Starting phenix.real_space_refine on Thu Mar 5 01:03:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v1s_21016/03_2026/6v1s_21016.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v1s_21016/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6v1s_21016/03_2026/6v1s_21016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v1s_21016/03_2026/6v1s_21016.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v1s_21016/03_2026/6v1s_21016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v1s_21016/03_2026/6v1s_21016.map" } 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-dev-5986/lib/python3.9/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: 3.75, per 1000 atoms: 0.21 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: 1.56 Conformation dependent library (CDL) restraints added in 766.7 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: 0.62 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: 2.64 Time building geometry restraints manager: 2.06 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: 0.670 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.890 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 covalent geometry : bond 0.00710 (18264) covalent geometry : angle 0.74852 (24753) hydrogen bonds : bond 0.16611 ( 464) hydrogen bonds : angle 8.53744 ( 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 : 0.701 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: 0.6974 (tm-30) REVERT: C 528 ARG cc_start: 0.8511 (mpt90) cc_final: 0.8214 (mmt90) REVERT: D 432 ASN cc_start: 0.8963 (p0) cc_final: 0.8757 (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: 0.8029 (tt0) outliers start: 5 outliers final: 2 residues processed: 201 average time/residue: 0.1491 time to fit residues: 44.9124 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 : 0.726 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3354 r_free = 0.3354 target = 0.112040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.093773 restraints weight = 35380.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.095272 restraints weight = 23713.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.096291 restraints weight = 18095.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.096971 restraints weight = 15051.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.097405 restraints weight = 13311.802| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18264 Z= 0.194 Angle : 0.652 7.489 24753 Z= 0.350 Chirality : 0.047 0.173 2752 Planarity : 0.005 0.047 3251 Dihedral : 5.658 48.851 2477 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 1.76 % Allowed : 15.45 % Favored : 82.80 % 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: -4.54 (0.14), residues: 2263 helix: -2.57 (0.19), residues: 484 sheet: -2.40 (0.19), residues: 511 loop : -3.60 (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 0.014 0.001 TRP F 503 HIS 0.002 0.001 HIS Z 392 Details of bonding type rmsd covalent geometry : bond 0.00457 (18264) covalent geometry : angle 0.65185 (24753) hydrogen bonds : bond 0.04319 ( 464) hydrogen bonds : angle 6.51719 ( 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 205 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: B 307 LEU cc_start: 0.7361 (tp) cc_final: 0.6588 (pt) REVERT: B 390 ASN cc_start: 0.7921 (t0) cc_final: 0.7559 (t0) REVERT: B 536 GLN cc_start: 0.7596 (tm-30) cc_final: 0.7309 (tt0) REVERT: C 528 ARG cc_start: 0.8552 (mpt90) cc_final: 0.8259 (mmt90) REVERT: D 451 THR cc_start: 0.9347 (m) cc_final: 0.9125 (m) REVERT: D 534 ASN cc_start: 0.7856 (t0) cc_final: 0.7113 (m-40) REVERT: E 432 ASN cc_start: 0.9025 (p0) cc_final: 0.8704 (p0) REVERT: F 309 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8592 (pt) outliers start: 35 outliers final: 23 residues processed: 196 average time/residue: 0.1267 time to fit residues: 38.7413 Evaluate side-chains 173 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 406 VAL 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: 0.0670 chunk 118 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3382 r_free = 0.3382 target = 0.113878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.095634 restraints weight = 35645.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.097148 restraints weight = 23797.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.098095 restraints weight = 18127.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098860 restraints weight = 15152.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.099277 restraints weight = 13329.213| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18264 Z= 0.142 Angle : 0.580 7.085 24753 Z= 0.310 Chirality : 0.045 0.156 2752 Planarity : 0.005 0.045 3251 Dihedral : 5.151 52.394 2475 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.56 % Allowed : 17.65 % Favored : 79.79 % 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: -3.95 (0.15), residues: 2263 helix: -1.86 (0.21), residues: 489 sheet: -2.07 (0.20), residues: 511 loop : -3.30 (0.14), residues: 1263 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 0.015 0.001 PHE B 487 TRP 0.011 0.001 TRP F 503 HIS 0.001 0.001 HIS Z 206 Details of bonding type rmsd covalent geometry : bond 0.00332 (18264) covalent geometry : angle 0.57986 (24753) hydrogen bonds : bond 0.03572 ( 464) hydrogen bonds : angle 5.90420 ( 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 230 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 179 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 307 LEU cc_start: 0.7234 (tp) cc_final: 0.6641 (pt) REVERT: B 390 ASN cc_start: 0.7988 (t0) cc_final: 0.7587 (t0) REVERT: C 426 GLU cc_start: 0.8173 (tp30) cc_final: 0.7821 (tp30) REVERT: D 534 ASN cc_start: 0.7654 (t0) cc_final: 0.7170 (m-40) REVERT: E 432 ASN cc_start: 0.8996 (p0) cc_final: 0.8561 (p0) REVERT: F 390 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8919 (t0) REVERT: F 527 GLU cc_start: 0.8176 (tt0) cc_final: 0.7923 (tt0) REVERT: G 385 GLU cc_start: 0.8035 (mp0) cc_final: 0.7706 (mp0) REVERT: G 417 ASP cc_start: 0.8741 (t0) cc_final: 0.8358 (t0) outliers start: 51 outliers final: 29 residues processed: 219 average time/residue: 0.1123 time to fit residues: 39.8080 Evaluate side-chains 193 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 478 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 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 410 THR Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 260 ASN Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 308 ILE 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 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: 7.9990 chunk 140 optimal weight: 6.9990 chunk 199 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 212 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 62 optimal weight: 0.0670 chunk 195 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 GLN C 509 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.117432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.099547 restraints weight = 35036.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.101110 restraints weight = 22888.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.102254 restraints weight = 17042.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.102979 restraints weight = 13994.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103471 restraints weight = 12190.433| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1972 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= 0.094 Angle : 0.530 7.306 24753 Z= 0.281 Chirality : 0.043 0.153 2752 Planarity : 0.004 0.042 3251 Dihedral : 4.686 59.891 2475 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.36 % Allowed : 18.71 % Favored : 78.94 % 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: -3.37 (0.15), residues: 2263 helix: -1.24 (0.22), residues: 487 sheet: -1.72 (0.20), residues: 519 loop : -2.99 (0.15), residues: 1257 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 F 455 TRP 0.005 0.001 TRP F 503 HIS 0.002 0.001 HIS Z 164 Details of bonding type rmsd covalent geometry : bond 0.00202 (18264) covalent geometry : angle 0.53034 (24753) hydrogen bonds : bond 0.02818 ( 464) hydrogen bonds : angle 5.41387 ( 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 246 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 307 LEU cc_start: 0.7181 (tp) cc_final: 0.6691 (pt) REVERT: B 390 ASN cc_start: 0.7774 (t0) cc_final: 0.7419 (t0) REVERT: D 534 ASN cc_start: 0.7528 (t0) cc_final: 0.7109 (m-40) REVERT: E 432 ASN cc_start: 0.8951 (p0) cc_final: 0.8485 (p0) REVERT: F 527 GLU cc_start: 0.8173 (tt0) cc_final: 0.7854 (tt0) REVERT: G 385 GLU cc_start: 0.7915 (mp0) cc_final: 0.7672 (mp0) REVERT: G 417 ASP cc_start: 0.8649 (t0) cc_final: 0.8230 (t0) REVERT: G 518 ILE cc_start: 0.8371 (mp) cc_final: 0.7403 (pt) outliers start: 47 outliers final: 29 residues processed: 232 average time/residue: 0.1182 time to fit residues: 43.7345 Evaluate side-chains 186 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 300 VAL 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 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 C residue 509 GLN 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 278 SER Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 288 GLU 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 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: 9.9990 chunk 65 optimal weight: 0.4980 chunk 49 optimal weight: 7.9990 chunk 69 optimal weight: 0.0870 chunk 96 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 overall best weight: 3.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN B 390 ASN E 495 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.094741 restraints weight = 35409.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096237 restraints weight = 23553.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.097269 restraints weight = 17871.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.097986 restraints weight = 14794.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.098460 restraints weight = 12983.026| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18264 Z= 0.187 Angle : 0.609 7.524 24753 Z= 0.324 Chirality : 0.045 0.174 2752 Planarity : 0.005 0.074 3251 Dihedral : 4.912 48.166 2473 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 2.96 % Allowed : 20.21 % Favored : 76.83 % 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: -3.34 (0.15), residues: 2263 helix: -1.25 (0.22), residues: 488 sheet: -1.58 (0.20), residues: 515 loop : -3.01 (0.15), residues: 1260 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 0.017 0.002 PHE B 487 TRP 0.011 0.001 TRP F 503 HIS 0.001 0.001 HIS Z 206 Details of bonding type rmsd covalent geometry : bond 0.00442 (18264) covalent geometry : angle 0.60945 (24753) hydrogen bonds : bond 0.03632 ( 464) hydrogen bonds : angle 5.59560 ( 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 226 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 167 time to evaluate : 0.697 Fit side-chains REVERT: A 241 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7965 (mt) REVERT: B 307 LEU cc_start: 0.7207 (tp) cc_final: 0.6621 (pt) REVERT: D 534 ASN cc_start: 0.7681 (t0) cc_final: 0.7131 (m-40) REVERT: E 432 ASN cc_start: 0.8911 (p0) cc_final: 0.8491 (p0) REVERT: F 527 GLU cc_start: 0.8198 (tt0) cc_final: 0.7944 (tt0) outliers start: 59 outliers final: 42 residues processed: 216 average time/residue: 0.1231 time to fit residues: 42.3808 Evaluate side-chains 196 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 432 ASN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 297 TYR 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 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 264 SER 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 300 VAL Chi-restraints excluded: chain E residue 390 ASN 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 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 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: 0.9980 chunk 133 optimal weight: 20.0000 chunk 67 optimal weight: 0.3980 chunk 192 optimal weight: 7.9990 chunk 139 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 49 optimal weight: 0.0970 chunk 96 optimal weight: 8.9990 chunk 191 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.123688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104350 restraints weight = 34127.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106499 restraints weight = 20248.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107901 restraints weight = 14294.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108855 restraints weight = 11343.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109429 restraints weight = 9695.237| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2244 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= 0.093 Angle : 0.532 7.427 24753 Z= 0.281 Chirality : 0.043 0.175 2752 Planarity : 0.004 0.054 3251 Dihedral : 4.415 45.721 2473 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.21 % Allowed : 21.01 % Favored : 76.78 % 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: -2.96 (0.16), residues: 2263 helix: -0.86 (0.23), residues: 490 sheet: -1.39 (0.21), residues: 505 loop : -2.77 (0.15), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 458 TYR 0.018 0.001 TYR C 464 PHE 0.009 0.001 PHE F 455 TRP 0.006 0.001 TRP F 503 HIS 0.001 0.001 HIS Z 164 Details of bonding type rmsd covalent geometry : bond 0.00201 (18264) covalent geometry : angle 0.53197 (24753) hydrogen bonds : bond 0.02692 ( 464) hydrogen bonds : angle 5.18998 ( 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 215 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 536 GLN cc_start: 0.7061 (mp-120) cc_final: 0.6804 (mp10) REVERT: B 307 LEU cc_start: 0.7055 (tp) cc_final: 0.6819 (pt) REVERT: B 390 ASN cc_start: 0.7927 (t0) cc_final: 0.7420 (t0) REVERT: C 426 GLU cc_start: 0.8351 (tp30) cc_final: 0.7775 (tp30) REVERT: D 432 ASN cc_start: 0.8414 (p0) cc_final: 0.8196 (p0) REVERT: D 534 ASN cc_start: 0.7479 (t0) cc_final: 0.7062 (m-40) REVERT: E 432 ASN cc_start: 0.8893 (p0) cc_final: 0.8414 (p0) REVERT: F 527 GLU cc_start: 0.8276 (tt0) cc_final: 0.7974 (tt0) REVERT: Z 254 MET cc_start: 0.5576 (ppp) cc_final: 0.5046 (ppp) outliers start: 44 outliers final: 32 residues processed: 204 average time/residue: 0.1124 time to fit residues: 37.4694 Evaluate side-chains 186 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 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 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 308 ILE Chi-restraints excluded: chain E residue 390 ASN Chi-restraints excluded: chain E residue 509 GLN Chi-restraints excluded: chain F residue 278 SER 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 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: 9.9990 chunk 10 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 482 GLN E 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.092569 restraints weight = 35959.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.094188 restraints weight = 23285.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.095312 restraints weight = 17329.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.096024 restraints weight = 14182.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.096536 restraints weight = 12411.952| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 18264 Z= 0.268 Angle : 0.687 8.183 24753 Z= 0.367 Chirality : 0.048 0.189 2752 Planarity : 0.005 0.062 3251 Dihedral : 5.250 54.222 2473 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 3.01 % Allowed : 20.61 % Favored : 76.38 % 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: -3.20 (0.16), residues: 2263 helix: -1.22 (0.22), residues: 488 sheet: -1.52 (0.21), residues: 491 loop : -2.85 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 458 TYR 0.022 0.002 TYR F 261 PHE 0.024 0.002 PHE D 281 TRP 0.014 0.002 TRP F 503 HIS 0.004 0.001 HIS Z 206 Details of bonding type rmsd covalent geometry : bond 0.00641 (18264) covalent geometry : angle 0.68743 (24753) hydrogen bonds : bond 0.04106 ( 464) hydrogen bonds : angle 5.77391 ( 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 214 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 154 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 241 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.8006 (mt) REVERT: B 470 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7744 (pp) REVERT: C 426 GLU cc_start: 0.8490 (tp30) cc_final: 0.8240 (tp30) REVERT: D 534 ASN cc_start: 0.7745 (t0) cc_final: 0.7027 (m-40) REVERT: E 432 ASN cc_start: 0.8911 (p0) cc_final: 0.8572 (p0) REVERT: F 527 GLU cc_start: 0.8215 (tt0) cc_final: 0.7962 (tt0) REVERT: Z 254 MET cc_start: 0.5846 (ppp) cc_final: 0.5270 (ppp) outliers start: 60 outliers final: 50 residues processed: 204 average time/residue: 0.1144 time to fit residues: 38.0866 Evaluate side-chains 200 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 451 THR Chi-restraints excluded: chain B residue 459 LEU 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 294 VAL 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 483 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 518 ILE 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 300 VAL Chi-restraints excluded: chain E residue 406 VAL 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 287 THR 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 288 GLU 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 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 362 VAL Chi-restraints excluded: chain Z residue 414 VAL Chi-restraints excluded: chain Z residue 415 ASP 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: 0.8980 chunk 186 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN G 536 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.120001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.100217 restraints weight = 34577.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102374 restraints weight = 20501.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.103782 restraints weight = 14449.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.104666 restraints weight = 11497.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105308 restraints weight = 9888.646| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18264 Z= 0.139 Angle : 0.581 8.022 24753 Z= 0.310 Chirality : 0.045 0.175 2752 Planarity : 0.004 0.055 3251 Dihedral : 4.863 51.520 2473 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.01 % Allowed : 21.61 % Favored : 75.38 % 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: -3.03 (0.16), residues: 2263 helix: -1.01 (0.23), residues: 489 sheet: -1.43 (0.21), residues: 521 loop : -2.77 (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 E 257 PHE 0.014 0.001 PHE B 487 TRP 0.010 0.001 TRP B 245 HIS 0.002 0.001 HIS Z 206 Details of bonding type rmsd covalent geometry : bond 0.00323 (18264) covalent geometry : angle 0.58150 (24753) hydrogen bonds : bond 0.03234 ( 464) hydrogen bonds : angle 5.45345 ( 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 220 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 160 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 241 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.8047 (mt) REVERT: A 536 GLN cc_start: 0.6970 (mp-120) cc_final: 0.6758 (mp10) REVERT: C 426 GLU cc_start: 0.8372 (tp30) cc_final: 0.7965 (tp30) REVERT: C 456 SER cc_start: 0.8141 (t) cc_final: 0.7771 (m) REVERT: C 511 ASP cc_start: 0.7600 (t0) cc_final: 0.7377 (t70) REVERT: D 432 ASN cc_start: 0.8469 (p0) cc_final: 0.8234 (p0) REVERT: D 534 ASN cc_start: 0.7617 (t0) cc_final: 0.7132 (m-40) REVERT: E 432 ASN cc_start: 0.8941 (p0) cc_final: 0.8484 (p0) REVERT: F 527 GLU cc_start: 0.8287 (tt0) cc_final: 0.7985 (tt0) REVERT: Z 254 MET cc_start: 0.5839 (ppp) cc_final: 0.5263 (ppp) REVERT: Z 353 MET cc_start: 0.5710 (ttp) cc_final: 0.5321 (ttp) outliers start: 60 outliers final: 53 residues processed: 209 average time/residue: 0.1142 time to fit residues: 38.3111 Evaluate side-chains 207 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 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 294 VAL 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 478 LEU Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 480 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 308 ILE Chi-restraints excluded: chain E residue 390 ASN Chi-restraints excluded: chain E residue 509 GLN 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 459 LEU Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 288 GLU 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 83 LEU 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 242 LEU 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: 9.9990 chunk 26 optimal weight: 9.9990 chunk 218 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 213 optimal weight: 30.0000 chunk 121 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 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 = 0.3478 r_free = 0.3478 target = 0.119869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.100433 restraints weight = 34123.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.102592 restraints weight = 19970.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.104005 restraints weight = 13931.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104928 restraints weight = 10983.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105543 restraints weight = 9390.037| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 0.034 18264 Z= 0.126 Angle : 0.567 8.917 24753 Z= 0.301 Chirality : 0.044 0.175 2752 Planarity : 0.004 0.050 3251 Dihedral : 4.671 50.446 2473 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.01 % Allowed : 21.82 % Favored : 75.18 % 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: -2.89 (0.16), residues: 2263 helix: -0.90 (0.23), residues: 490 sheet: -1.34 (0.21), residues: 521 loop : -2.69 (0.15), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 290 TYR 0.011 0.001 TYR E 257 PHE 0.014 0.001 PHE B 487 TRP 0.009 0.001 TRP B 245 HIS 0.002 0.001 HIS Z 206 Details of bonding type rmsd covalent geometry : bond 0.00292 (18264) covalent geometry : angle 0.56739 (24753) hydrogen bonds : bond 0.03056 ( 464) hydrogen bonds : angle 5.29488 ( 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 220 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 160 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 390 ASN cc_start: 0.8062 (t0) cc_final: 0.7594 (t0) REVERT: C 426 GLU cc_start: 0.8344 (tp30) cc_final: 0.7900 (tp30) REVERT: D 432 ASN cc_start: 0.8503 (p0) cc_final: 0.8257 (p0) REVERT: D 534 ASN cc_start: 0.7579 (t0) cc_final: 0.7136 (m-40) REVERT: E 432 ASN cc_start: 0.8940 (p0) cc_final: 0.8511 (p0) REVERT: F 527 GLU cc_start: 0.8275 (tt0) cc_final: 0.7965 (tt0) REVERT: Z 232 LYS cc_start: 0.6910 (mmmt) cc_final: 0.6620 (tppt) REVERT: Z 254 MET cc_start: 0.5893 (ppp) cc_final: 0.5314 (ppp) REVERT: Z 353 MET cc_start: 0.5546 (ttp) cc_final: 0.5190 (ttp) outliers start: 60 outliers final: 55 residues processed: 207 average time/residue: 0.1137 time to fit residues: 38.2419 Evaluate side-chains 207 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 297 TYR 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 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 415 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 480 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 300 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 390 ASN Chi-restraints excluded: chain E residue 509 GLN Chi-restraints excluded: chain E residue 516 SER 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 459 LEU Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 288 GLU 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 83 LEU 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 242 LEU 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: 9.9990 chunk 223 optimal weight: 30.0000 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 25 optimal weight: 0.0020 chunk 94 optimal weight: 0.0970 chunk 95 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 overall best weight: 2.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101369 restraints weight = 34266.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103554 restraints weight = 20253.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.104993 restraints weight = 14240.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105909 restraints weight = 11270.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106546 restraints weight = 9682.098| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18264 Z= 0.122 Angle : 0.565 8.372 24753 Z= 0.300 Chirality : 0.044 0.184 2752 Planarity : 0.004 0.050 3251 Dihedral : 4.603 50.316 2473 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.96 % Allowed : 22.02 % Favored : 75.03 % 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: -2.78 (0.16), residues: 2263 helix: -0.82 (0.23), residues: 490 sheet: -1.25 (0.22), residues: 505 loop : -2.62 (0.15), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 290 TYR 0.011 0.001 TYR E 257 PHE 0.013 0.001 PHE B 487 TRP 0.009 0.001 TRP B 245 HIS 0.002 0.001 HIS Z 206 Details of bonding type rmsd covalent geometry : bond 0.00282 (18264) covalent geometry : angle 0.56518 (24753) hydrogen bonds : bond 0.02996 ( 464) hydrogen bonds : angle 5.20427 ( 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 217 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 158 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 426 GLU cc_start: 0.8350 (tp30) cc_final: 0.7853 (tp30) REVERT: D 432 ASN cc_start: 0.8484 (p0) cc_final: 0.8241 (p0) REVERT: D 534 ASN cc_start: 0.7563 (t0) cc_final: 0.7131 (m-40) REVERT: E 432 ASN cc_start: 0.8944 (p0) cc_final: 0.8458 (p0) REVERT: F 527 GLU cc_start: 0.8291 (tt0) cc_final: 0.7994 (tt0) REVERT: Z 232 LYS cc_start: 0.6960 (mmmt) cc_final: 0.6704 (tppt) REVERT: Z 254 MET cc_start: 0.5913 (ppp) cc_final: 0.5373 (ppp) REVERT: Z 353 MET cc_start: 0.5518 (ttp) cc_final: 0.5179 (ttp) outliers start: 59 outliers final: 57 residues processed: 204 average time/residue: 0.1201 time to fit residues: 39.4777 Evaluate side-chains 209 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 152 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 297 TYR 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 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 294 VAL 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 478 LEU Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 480 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 308 ILE Chi-restraints excluded: chain E residue 390 ASN Chi-restraints excluded: chain E residue 509 GLN Chi-restraints excluded: chain E residue 516 SER 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 459 LEU Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 288 GLU 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 83 LEU 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 242 LEU 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: 5.9990 chunk 216 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN Z 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.098184 restraints weight = 34953.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.100322 restraints weight = 20779.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.101717 restraints weight = 14669.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.102631 restraints weight = 11705.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103202 restraints weight = 10072.995| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 18264 Z= 0.216 Angle : 0.647 7.822 24753 Z= 0.345 Chirality : 0.047 0.191 2752 Planarity : 0.005 0.055 3251 Dihedral : 5.081 54.408 2473 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.06 % Allowed : 22.07 % Favored : 74.87 % 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: -2.96 (0.16), residues: 2263 helix: -1.03 (0.23), residues: 487 sheet: -1.30 (0.21), residues: 515 loop : -2.74 (0.15), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 290 TYR 0.018 0.002 TYR F 261 PHE 0.019 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 covalent geometry : bond 0.00513 (18264) covalent geometry : angle 0.64733 (24753) hydrogen bonds : bond 0.03737 ( 464) hydrogen bonds : angle 5.57169 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2368.23 seconds wall clock time: 42 minutes 6.15 seconds (2526.15 seconds total)