb=" N SER B 42 " pdb=" CA SER B 42 " pdb=" C SER B 42 " ideal model delta sigma weight residual 108.34 111.36 -3.02 1.31e+00 5.83e-01 5.30e+00 angle pdb=" C PHE B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 121.61 124.52 -2.91 1.39e+00 5.18e-01 4.38e+00 angle pdb=" C GLU C 391 " pdb=" N SER C 392 " pdb=" CA SER C 392 " ideal model delta sigma weight residual 120.82 123.93 -3.11 1.50e+00 4.44e-01 4.30e+00 angle pdb=" N GLU C 579 " pdb=" CA GLU C 579 " pdb=" C GLU C 579 " ideal model delta sigma weight residual 114.04 111.65 2.39 1.24e+00 6.50e-01 3.72e+00 angle pdb=" C PRO B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 121.54 125.19 -3.65 1.91e+00 2.74e-01 3.65e+00 ... (remaining 17344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 7468 21.45 - 42.89: 320 42.89 - 64.34: 76 64.34 - 85.79: 20 85.79 - 107.23: 50 Dihedral angle restraints: 7934 sinusoidal: 3463 harmonic: 4471 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 670 " pdb=" CB CYS C 670 " ideal model delta sinusoidal sigma weight residual 93.00 19.20 73.80 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS B 458 " pdb=" SG CYS B 458 " pdb=" SG CYS B 466 " pdb=" CB CYS B 466 " ideal model delta sinusoidal sigma weight residual 93.00 20.12 72.88 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual 93.00 37.20 55.80 1 1.00e+01 1.00e-02 4.20e+01 ... (remaining 7931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1698 0.055 - 0.110: 257 0.110 - 0.165: 34 0.165 - 0.220: 1 0.220 - 0.275: 1 Chirality restraints: 1991 Sorted by residual: chirality pdb=" C1 NAG C 901 " pdb=" ND2 ASN C 303 " pdb=" C2 NAG C 901 " pdb=" O5 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG B 704 " pdb=" ND2 ASN B 383 " pdb=" C2 NAG B 704 " pdb=" O5 NAG B 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" C1 NAG B 702 " pdb=" ND2 ASN B 390 " pdb=" C2 NAG B 702 " pdb=" O5 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 1988 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 414 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO C 415 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 415 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 415 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 587 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO C 588 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 588 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 588 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 387 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO C 388 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 388 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 388 " -0.017 5.00e-02 4.00e+02 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1643 2.76 - 3.30: 11035 3.30 - 3.83: 19852 3.83 - 4.37: 21762 4.37 - 4.90: 38463 Nonbonded interactions: 92755 Sorted by model distance: nonbonded pdb=" OG SER B 229 " pdb=" OG1 THR B 243 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR B 369 " pdb=" OG1 THR B 399 " model vdw 2.299 3.040 nonbonded pdb=" O HIS B 425 " pdb=" OH TYR B 500 " model vdw 2.300 3.040 nonbonded pdb=" O SER B 489 " pdb=" OG SER B 489 " model vdw 2.312 3.040 nonbonded pdb=" O TRP B 539 " pdb=" OG1 THR B 575 " model vdw 2.315 3.040 ... (remaining 92750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 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: 0.100 Set scattering table: 0.120 Process input model: 31.270 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.140 ------------------------------------------------------------------------------- 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 : 1.410 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: 0.3552 time to fit residues: 67.9986 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 : 1.407 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 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 : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.7270 (ttp) cc_final: 0.6970 (ttm) REVERT: B 202 ASN cc_start: 0.5876 (OUTLIER) cc_final: 0.5600 (p0) REVERT: B 302 MET cc_start: 0.8023 (ptm) cc_final: 0.7768 (ptm) REVERT: B 352 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7704 (mmtt) REVERT: B 592 MET cc_start: 0.3685 (tpp) cc_final: 0.3192 (tpt) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.2594 time to fit residues: 26.1160 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 : 1.703 ------------------------------------------------------------------------------- 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 76 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12758 Z= 0.385 Angle : 0.782 8.571 17349 Z= 0.403 Chirality : 0.051 0.289 1991 Planarity : 0.005 0.064 2182 Dihedral : 9.420 64.956 2044 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.61 % Allowed : 13.85 % Favored : 83.54 % Cbeta Deviations : 0.07 % 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: -1.37 (0.20), residues: 1514 helix: 0.50 (0.41), residues: 157 sheet: -0.48 (0.19), residues: 649 loop : -1.61 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 440 HIS 0.012 0.002 HIS A 196 PHE 0.029 0.003 PHE C 217 TYR 0.027 0.002 TYR B 453 ARG 0.016 0.001 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 87 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 51 time to evaluate : 1.501 Fit side-chains revert: symmetry clash REVERT: B 55 MET cc_start: 0.3766 (tpp) cc_final: 0.3364 (tpt) REVERT: B 142 MET cc_start: 0.7645 (ttp) cc_final: 0.7342 (ttm) REVERT: B 202 ASN cc_start: 0.6036 (OUTLIER) cc_final: 0.4968 (t0) REVERT: B 592 MET cc_start: 0.4068 (tpp) cc_final: 0.3692 (tpp) outliers start: 36 outliers final: 20 residues processed: 81 average time/residue: 0.2243 time to fit residues: 28.8911 Evaluate side-chains 65 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 805 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 5.9990 chunk 103 optimal weight: 0.0670 chunk 71 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 overall best weight: 2.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 104 ASN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12758 Z= 0.296 Angle : 0.670 10.374 17349 Z= 0.341 Chirality : 0.047 0.290 1991 Planarity : 0.004 0.053 2182 Dihedral : 7.862 53.156 2044 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.76 % Allowed : 16.32 % Favored : 80.93 % 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: -1.12 (0.21), residues: 1514 helix: 0.85 (0.42), residues: 157 sheet: -0.31 (0.20), residues: 630 loop : -1.47 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 440 HIS 0.009 0.001 HIS A 196 PHE 0.033 0.002 PHE B 72 TYR 0.013 0.002 TYR B 453 ARG 0.005 0.001 ARG A 61 *********************** 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 90 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 52 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: B 55 MET cc_start: 0.4070 (tpp) cc_final: 0.3644 (tpt) REVERT: B 142 MET cc_start: 0.7463 (ttp) cc_final: 0.7117 (ttm) REVERT: B 490 LYS cc_start: 0.7377 (mmtt) cc_final: 0.6986 (mmtt) REVERT: B 592 MET cc_start: 0.4137 (tpp) cc_final: 0.3725 (tpp) REVERT: C 743 LYS cc_start: 0.8274 (tptt) cc_final: 0.7613 (mmtt) outliers start: 38 outliers final: 23 residues processed: 85 average time/residue: 0.2171 time to fit residues: 29.5782 Evaluate side-chains 71 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 131 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12758 Z= 0.275 Angle : 0.654 10.288 17349 Z= 0.333 Chirality : 0.046 0.270 1991 Planarity : 0.004 0.057 2182 Dihedral : 7.295 53.294 2044 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.34 % Allowed : 17.91 % Favored : 78.75 % 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: -1.02 (0.21), residues: 1514 helix: 0.97 (0.42), residues: 156 sheet: -0.27 (0.20), residues: 618 loop : -1.38 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 440 HIS 0.017 0.002 HIS A 196 PHE 0.027 0.002 PHE B 72 TYR 0.015 0.002 TYR C 393 ARG 0.006 0.001 ARG A 61 *********************** 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 96 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 50 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.4342 (tpp) cc_final: 0.3904 (tpt) REVERT: B 142 MET cc_start: 0.7477 (ttp) cc_final: 0.7177 (ttm) REVERT: B 592 MET cc_start: 0.4313 (tpp) cc_final: 0.3884 (tpp) REVERT: C 743 LYS cc_start: 0.8362 (tptt) cc_final: 0.7676 (mmtt) outliers start: 46 outliers final: 26 residues processed: 91 average time/residue: 0.2232 time to fit residues: 32.7838 Evaluate side-chains 73 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 431 VAL 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 829 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 9.9990 chunk 131 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 0.0980 chunk 76 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12758 Z= 0.159 Angle : 0.589 10.005 17349 Z= 0.291 Chirality : 0.045 0.302 1991 Planarity : 0.004 0.058 2182 Dihedral : 6.624 52.854 2044 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.39 % Allowed : 18.42 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1514 helix: 1.19 (0.43), residues: 162 sheet: -0.07 (0.20), residues: 634 loop : -1.17 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 440 HIS 0.016 0.001 HIS A 196 PHE 0.018 0.001 PHE B 72 TYR 0.014 0.001 TYR C 555 ARG 0.003 0.000 ARG B 479 *********************** 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 87 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 54 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.4112 (tpp) cc_final: 0.3769 (tpt) REVERT: B 142 MET cc_start: 0.7368 (ttp) cc_final: 0.7093 (ttm) REVERT: B 592 MET cc_start: 0.4287 (tpp) cc_final: 0.3864 (tpp) REVERT: C 743 LYS cc_start: 0.8522 (tptt) cc_final: 0.7858 (mmtt) outliers start: 33 outliers final: 27 residues processed: 84 average time/residue: 0.1983 time to fit residues: 27.5466 Evaluate side-chains 76 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 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 325 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 616 SER Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 795 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 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 148 ASN A 196 HIS C 202 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.4949 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= 0.191 Angle : 0.589 11.892 17349 Z= 0.291 Chirality : 0.044 0.291 1991 Planarity : 0.004 0.052 2182 Dihedral : 6.429 52.158 2044 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.19 % Allowed : 18.27 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1514 helix: 1.25 (0.43), residues: 162 sheet: -0.03 (0.20), residues: 626 loop : -1.14 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 440 HIS 0.006 0.001 HIS A 196 PHE 0.017 0.001 PHE B 72 TYR 0.022 0.001 TYR B 396 ARG 0.003 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 96 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 52 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.4179 (tpp) cc_final: 0.3749 (tpt) REVERT: B 142 MET cc_start: 0.7384 (ttp) cc_final: 0.7132 (ttm) REVERT: B 438 MET cc_start: 0.5972 (ttt) cc_final: 0.5674 (ppp) REVERT: B 592 MET cc_start: 0.4304 (tpp) cc_final: 0.3850 (tpp) outliers start: 44 outliers final: 36 residues processed: 91 average time/residue: 0.2086 time to fit residues: 30.9185 Evaluate side-chains 84 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 48 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 616 SER Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 819 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN C 143 ASN C 202 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12758 Z= 0.253 Angle : 0.636 10.723 17349 Z= 0.322 Chirality : 0.045 0.274 1991 Planarity : 0.004 0.055 2182 Dihedral : 6.435 54.537 2044 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.55 % Allowed : 18.56 % Favored : 77.88 % 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: -0.76 (0.21), residues: 1514 helix: 1.39 (0.44), residues: 150 sheet: -0.21 (0.20), residues: 633 loop : -1.13 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP B 440 HIS 0.006 0.001 HIS A 196 PHE 0.020 0.002 PHE B 72 TYR 0.016 0.002 TYR B 396 ARG 0.008 0.001 ARG A 147 *********************** 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 101 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 52 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6657 (ttm) REVERT: B 55 MET cc_start: 0.4221 (tpp) cc_final: 0.3900 (tpt) REVERT: B 142 MET cc_start: 0.7556 (ttp) cc_final: 0.7299 (ttm) REVERT: B 202 ASN cc_start: 0.6660 (OUTLIER) cc_final: 0.6385 (p0) REVERT: B 440 TRP cc_start: 0.7916 (m100) cc_final: 0.7473 (m100) REVERT: B 592 MET cc_start: 0.4290 (tpp) cc_final: 0.3841 (tpp) outliers start: 49 outliers final: 38 residues processed: 94 average time/residue: 0.2149 time to fit residues: 32.3563 Evaluate side-chains 91 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 51 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 616 SER Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 825 MET Chi-restraints excluded: chain C residue 829 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 135 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS C 143 ASN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.6611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 12758 Z= 0.511 Angle : 0.896 11.444 17349 Z= 0.465 Chirality : 0.053 0.458 1991 Planarity : 0.006 0.062 2182 Dihedral : 7.622 57.481 2044 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.70 % Allowed : 18.64 % Favored : 77.66 % 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: -1.54 (0.21), residues: 1514 helix: 0.05 (0.40), residues: 144 sheet: -0.60 (0.20), residues: 641 loop : -1.59 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 440 HIS 0.015 0.002 HIS A 196 PHE 0.037 0.003 PHE C 217 TYR 0.026 0.003 TYR B 396 ARG 0.008 0.001 ARG A 61 *********************** 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 104 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 53 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.4611 (tpp) cc_final: 0.4228 (tpt) REVERT: B 142 MET cc_start: 0.7672 (ttp) cc_final: 0.7320 (ttm) REVERT: B 202 ASN cc_start: 0.7108 (OUTLIER) cc_final: 0.6872 (p0) REVERT: B 352 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7913 (mmtt) REVERT: B 592 MET cc_start: 0.4422 (tpp) cc_final: 0.3929 (tpp) REVERT: C 167 ARG cc_start: 0.7010 (mtt180) cc_final: 0.6775 (tmt-80) REVERT: C 827 VAL cc_start: 0.2143 (OUTLIER) cc_final: 0.1869 (m) outliers start: 51 outliers final: 38 residues processed: 96 average time/residue: 0.2229 time to fit residues: 33.6354 Evaluate side-chains 90 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 50 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 827 VAL Chi-restraints excluded: chain C residue 829 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 HIS C 202 HIS C 344 HIS C 420 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12758 Z= 0.236 Angle : 0.670 10.591 17349 Z= 0.337 Chirality : 0.047 0.276 1991 Planarity : 0.004 0.059 2182 Dihedral : 6.810 58.461 2044 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.83 % Allowed : 19.65 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.16 (0.21), residues: 1514 helix: 1.02 (0.43), residues: 144 sheet: -0.51 (0.20), residues: 639 loop : -1.33 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 333 HIS 0.016 0.001 HIS A 196 PHE 0.028 0.002 PHE B 332 TYR 0.017 0.002 TYR B 396 ARG 0.003 0.000 ARG A 61 ********************** 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 90 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 51 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.4528 (tpp) cc_final: 0.4179 (tpt) REVERT: B 142 MET cc_start: 0.7502 (ttp) cc_final: 0.7268 (ttm) REVERT: B 202 ASN cc_start: 0.6873 (OUTLIER) cc_final: 0.6569 (p0) REVERT: B 333 TRP cc_start: 0.7751 (t-100) cc_final: 0.7517 (t-100) REVERT: B 592 MET cc_start: 0.4458 (tpp) cc_final: 0.3961 (tpp) REVERT: C 827 VAL cc_start: 0.2040 (OUTLIER) cc_final: 0.1675 (m) outliers start: 39 outliers final: 34 residues processed: 85 average time/residue: 0.2083 time to fit residues: 28.8348 Evaluate side-chains 83 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 47 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 827 VAL Chi-restraints excluded: chain C residue 829 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.113497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.094265 restraints weight = 82283.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.092906 restraints weight = 52501.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.092887 restraints weight = 47139.996| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.6438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12758 Z= 0.226 Angle : 0.657 12.550 17349 Z= 0.331 Chirality : 0.047 0.283 1991 Planarity : 0.004 0.058 2182 Dihedral : 6.455 53.684 2044 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.97 % Allowed : 19.65 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.04 (0.21), residues: 1514 helix: 0.98 (0.43), residues: 157 sheet: -0.37 (0.20), residues: 622 loop : -1.32 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 333 HIS 0.014 0.001 HIS A 196 PHE 0.021 0.002 PHE B 332 TYR 0.015 0.002 TYR C 79 ARG 0.004 0.000 ARG A 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2528.73 seconds wall clock time: 47 minutes 17.34 seconds (2837.34 seconds total)