Starting phenix.real_space_refine on Sat Sep 12 19:22:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v1s_21016/09_2026/6v1s_21016.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v1s_21016/09_2026/6v1s_21016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v1s_21016/09_2026/6v1s_21016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v1s_21016/09_2026/6v1s_21016.map" model { file = "/net/cci-nas-00/data/ceres_data/6v1s_21016/09_2026/6v1s_21016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v1s_21016/09_2026/6v1s_21016.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6v1s_21016/09_2026/6v1s_21016.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v1s_21016/09_2026/6v1s_21016.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 26 5.16 5 C 11235 2.51 5 N 2935 2.21 5 O 3754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17964 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2114 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain breaks: 1 Chain: "B" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2081 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 12, 'TRANS': 255} Chain breaks: 1 Chain: "C" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2058 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain breaks: 1 Chain: "D" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2122 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 1 Chain: "E" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2153 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 12, 'TRANS': 263} Chain breaks: 1 Chain: "F" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2114 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain breaks: 1 Chain: "G" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2122 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 1 Chain: "Z" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3186 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.68, per 1000 atoms: 0.20 Number of scatterers: 17964 At special positions: 0 Unit cell: (136.73, 123.17, 119.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 26 16.00 O 3754 8.00 N 2935 7.00 C 11235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 740.4 milliseconds 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4278 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 42 sheets defined 22.4% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 248 through 253 removed outlier: 4.234A pdb=" N GLN A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 253' Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.029A pdb=" N ILE A 429 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 502 through 506 removed outlier: 4.030A pdb=" N ASP A 505 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.823A pdb=" N GLU A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 464 through 473 removed outlier: 3.858A pdb=" N ALA B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 512 removed outlier: 4.467A pdb=" N TYR B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 290 removed outlier: 4.102A pdb=" N ARG C 290 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 473 removed outlier: 3.621A pdb=" N ALA C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 513 removed outlier: 3.759A pdb=" N ILE C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 555 removed outlier: 4.399A pdb=" N GLU C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 555 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 272 through 278 Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 464 through 469 Processing helix chain 'D' and resid 507 through 513 removed outlier: 3.814A pdb=" N ILE D 513 " --> pdb=" O GLN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 removed outlier: 4.099A pdb=" N GLU D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 247 through 251 removed outlier: 3.642A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.738A pdb=" N ILE E 429 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 473 removed outlier: 3.786A pdb=" N ALA E 472 " --> pdb=" O LYS E 468 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY E 473 " --> pdb=" O LYS E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 511 Processing helix chain 'E' and resid 546 through 556 removed outlier: 4.816A pdb=" N GLU E 552 " --> pdb=" O GLY E 548 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE E 555 " --> pdb=" O ILE E 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 272 through 279 removed outlier: 3.872A pdb=" N GLY F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 463 through 473 removed outlier: 3.616A pdb=" N LEU F 467 " --> pdb=" O ASN F 463 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA F 472 " --> pdb=" O LYS F 468 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY F 473 " --> pdb=" O LYS F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 513 removed outlier: 3.581A pdb=" N ILE F 510 " --> pdb=" O TYR F 506 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE F 513 " --> pdb=" O GLN F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 555 removed outlier: 4.185A pdb=" N GLU F 552 " --> pdb=" O GLY F 548 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 234 removed outlier: 3.506A pdb=" N GLY G 234 " --> pdb=" O TYR G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 290 removed outlier: 3.589A pdb=" N ARG G 290 " --> pdb=" O THR G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.997A pdb=" N ILE G 429 " --> pdb=" O GLU G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 471 Processing helix chain 'G' and resid 502 through 505 removed outlier: 4.225A pdb=" N ASP G 505 " --> pdb=" O SER G 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 502 through 505' Processing helix chain 'G' and resid 506 through 514 removed outlier: 3.654A pdb=" N ILE G 513 " --> pdb=" O GLN G 509 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER G 514 " --> pdb=" O ILE G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 555 removed outlier: 4.040A pdb=" N GLU G 552 " --> pdb=" O GLY G 548 " (cutoff:3.500A) Processing helix chain 'Z' and resid 28 through 34 Processing helix chain 'Z' and resid 39 through 50 removed outlier: 3.949A pdb=" N LYS Z 50 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 62 removed outlier: 3.765A pdb=" N THR Z 62 " --> pdb=" O LYS Z 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 67 through 72 removed outlier: 4.014A pdb=" N ILE Z 71 " --> pdb=" O TYR Z 67 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU Z 72 " --> pdb=" O ASP Z 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 67 through 72' Processing helix chain 'Z' and resid 77 through 88 Processing helix chain 'Z' and resid 122 through 133 removed outlier: 3.540A pdb=" N ILE Z 133 " --> pdb=" O PHE Z 129 " (cutoff:3.500A) Processing helix chain 'Z' and resid 223 through 236 Processing helix chain 'Z' and resid 237 through 239 No H-bonds generated for 'chain 'Z' and resid 237 through 239' Processing helix chain 'Z' and resid 243 through 256 Processing helix chain 'Z' and resid 257 through 267 removed outlier: 4.644A pdb=" N ASN Z 263 " --> pdb=" O THR Z 259 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU Z 265 " --> pdb=" O ILE Z 261 " (cutoff:3.500A) Processing helix chain 'Z' and resid 268 through 273 Processing helix chain 'Z' and resid 275 through 291 Processing helix chain 'Z' and resid 306 through 310 removed outlier: 3.807A pdb=" N GLY Z 310 " --> pdb=" O GLN Z 307 " (cutoff:3.500A) Processing helix chain 'Z' and resid 315 through 319 Processing helix chain 'Z' and resid 322 through 333 removed outlier: 3.684A pdb=" N ILE Z 326 " --> pdb=" O LYS Z 322 " (cutoff:3.500A) Processing helix chain 'Z' and resid 375 through 379 removed outlier: 3.678A pdb=" N ILE Z 379 " --> pdb=" O LEU Z 376 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 237 Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 311 removed outlier: 5.003A pdb=" N VAL A 300 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A 398 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN A 392 " --> pdb=" O LYS A 306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 311 removed outlier: 5.003A pdb=" N VAL A 300 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A 398 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN A 392 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 387 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.838A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN A 482 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASN A 411 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N THR A 480 " --> pdb=" O ASN A 411 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL A 413 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU A 478 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA6, first strand: chain 'A' and resid 514 through 520 Processing sheet with id=AA7, first strand: chain 'B' and resid 235 through 237 Processing sheet with id=AA8, first strand: chain 'B' and resid 299 through 311 removed outlier: 4.624A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 299 through 311 removed outlier: 4.624A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 387 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 403 through 406 removed outlier: 7.030A pdb=" N TYR B 404 " --> pdb=" O ASN B 432 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 422 through 423 removed outlier: 3.744A pdb=" N GLN B 482 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN B 411 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N THR B 480 " --> pdb=" O ASN B 411 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL B 413 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU B 478 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 514 through 519 Processing sheet with id=AB4, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AB5, first strand: chain 'C' and resid 299 through 311 removed outlier: 4.636A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 403 through 405 removed outlier: 6.313A pdb=" N LYS C 405 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN C 431 " --> pdb=" O LYS C 405 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 417 through 422 removed outlier: 6.934A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 514 through 519 Processing sheet with id=AB9, first strand: chain 'D' and resid 235 through 237 Processing sheet with id=AC1, first strand: chain 'D' and resid 298 through 311 removed outlier: 4.661A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 405 through 406 removed outlier: 3.521A pdb=" N VAL D 406 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY D 430 " --> pdb=" O VAL D 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 417 through 422 removed outlier: 4.795A pdb=" N THR D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU D 414 " --> pdb=" O THR D 418 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR D 409 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 489 through 491 removed outlier: 4.426A pdb=" N ASN D 491 " --> pdb=" O GLN D 495 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLN D 495 " --> pdb=" O ASN D 491 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 514 through 520 Processing sheet with id=AC6, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AC7, first strand: chain 'E' and resid 298 through 311 removed outlier: 4.976A pdb=" N VAL E 300 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR E 398 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYS E 306 " --> pdb=" O ASN E 392 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN E 392 " --> pdb=" O LYS E 306 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN E 397 " --> pdb=" O ASP E 437 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP E 437 " --> pdb=" O ASN E 397 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 298 through 311 removed outlier: 4.976A pdb=" N VAL E 300 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR E 398 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYS E 306 " --> pdb=" O ASN E 392 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN E 392 " --> pdb=" O LYS E 306 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 418 through 422 removed outlier: 3.835A pdb=" N SER E 420 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR E 409 " --> pdb=" O THR E 481 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 515 through 520 Processing sheet with id=AD2, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AD3, first strand: chain 'F' and resid 298 through 311 removed outlier: 4.453A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 298 through 311 removed outlier: 4.453A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA F 387 " --> pdb=" O ILE F 462 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 403 through 406 removed outlier: 6.892A pdb=" N TYR F 404 " --> pdb=" O ASN F 432 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 421 through 423 removed outlier: 3.860A pdb=" N GLN F 482 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASN F 411 " --> pdb=" O THR F 480 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N THR F 480 " --> pdb=" O ASN F 411 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL F 413 " --> pdb=" O LEU F 478 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU F 478 " --> pdb=" O VAL F 413 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 514 through 520 Processing sheet with id=AD8, first strand: chain 'G' and resid 236 through 238 Processing sheet with id=AD9, first strand: chain 'G' and resid 298 through 311 removed outlier: 4.492A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.822A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 515 through 520 Processing sheet with id=AE3, first strand: chain 'Z' and resid 96 through 101 removed outlier: 3.503A pdb=" N ALA Z 210 " --> pdb=" O LEU Z 162 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL Z 214 " --> pdb=" O LYS Z 166 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS Z 205 " --> pdb=" O VAL Z 201 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL Z 201 " --> pdb=" O LYS Z 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR Z 207 " --> pdb=" O ARG Z 199 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ARG Z 199 " --> pdb=" O TYR Z 207 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS Z 209 " --> pdb=" O ILE Z 197 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE Z 197 " --> pdb=" O LYS Z 209 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU Z 211 " --> pdb=" O ASP Z 195 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER Z 213 " --> pdb=" O LYS Z 193 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS Z 193 " --> pdb=" O SER Z 213 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER Z 191 " --> pdb=" O VAL Z 215 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Z' and resid 143 through 146 Processing sheet with id=AE5, first strand: chain 'Z' and resid 298 through 304 removed outlier: 3.970A pdb=" N ILE Z 361 " --> pdb=" O SER Z 304 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL Z 362 " --> pdb=" O LEU Z 412 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL Z 414 " --> pdb=" O VAL Z 362 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR Z 366 " --> pdb=" O ALA Z 416 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU Z 418 " --> pdb=" O THR Z 366 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE Z 409 " --> pdb=" O LYS Z 405 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS Z 405 " --> pdb=" O ILE Z 409 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS Z 411 " --> pdb=" O SER Z 403 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER Z 403 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE Z 413 " --> pdb=" O ILE Z 401 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE Z 401 " --> pdb=" O ILE Z 413 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP Z 415 " --> pdb=" O ASN Z 399 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Z' and resid 344 through 347 488 hydrogen bonds defined for protein. 1284 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: 3.00 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5043 1.33 - 1.45: 2853 1.45 - 1.57: 10316 1.57 - 1.69: 0 1.69 - 1.80: 52 Bond restraints: 18264 Sorted by residual: bond pdb=" CA TRP F 503 " pdb=" C TRP F 503 " ideal model delta sigma weight residual 1.523 1.451 0.072 1.80e-02 3.09e+03 1.62e+01 bond pdb=" CA TRP D 503 " pdb=" C TRP D 503 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.80e-02 3.09e+03 1.48e+01 bond pdb=" C GLN Z 118 " pdb=" N ASN Z 119 " ideal model delta sigma weight residual 1.332 1.308 0.025 1.40e-02 5.10e+03 3.11e+00 bond pdb=" C THR D 400 " pdb=" N ALA D 401 " ideal model delta sigma weight residual 1.340 1.238 0.102 5.87e-02 2.90e+02 3.01e+00 bond pdb=" CG LEU E 433 " pdb=" CD2 LEU E 433 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.95e+00 ... (remaining 18259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 23739 1.66 - 3.33: 887 3.33 - 4.99: 98 4.99 - 6.66: 19 6.66 - 8.32: 10 Bond angle restraints: 24753 Sorted by residual: angle pdb=" N GLY B 485 " pdb=" CA GLY B 485 " pdb=" C GLY B 485 " ideal model delta sigma weight residual 110.77 115.48 -4.71 1.59e+00 3.96e-01 8.79e+00 angle pdb=" CA TYR B 439 " pdb=" CB TYR B 439 " pdb=" CG TYR B 439 " ideal model delta sigma weight residual 113.90 108.81 5.09 1.80e+00 3.09e-01 8.00e+00 angle pdb=" C TYR D 439 " pdb=" N PRO D 440 " pdb=" CA PRO D 440 " ideal model delta sigma weight residual 120.79 117.18 3.61 1.30e+00 5.92e-01 7.69e+00 angle pdb=" N ILE A 507 " pdb=" CA ILE A 507 " pdb=" C ILE A 507 " ideal model delta sigma weight residual 113.39 109.31 4.08 1.47e+00 4.63e-01 7.69e+00 angle pdb=" C LEU C 414 " pdb=" N ASP C 415 " pdb=" CA ASP C 415 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.65e+00 ... (remaining 24748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 9944 17.66 - 35.32: 988 35.32 - 52.99: 170 52.99 - 70.65: 29 70.65 - 88.31: 14 Dihedral angle restraints: 11145 sinusoidal: 4453 harmonic: 6692 Sorted by residual: dihedral pdb=" CA LYS C 490 " pdb=" C LYS C 490 " pdb=" N ASN C 491 " pdb=" CA ASN C 491 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA MET C 304 " pdb=" C MET C 304 " pdb=" N GLU C 305 " pdb=" CA GLU C 305 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TYR E 404 " pdb=" C TYR E 404 " pdb=" N LYS E 405 " pdb=" CA LYS E 405 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 11142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1596 0.036 - 0.072: 752 0.072 - 0.109: 302 0.109 - 0.145: 95 0.145 - 0.181: 7 Chirality restraints: 2752 Sorted by residual: chirality pdb=" CA ASN B 432 " pdb=" N ASN B 432 " pdb=" C ASN B 432 " pdb=" CB ASN B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CA TYR D 404 " pdb=" N TYR D 404 " pdb=" C TYR D 404 " pdb=" CB TYR D 404 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA ASN C 432 " pdb=" N ASN C 432 " pdb=" C ASN C 432 " pdb=" CB ASN C 432 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 2749 not shown) Planarity restraints: 3251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 291 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO F 292 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 292 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 292 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN Z 273 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO Z 274 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO Z 274 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO Z 274 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 434 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO D 435 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 435 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 435 " 0.031 5.00e-02 4.00e+02 ... (remaining 3248 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1693 2.72 - 3.27: 18050 3.27 - 3.81: 25949 3.81 - 4.36: 30789 4.36 - 4.90: 55070 Nonbonded interactions: 131551 Sorted by model distance: nonbonded pdb=" OD1 ASN B 450 " pdb=" OG1 THR B 451 " model vdw 2.181 3.040 nonbonded pdb=" OD2 ASP Z 219 " pdb=" OG1 THR Z 299 " model vdw 2.199 3.040 nonbonded pdb=" O PHE Z 320 " pdb=" OG1 THR Z 410 " model vdw 2.202 3.040 nonbonded pdb=" ND2 ASN D 260 " pdb=" O LYS D 541 " model vdw 2.211 3.120 nonbonded pdb=" OE1 GLN E 482 " pdb=" OH TYR F 439 " model vdw 2.217 3.040 ... (remaining 131546 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 'A' and resid 224 through 902) selection = (chain 'B' and resid 224 through 902) selection = chain 'C' selection = (chain 'D' and resid 224 through 902) selection = (chain 'E' and resid 224 through 902) selection = (chain 'F' and resid 224 through 902) selection = (chain 'G' and resid 224 through 902) } 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: 0.940 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.660 Find NCS groups from input model: 0.440 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 18264 Z= 0.302 Angle : 0.749 8.322 24753 Z= 0.411 Chirality : 0.049 0.181 2752 Planarity : 0.005 0.058 3251 Dihedral : 14.400 88.309 6867 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % Rotamer: Outliers : 0.25 % Allowed : 11.38 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.42 (0.13), residues: 2263 helix: -3.62 (0.15), residues: 473 sheet: -2.77 (0.19), residues: 507 loop : -4.11 (0.13), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 529 TYR 0.020 0.002 TYR E 257 PHE 0.024 0.002 PHE B 487 TRP 0.019 0.002 TRP F 503 HIS 0.001 0.001 HIS Z 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.30 (18264) covalent geometry : angle 0.74852 / 0.41 (24753) hydrogen bonds : bond 0.16611 / 9.87 ( 464) hydrogen bonds : angle 8.53744 / 6.04 ( 1284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 196 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 307 LEU cc_start: 0.7715 (tp) cc_final: 0.6916 (pt) REVERT: B 536 GLN cc_start: 0.7614 (tm-30) cc_final: 0.6973 (tm-30) REVERT: C 528 ARG cc_start: 0.8511 (mpt90) cc_final: 0.8216 (mmt90) REVERT: D 432 ASN cc_start: 0.8963 (p0) cc_final: 0.8761 (p0) REVERT: D 505 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8612 (p0) REVERT: D 534 ASN cc_start: 0.7959 (t0) cc_final: 0.7113 (m-40) REVERT: E 432 ASN cc_start: 0.9063 (p0) cc_final: 0.8701 (p0) REVERT: F 527 GLU cc_start: 0.8232 (tt0) cc_final: 0.8030 (tt0) outliers start: 5 outliers final: 2 residues processed: 201 average time/residue: 0.1333 time to fit residues: 40.4574 Evaluate side-chains 142 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain G residue 447 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 ASN A 432 ASN A 466 GLN B 486 ASN C 486 ASN C 509 GLN D 252 GLN D 466 GLN D 509 GLN E 482 GLN E 486 ASN F 454 GLN F 486 ASN G 432 ASN ** Z 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 392 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.093222 restraints weight = 35441.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.094881 restraints weight = 23160.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.095983 restraints weight = 17228.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.096736 restraints weight = 14150.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.097166 restraints weight = 12382.613| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 18264 Z= 0.194 Angle : 0.654 7.496 24753 Z= 0.351 Chirality : 0.047 0.174 2752 Planarity : 0.005 0.048 3251 Dihedral : 5.667 48.634 2477 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 1.60 % Allowed : 15.50 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.14), residues: 2263 helix: -2.58 (0.19), residues: 484 sheet: -2.40 (0.19), residues: 511 loop : -3.61 (0.14), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 458 TYR 0.020 0.002 TYR B 396 PHE 0.017 0.002 PHE B 487 TRP 0.015 0.001 TRP F 503 HIS 0.002 0.001 HIS Z 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (18264) covalent geometry : angle 0.65357 / 0.35 (24753) hydrogen bonds : bond 0.04365 / 2.74 ( 464) hydrogen bonds : angle 6.54747 / 4.56 ( 1284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: B 307 LEU cc_start: 0.7364 (tp) cc_final: 0.6589 (pt) REVERT: B 390 ASN cc_start: 0.7914 (t0) cc_final: 0.7550 (t0) REVERT: B 458 ARG cc_start: 0.8711 (mtp85) cc_final: 0.8505 (mtp85) REVERT: C 450 ASN cc_start: 0.8100 (p0) cc_final: 0.7859 (p0) REVERT: C 528 ARG cc_start: 0.8551 (mpt90) cc_final: 0.8260 (mmt90) REVERT: D 534 ASN cc_start: 0.7862 (t0) cc_final: 0.7115 (m-40) REVERT: E 432 ASN cc_start: 0.9027 (p0) cc_final: 0.8701 (p0) REVERT: F 309 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8590 (pt) outliers start: 32 outliers final: 22 residues processed: 194 average time/residue: 0.1180 time to fit residues: 36.0600 Evaluate side-chains 167 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 265 LEU Chi-restraints excluded: chain Z residue 362 VAL Chi-restraints excluded: chain Z residue 414 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 195 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN F 454 GLN G 390 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.115579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.097519 restraints weight = 35325.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.099065 restraints weight = 23241.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.100130 restraints weight = 17497.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.100752 restraints weight = 14427.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.101291 restraints weight = 12732.561| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18264 Z= 0.107 Angle : 0.546 6.831 24753 Z= 0.292 Chirality : 0.044 0.148 2752 Planarity : 0.004 0.044 3251 Dihedral : 4.947 55.498 2475 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.36 % Allowed : 16.75 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.15), residues: 2263 helix: -1.72 (0.21), residues: 484 sheet: -2.03 (0.20), residues: 511 loop : -3.25 (0.14), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 458 TYR 0.009 0.001 TYR C 230 PHE 0.012 0.001 PHE B 487 TRP 0.008 0.001 TRP F 503 HIS 0.001 0.001 HIS Z 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (18264) covalent geometry : angle 0.54592 / 0.29 (24753) hydrogen bonds : bond 0.03227 / 2.04 ( 464) hydrogen bonds : angle 5.75735 / 4.00 ( 1284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 307 LEU cc_start: 0.7259 (tp) cc_final: 0.6703 (pt) REVERT: B 390 ASN cc_start: 0.7889 (t0) cc_final: 0.7503 (t0) REVERT: C 426 GLU cc_start: 0.8175 (tp30) cc_final: 0.7757 (tp30) REVERT: C 528 ARG cc_start: 0.8494 (mpt90) cc_final: 0.8265 (mmt90) REVERT: D 534 ASN cc_start: 0.7610 (t0) cc_final: 0.7161 (m-40) REVERT: E 432 ASN cc_start: 0.9007 (p0) cc_final: 0.8573 (p0) REVERT: F 390 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8855 (t0) REVERT: F 527 GLU cc_start: 0.8125 (tt0) cc_final: 0.7814 (tt0) REVERT: G 385 GLU cc_start: 0.8004 (mp0) cc_final: 0.7693 (mp0) REVERT: G 417 ASP cc_start: 0.8717 (t0) cc_final: 0.8333 (t0) outliers start: 47 outliers final: 21 residues processed: 222 average time/residue: 0.1184 time to fit residues: 41.6534 Evaluate side-chains 182 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 434 SER Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 260 ASN Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 414 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 178 optimal weight: 4.9990 chunk 140 optimal weight: 0.0070 chunk 199 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 94 optimal weight: 0.0770 chunk 113 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 overall best weight: 1.3360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN C 425 GLN C 509 GLN E 390 ASN E 495 GLN F 390 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.116207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.098189 restraints weight = 35291.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099761 restraints weight = 23269.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100806 restraints weight = 17510.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101497 restraints weight = 14512.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.102010 restraints weight = 12708.981| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18264 Z= 0.102 Angle : 0.536 6.817 24753 Z= 0.285 Chirality : 0.044 0.152 2752 Planarity : 0.004 0.065 3251 Dihedral : 4.592 41.251 2473 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.46 % Allowed : 18.36 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.15), residues: 2263 helix: -1.26 (0.22), residues: 485 sheet: -1.77 (0.20), residues: 521 loop : -3.01 (0.15), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 458 TYR 0.021 0.001 TYR F 396 PHE 0.012 0.001 PHE F 455 TRP 0.007 0.001 TRP F 503 HIS 0.001 0.001 HIS Z 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (18264) covalent geometry : angle 0.53610 / 0.29 (24753) hydrogen bonds : bond 0.02964 / 1.88 ( 464) hydrogen bonds : angle 5.44117 / 3.77 ( 1284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: B 307 LEU cc_start: 0.7187 (tp) cc_final: 0.6712 (pt) REVERT: B 390 ASN cc_start: 0.7828 (t0) cc_final: 0.7466 (t0) REVERT: C 403 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7830 (mtt) REVERT: C 404 TYR cc_start: 0.8663 (m-80) cc_final: 0.8452 (m-80) REVERT: C 528 ARG cc_start: 0.8489 (mpt90) cc_final: 0.8274 (mmt90) REVERT: D 534 ASN cc_start: 0.7568 (t0) cc_final: 0.7131 (m-40) REVERT: E 432 ASN cc_start: 0.8971 (p0) cc_final: 0.8522 (p0) REVERT: F 527 GLU cc_start: 0.8160 (tt0) cc_final: 0.7857 (tt0) REVERT: G 385 GLU cc_start: 0.7968 (mp0) cc_final: 0.7687 (mp0) REVERT: G 417 ASP cc_start: 0.8671 (t0) cc_final: 0.8263 (t0) REVERT: Z 232 LYS cc_start: 0.6946 (mmmt) cc_final: 0.6699 (tppt) REVERT: Z 254 MET cc_start: 0.6457 (ppp) cc_final: 0.6105 (ppp) outliers start: 49 outliers final: 32 residues processed: 214 average time/residue: 0.1143 time to fit residues: 39.6183 Evaluate side-chains 184 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 434 SER Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 451 THR Chi-restraints excluded: chain F residue 470 LEU Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 414 VAL Chi-restraints excluded: chain Z residue 419 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 17 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 139 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 390 ASN E 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101492 restraints weight = 34093.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.103668 restraints weight = 20002.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.105089 restraints weight = 13909.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105986 restraints weight = 10967.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106636 restraints weight = 9369.984| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18264 Z= 0.130 Angle : 0.555 7.018 24753 Z= 0.294 Chirality : 0.044 0.166 2752 Planarity : 0.004 0.054 3251 Dihedral : 4.626 43.652 2473 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.91 % Allowed : 19.06 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.16), residues: 2263 helix: -1.11 (0.23), residues: 490 sheet: -1.61 (0.20), residues: 521 loop : -2.93 (0.15), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 458 TYR 0.012 0.001 TYR E 257 PHE 0.014 0.001 PHE B 487 TRP 0.009 0.001 TRP F 503 HIS 0.001 0.000 HIS Z 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (18264) covalent geometry : angle 0.55547 / 0.29 (24753) hydrogen bonds : bond 0.03138 / 2.01 ( 464) hydrogen bonds : angle 5.38474 / 3.72 ( 1284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 159 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 307 LEU cc_start: 0.7130 (tp) cc_final: 0.6620 (pt) REVERT: B 390 ASN cc_start: 0.7990 (t0) cc_final: 0.7496 (t0) REVERT: C 403 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7902 (mtt) REVERT: C 450 ASN cc_start: 0.7922 (p0) cc_final: 0.7679 (p0) REVERT: D 534 ASN cc_start: 0.7645 (t0) cc_final: 0.7101 (m-40) REVERT: E 432 ASN cc_start: 0.8916 (p0) cc_final: 0.8447 (p0) REVERT: F 527 GLU cc_start: 0.8274 (tt0) cc_final: 0.7990 (tt0) REVERT: G 385 GLU cc_start: 0.8006 (mp0) cc_final: 0.7719 (mp0) outliers start: 58 outliers final: 43 residues processed: 205 average time/residue: 0.1135 time to fit residues: 37.8569 Evaluate side-chains 187 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 434 SER Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 451 THR Chi-restraints excluded: chain F residue 470 LEU Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 414 VAL Chi-restraints excluded: chain Z residue 419 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 201 optimal weight: 0.4980 chunk 133 optimal weight: 20.0000 chunk 67 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103664 restraints weight = 34227.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105861 restraints weight = 19943.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107319 restraints weight = 13934.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108270 restraints weight = 10994.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.108919 restraints weight = 9388.936| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18264 Z= 0.095 Angle : 0.523 6.766 24753 Z= 0.276 Chirality : 0.043 0.152 2752 Planarity : 0.004 0.046 3251 Dihedral : 4.359 42.836 2473 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.41 % Allowed : 19.71 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.16), residues: 2263 helix: -0.84 (0.23), residues: 490 sheet: -1.37 (0.21), residues: 505 loop : -2.76 (0.15), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 458 TYR 0.009 0.001 TYR C 230 PHE 0.011 0.001 PHE B 487 TRP 0.006 0.001 TRP B 245 HIS 0.001 0.000 HIS Z 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (18264) covalent geometry : angle 0.52293 / 0.28 (24753) hydrogen bonds : bond 0.02712 / 1.74 ( 464) hydrogen bonds : angle 5.14528 / 3.55 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 172 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 307 LEU cc_start: 0.7116 (tp) cc_final: 0.6659 (pt) REVERT: C 403 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7845 (mtt) REVERT: C 404 TYR cc_start: 0.8637 (m-80) cc_final: 0.8435 (m-80) REVERT: C 450 ASN cc_start: 0.7787 (p0) cc_final: 0.7521 (p0) REVERT: D 432 ASN cc_start: 0.8387 (p0) cc_final: 0.8184 (p0) REVERT: D 534 ASN cc_start: 0.7514 (t0) cc_final: 0.7068 (m-40) REVERT: E 432 ASN cc_start: 0.8877 (p0) cc_final: 0.8352 (p0) REVERT: F 527 GLU cc_start: 0.8271 (tt0) cc_final: 0.7954 (tt0) REVERT: G 385 GLU cc_start: 0.7902 (mp0) cc_final: 0.7678 (mp0) REVERT: G 417 ASP cc_start: 0.8680 (t0) cc_final: 0.8361 (t0) REVERT: Z 232 LYS cc_start: 0.6977 (mmmt) cc_final: 0.6674 (tppt) REVERT: Z 254 MET cc_start: 0.6006 (ppp) cc_final: 0.5401 (ppp) outliers start: 48 outliers final: 36 residues processed: 206 average time/residue: 0.1111 time to fit residues: 36.8786 Evaluate side-chains 186 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 434 SER Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 451 THR Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 414 VAL Chi-restraints excluded: chain Z residue 419 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 149 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 7 optimal weight: 0.0870 chunk 66 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 overall best weight: 4.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.099117 restraints weight = 34464.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101242 restraints weight = 20339.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102595 restraints weight = 14291.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.103561 restraints weight = 11311.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.104169 restraints weight = 9670.152| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 18264 Z= 0.199 Angle : 0.616 7.474 24753 Z= 0.328 Chirality : 0.046 0.178 2752 Planarity : 0.004 0.054 3251 Dihedral : 4.894 49.916 2473 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.76 % Allowed : 20.66 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.16), residues: 2263 helix: -1.03 (0.23), residues: 488 sheet: -1.35 (0.21), residues: 515 loop : -2.83 (0.15), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Z 40 TYR 0.017 0.002 TYR B 297 PHE 0.018 0.002 PHE B 487 TRP 0.012 0.001 TRP F 503 HIS 0.003 0.001 HIS Z 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (18264) covalent geometry : angle 0.61639 / 0.33 (24753) hydrogen bonds : bond 0.03608 / 2.33 ( 464) hydrogen bonds : angle 5.47229 / 3.78 ( 1284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 154 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 241 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7971 (mt) REVERT: B 307 LEU cc_start: 0.7283 (tp) cc_final: 0.6681 (pt) REVERT: C 426 GLU cc_start: 0.8417 (tp30) cc_final: 0.8084 (tp30) REVERT: D 432 ASN cc_start: 0.8528 (p0) cc_final: 0.8278 (p0) REVERT: D 534 ASN cc_start: 0.7716 (t0) cc_final: 0.6981 (m-40) REVERT: E 216 ASP cc_start: 0.7597 (p0) cc_final: 0.7397 (p0) REVERT: E 432 ASN cc_start: 0.8894 (p0) cc_final: 0.8433 (p0) REVERT: F 527 GLU cc_start: 0.8308 (tt0) cc_final: 0.8017 (tt0) REVERT: G 417 ASP cc_start: 0.8714 (t0) cc_final: 0.8273 (t0) REVERT: Z 254 MET cc_start: 0.6433 (ppp) cc_final: 0.5802 (ppp) outliers start: 55 outliers final: 50 residues processed: 198 average time/residue: 0.1131 time to fit residues: 36.6275 Evaluate side-chains 195 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain E residue 509 GLN Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 451 THR Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 414 VAL Chi-restraints excluded: chain Z residue 419 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 177 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.120178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.100817 restraints weight = 34182.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102937 restraints weight = 20072.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104340 restraints weight = 14096.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105270 restraints weight = 11127.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105842 restraints weight = 9503.973| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18264 Z= 0.139 Angle : 0.571 8.149 24753 Z= 0.303 Chirality : 0.044 0.175 2752 Planarity : 0.004 0.051 3251 Dihedral : 4.729 49.759 2473 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.01 % Allowed : 20.91 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.16), residues: 2263 helix: -0.91 (0.23), residues: 489 sheet: -1.37 (0.21), residues: 521 loop : -2.72 (0.15), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 458 TYR 0.012 0.001 TYR B 297 PHE 0.015 0.001 PHE B 487 TRP 0.009 0.001 TRP F 503 HIS 0.003 0.001 HIS Z 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (18264) covalent geometry : angle 0.57055 / 0.30 (24753) hydrogen bonds : bond 0.03179 / 2.04 ( 464) hydrogen bonds : angle 5.33580 / 3.69 ( 1284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 154 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 241 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.8031 (mt) REVERT: B 307 LEU cc_start: 0.7257 (tp) cc_final: 0.6702 (pt) REVERT: C 426 GLU cc_start: 0.8356 (tp30) cc_final: 0.7952 (tp30) REVERT: C 456 SER cc_start: 0.8012 (t) cc_final: 0.7759 (m) REVERT: C 511 ASP cc_start: 0.7601 (t0) cc_final: 0.7396 (t70) REVERT: D 432 ASN cc_start: 0.8522 (p0) cc_final: 0.8278 (p0) REVERT: D 534 ASN cc_start: 0.7628 (t0) cc_final: 0.7118 (m-40) REVERT: E 432 ASN cc_start: 0.8935 (p0) cc_final: 0.8449 (p0) REVERT: F 527 GLU cc_start: 0.8300 (tt0) cc_final: 0.7979 (tt0) REVERT: Z 254 MET cc_start: 0.6366 (ppp) cc_final: 0.5650 (ppp) REVERT: Z 353 MET cc_start: 0.5143 (ttp) cc_final: 0.4715 (ttp) outliers start: 60 outliers final: 53 residues processed: 200 average time/residue: 0.1131 time to fit residues: 36.9715 Evaluate side-chains 203 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 509 GLN Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain E residue 509 GLN Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 451 THR Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 414 VAL Chi-restraints excluded: chain Z residue 419 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 223 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 213 optimal weight: 30.0000 chunk 121 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.120764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101705 restraints weight = 33999.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103535 restraints weight = 19848.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105089 restraints weight = 14673.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105378 restraints weight = 11017.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105599 restraints weight = 10746.946| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18264 Z= 0.129 Angle : 0.564 7.939 24753 Z= 0.299 Chirality : 0.044 0.179 2752 Planarity : 0.004 0.049 3251 Dihedral : 4.619 49.705 2473 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.06 % Allowed : 21.26 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.16), residues: 2263 helix: -0.84 (0.23), residues: 490 sheet: -1.30 (0.21), residues: 521 loop : -2.65 (0.15), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 40 TYR 0.011 0.001 TYR B 297 PHE 0.014 0.001 PHE B 487 TRP 0.008 0.001 TRP F 503 HIS 0.003 0.001 HIS Z 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (18264) covalent geometry : angle 0.56370 / 0.30 (24753) hydrogen bonds : bond 0.03047 / 1.96 ( 464) hydrogen bonds : angle 5.23327 / 3.62 ( 1284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 155 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: B 307 LEU cc_start: 0.7209 (tp) cc_final: 0.6690 (pt) REVERT: C 426 GLU cc_start: 0.8323 (tp30) cc_final: 0.7881 (tp30) REVERT: C 456 SER cc_start: 0.7995 (t) cc_final: 0.7703 (m) REVERT: D 432 ASN cc_start: 0.8492 (p0) cc_final: 0.8232 (p0) REVERT: D 534 ASN cc_start: 0.7625 (t0) cc_final: 0.7126 (m-40) REVERT: E 432 ASN cc_start: 0.8874 (p0) cc_final: 0.8418 (p0) REVERT: F 527 GLU cc_start: 0.8325 (tt0) cc_final: 0.8005 (tt0) REVERT: Z 232 LYS cc_start: 0.7022 (mmmt) cc_final: 0.6747 (tppt) REVERT: Z 254 MET cc_start: 0.6458 (ppp) cc_final: 0.5733 (ppp) REVERT: Z 353 MET cc_start: 0.5026 (ttp) cc_final: 0.4603 (ttp) outliers start: 61 outliers final: 56 residues processed: 201 average time/residue: 0.1165 time to fit residues: 37.9691 Evaluate side-chains 207 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 151 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 509 GLN Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain E residue 509 GLN Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 451 THR Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 192 ILE Chi-restraints excluded: chain Z residue 414 VAL Chi-restraints excluded: chain Z residue 419 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 53 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 223 optimal weight: 30.0000 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 25 optimal weight: 0.0470 chunk 94 optimal weight: 0.0020 chunk 95 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.103112 restraints weight = 33814.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.105256 restraints weight = 19820.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106673 restraints weight = 13878.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107613 restraints weight = 10957.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.108198 restraints weight = 9327.020| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18264 Z= 0.103 Angle : 0.536 8.140 24753 Z= 0.284 Chirality : 0.043 0.179 2752 Planarity : 0.004 0.045 3251 Dihedral : 4.406 48.634 2473 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.61 % Allowed : 21.82 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.16), residues: 2263 helix: -0.65 (0.24), residues: 490 sheet: -1.16 (0.22), residues: 505 loop : -2.55 (0.15), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 458 TYR 0.010 0.001 TYR C 230 PHE 0.012 0.001 PHE B 487 TRP 0.007 0.001 TRP B 245 HIS 0.003 0.001 HIS Z 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (18264) covalent geometry : angle 0.53627 / 0.28 (24753) hydrogen bonds : bond 0.02728 / 1.75 ( 464) hydrogen bonds : angle 5.00781 / 3.47 ( 1284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 304 MET cc_start: 0.8080 (tmm) cc_final: 0.7832 (tmm) REVERT: B 307 LEU cc_start: 0.7048 (tp) cc_final: 0.6764 (pt) REVERT: C 404 TYR cc_start: 0.8685 (m-80) cc_final: 0.8463 (m-80) REVERT: C 426 GLU cc_start: 0.8375 (tp30) cc_final: 0.7807 (tp30) REVERT: D 534 ASN cc_start: 0.7561 (t0) cc_final: 0.7107 (m-40) REVERT: E 432 ASN cc_start: 0.8922 (p0) cc_final: 0.8438 (p0) REVERT: F 527 GLU cc_start: 0.8309 (tt0) cc_final: 0.7983 (tt0) REVERT: G 245 TRP cc_start: 0.8592 (t-100) cc_final: 0.8343 (t-100) REVERT: Z 232 LYS cc_start: 0.6950 (mmmt) cc_final: 0.6634 (tppt) REVERT: Z 254 MET cc_start: 0.6081 (ppp) cc_final: 0.5374 (ppp) REVERT: Z 353 MET cc_start: 0.4981 (ttp) cc_final: 0.4566 (ttp) outliers start: 52 outliers final: 48 residues processed: 202 average time/residue: 0.1122 time to fit residues: 36.5606 Evaluate side-chains 203 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 509 GLN Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 451 THR Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 192 ILE Chi-restraints excluded: chain Z residue 414 VAL Chi-restraints excluded: chain Z residue 419 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 225 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 0.0870 overall best weight: 2.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.120848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.101375 restraints weight = 34283.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.103522 restraints weight = 20133.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.104943 restraints weight = 14061.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105871 restraints weight = 11080.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106450 restraints weight = 9479.651| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18264 Z= 0.138 Angle : 0.570 8.400 24753 Z= 0.302 Chirality : 0.044 0.180 2752 Planarity : 0.004 0.048 3251 Dihedral : 4.557 50.914 2473 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.61 % Allowed : 21.97 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.16), residues: 2263 helix: -0.71 (0.23), residues: 490 sheet: -1.17 (0.22), residues: 505 loop : -2.51 (0.15), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 40 TYR 0.012 0.001 TYR F 261 PHE 0.014 0.001 PHE B 487 TRP 0.009 0.001 TRP F 503 HIS 0.002 0.001 HIS Z 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (18264) covalent geometry : angle 0.57010 / 0.30 (24753) hydrogen bonds : bond 0.03054 / 1.97 ( 464) hydrogen bonds : angle 5.12238 / 3.55 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2303.97 seconds wall clock time: 40 minutes 59.83 seconds (2459.83 seconds total)