Starting phenix.real_space_refine on Thu Feb 5 06:38:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mi9_23843/02_2026/7mi9_23843.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mi9_23843/02_2026/7mi9_23843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mi9_23843/02_2026/7mi9_23843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mi9_23843/02_2026/7mi9_23843.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mi9_23843/02_2026/7mi9_23843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mi9_23843/02_2026/7mi9_23843.map" } resolution = 3.89 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= 0.002 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 P 170 5.49 5 S 74 5.16 5 C 9521 2.51 5 N 2935 2.21 5 O 3224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15924 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2772 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 20, 'TRANS': 327} Chain: "B" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2696 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 18, 'TRANS': 319} Chain: "C" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2707 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 18, 'TRANS': 320} Chain: "D" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2696 Classifications: {'peptide': 339} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 320} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 786 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 786 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1639 Classifications: {'DNA': 80} Link IDs: {'rna3p': 79} Chain: "H" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1468 Classifications: {'DNA': 72} Link IDs: {'rna3p': 71} Chain: "I" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "J" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 124 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Time building chain proxies: 3.11, per 1000 atoms: 0.20 Number of scatterers: 15924 At special positions: 0 Unit cell: (119.574, 103.806, 185.274, 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) S 74 16.00 P 170 15.00 O 3224 8.00 N 2935 7.00 C 9521 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: 1.46 Conformation dependent library (CDL) restraints added in 513.1 milliseconds 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 15 sheets defined 45.9% alpha, 9.2% beta 47 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 269 through 278 removed outlier: 3.604A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 316 through 343 removed outlier: 3.914A pdb=" N CYS A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS A 331 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 419 through 438 removed outlier: 4.467A pdb=" N PHE A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 487 through 491 removed outlier: 3.798A pdb=" N PHE A 491 " --> pdb=" O THR A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 removed outlier: 3.591A pdb=" N LYS A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.931A pdb=" N THR B 257 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.671A pdb=" N THR B 306 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 336 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 353 through 368 Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 418 through 423 Processing helix chain 'B' and resid 424 through 437 removed outlier: 3.694A pdb=" N ARG B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 501 through 518 Processing helix chain 'B' and resid 531 through 546 removed outlier: 4.477A pdb=" N ALA B 539 " --> pdb=" O LEU B 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 277 Processing helix chain 'C' and resid 303 through 315 removed outlier: 3.574A pdb=" N ARG C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 333 removed outlier: 3.617A pdb=" N CYS C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 353 through 358 removed outlier: 3.880A pdb=" N MET C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 366 removed outlier: 3.689A pdb=" N MET C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 390 removed outlier: 3.717A pdb=" N GLY C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 394 removed outlier: 3.729A pdb=" N MET C 394 " --> pdb=" O PHE C 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 394' Processing helix chain 'C' and resid 417 through 441 removed outlier: 3.938A pdb=" N LEU C 422 " --> pdb=" O PRO C 418 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'C' and resid 467 through 472 removed outlier: 4.395A pdb=" N LEU C 471 " --> pdb=" O PRO C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 483 removed outlier: 3.973A pdb=" N VAL C 477 " --> pdb=" O ALA C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 518 removed outlier: 3.748A pdb=" N ALA C 510 " --> pdb=" O LYS C 506 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN C 518 " --> pdb=" O ARG C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 548 Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 269 through 279 removed outlier: 4.156A pdb=" N ARG D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 313 Processing helix chain 'D' and resid 316 through 342 removed outlier: 3.908A pdb=" N CYS D 320 " --> pdb=" O ASP D 316 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG D 326 " --> pdb=" O ASN D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 368 Processing helix chain 'D' and resid 375 through 392 removed outlier: 3.633A pdb=" N SER D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 441 removed outlier: 3.623A pdb=" N ARG D 432 " --> pdb=" O ALA D 428 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 433 " --> pdb=" O MET D 429 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 467 through 472 removed outlier: 3.681A pdb=" N LEU D 471 " --> pdb=" O PRO D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.679A pdb=" N ASN D 483 " --> pdb=" O MET D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 518 removed outlier: 3.577A pdb=" N MET D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 547 Processing helix chain 'E' and resid 13 through 26 removed outlier: 4.611A pdb=" N ARG E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 52 Processing helix chain 'F' and resid 13 through 26 removed outlier: 4.611A pdb=" N ARG F 19 " --> pdb=" O ARG F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 52 Processing sheet with id=AA1, first strand: chain 'A' and resid 222 through 226 removed outlier: 6.832A pdb=" N LEU A 222 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ALA A 261 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 224 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N PHE A 263 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 226 " --> pdb=" O PHE A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 253 removed outlier: 7.087A pdb=" N ILE A 242 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU A 251 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU A 240 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 233 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA4, first strand: chain 'A' and resid 519 through 521 Processing sheet with id=AA5, first strand: chain 'B' and resid 225 through 226 removed outlier: 6.132A pdb=" N VAL B 260 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 286 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU B 262 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP B 285 " --> pdb=" O MET B 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.759A pdb=" N ILE B 242 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AA8, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AA9, first strand: chain 'D' and resid 224 through 225 removed outlier: 7.982A pdb=" N LEU D 224 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL D 260 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL D 283 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 296 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS D 295 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL C 283 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 222 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C 260 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU C 224 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU C 262 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 226 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 248 through 253 removed outlier: 4.881A pdb=" N ALA C 250 " --> pdb=" O ILE C 242 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 491 through 493 Processing sheet with id=AB3, first strand: chain 'C' and resid 519 through 521 Processing sheet with id=AB4, first strand: chain 'D' and resid 231 through 236 Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 32 removed outlier: 5.515A pdb=" N TRP E 30 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLN E 37 " --> pdb=" O TRP E 30 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER F 79 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 78 through 80 removed outlier: 3.879A pdb=" N SER E 79 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN F 37 " --> pdb=" O TRP F 30 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TRP F 30 " --> pdb=" O GLN F 37 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.92 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: 3916 1.33 - 1.45: 4233 1.45 - 1.57: 8019 1.57 - 1.69: 336 1.69 - 1.82: 124 Bond restraints: 16628 Sorted by residual: bond pdb=" N GLY C 345 " pdb=" CA GLY C 345 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.98e+01 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.44e+01 bond pdb=" N ILE A 328 " pdb=" CA ILE A 328 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.18e-02 7.18e+03 1.40e+01 bond pdb=" O3' DT H 27 " pdb=" P DT H 28 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.29e+01 bond pdb=" CA ALA B 437 " pdb=" C ALA B 437 " ideal model delta sigma weight residual 1.523 1.479 0.043 1.41e-02 5.03e+03 9.47e+00 ... (remaining 16623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 22694 2.58 - 5.16: 470 5.16 - 7.75: 53 7.75 - 10.33: 6 10.33 - 12.91: 2 Bond angle restraints: 23225 Sorted by residual: angle pdb=" N ILE B 524 " pdb=" CA ILE B 524 " pdb=" C ILE B 524 " ideal model delta sigma weight residual 113.71 107.60 6.11 9.50e-01 1.11e+00 4.13e+01 angle pdb=" C ARG B 412 " pdb=" N ARG B 413 " pdb=" CA ARG B 413 " ideal model delta sigma weight residual 121.80 108.89 12.91 2.44e+00 1.68e-01 2.80e+01 angle pdb=" N PHE B 388 " pdb=" CA PHE B 388 " pdb=" C PHE B 388 " ideal model delta sigma weight residual 113.17 106.74 6.43 1.26e+00 6.30e-01 2.60e+01 angle pdb=" C4' DG H 39 " pdb=" C3' DG H 39 " pdb=" O3' DG H 39 " ideal model delta sigma weight residual 110.00 117.44 -7.44 1.50e+00 4.44e-01 2.46e+01 angle pdb=" C4' DT H 6 " pdb=" C3' DT H 6 " pdb=" O3' DT H 6 " ideal model delta sigma weight residual 110.00 117.40 -7.40 1.50e+00 4.44e-01 2.43e+01 ... (remaining 23220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 8490 34.99 - 69.97: 925 69.97 - 104.96: 41 104.96 - 139.94: 8 139.94 - 174.93: 5 Dihedral angle restraints: 9469 sinusoidal: 5001 harmonic: 4468 Sorted by residual: dihedral pdb=" CA ILE A 215 " pdb=" C ILE A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LEU A 478 " pdb=" C LEU A 478 " pdb=" N MET A 479 " pdb=" CA MET A 479 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLU B 243 " pdb=" C GLU B 243 " pdb=" N GLU B 244 " pdb=" CA GLU B 244 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 9466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2146 0.074 - 0.149: 355 0.149 - 0.223: 19 0.223 - 0.297: 1 0.297 - 0.372: 5 Chirality restraints: 2526 Sorted by residual: chirality pdb=" C3' DT H 6 " pdb=" C4' DT H 6 " pdb=" O3' DT H 6 " pdb=" C2' DT H 6 " both_signs ideal model delta sigma weight residual False -2.66 -2.29 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C3' DT G 10 " pdb=" C4' DT G 10 " pdb=" O3' DT G 10 " pdb=" C2' DT G 10 " both_signs ideal model delta sigma weight residual False -2.66 -2.29 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C3' DG H 10 " pdb=" C4' DG H 10 " pdb=" O3' DG H 10 " pdb=" C2' DG H 10 " both_signs ideal model delta sigma weight residual False -2.66 -2.31 -0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 2523 not shown) Planarity restraints: 2421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 466 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO A 467 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 370 " -0.062 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO D 371 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 371 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 371 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 550 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO C 551 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 551 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 551 " 0.039 5.00e-02 4.00e+02 ... (remaining 2418 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 337 2.59 - 3.16: 14547 3.16 - 3.74: 29004 3.74 - 4.32: 38425 4.32 - 4.90: 58256 Nonbonded interactions: 140569 Sorted by model distance: nonbonded pdb=" O ARG B 413 " pdb=" OP2 DT H 30 " model vdw 2.008 3.040 nonbonded pdb=" O GLN C 361 " pdb=" NE2 GLN C 361 " model vdw 2.117 3.120 nonbonded pdb=" O LEU A 323 " pdb=" CB TRP A 327 " model vdw 2.176 2.752 nonbonded pdb=" OD2 ASP A 490 " pdb=" NH2 ARG A 507 " model vdw 2.197 3.120 nonbonded pdb=" O PRO B 353 " pdb=" CD2 LEU B 357 " model vdw 2.202 3.460 ... (remaining 140564 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 221 through 379 or (resid 380 through 381 and (name N or n \ ame CA or name C or name O )) or resid 382 through 558)) selection = (chain 'B' and (resid 221 through 379 or (resid 380 through 381 and (name N or n \ ame CA or name C or name O )) or resid 382 through 558)) selection = (chain 'C' and (resid 221 through 379 or (resid 380 through 381 and (name N or n \ ame CA or name C or name O )) or resid 382 through 558)) selection = (chain 'D' and resid 221 through 558) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.540 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4923 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 : 0.006 0.054 16628 Z= 0.323 Angle : 0.907 12.909 23225 Z= 0.546 Chirality : 0.053 0.372 2526 Planarity : 0.007 0.113 2421 Dihedral : 24.159 174.930 6605 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 38.66 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.16 % Favored : 86.25 % Rotamer: Outliers : 2.08 % Allowed : 1.85 % Favored : 96.06 % Cbeta Deviations : 0.07 % 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 (0.20), residues: 1542 helix: -1.59 (0.19), residues: 677 sheet: -2.83 (0.46), residues: 111 loop : -2.78 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG C 514 TYR 0.037 0.003 TYR B 387 PHE 0.018 0.002 PHE B 556 TRP 0.033 0.003 TRP B 434 HIS 0.009 0.002 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00610 (16628) covalent geometry : angle 0.90736 (23225) hydrogen bonds : bond 0.18546 ( 631) hydrogen bonds : angle 8.11234 ( 1685) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 357 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.7780 (ttm) cc_final: 0.6765 (tpt) REVERT: A 508 PHE cc_start: 0.6403 (t80) cc_final: 0.6129 (t80) REVERT: B 293 MET cc_start: 0.6330 (mmt) cc_final: 0.6096 (mmm) REVERT: B 343 TRP cc_start: 0.5166 (OUTLIER) cc_final: 0.4940 (t-100) REVERT: B 429 MET cc_start: 0.7922 (mtm) cc_final: 0.7559 (mtp) REVERT: B 538 GLN cc_start: 0.8540 (tp40) cc_final: 0.8326 (tp40) REVERT: C 322 ASN cc_start: 0.6431 (m-40) cc_final: 0.5644 (m-40) REVERT: C 356 LEU cc_start: 0.5828 (tp) cc_final: 0.5627 (tp) REVERT: C 454 ARG cc_start: 0.5319 (tmt170) cc_final: 0.5060 (tpt-90) REVERT: C 472 ILE cc_start: 0.5861 (mp) cc_final: 0.5576 (mm) REVERT: D 236 ASP cc_start: 0.6354 (p0) cc_final: 0.6026 (p0) REVERT: D 358 MET cc_start: 0.6249 (tpt) cc_final: 0.5650 (tpt) REVERT: D 368 MET cc_start: 0.6404 (ptp) cc_final: 0.5783 (mmt) REVERT: D 407 PHE cc_start: 0.5802 (p90) cc_final: 0.5531 (p90) REVERT: D 410 ARG cc_start: 0.3449 (mmm160) cc_final: 0.3094 (tmt170) REVERT: D 479 MET cc_start: 0.5382 (mmm) cc_final: 0.4807 (mtp) REVERT: E 1 MET cc_start: 0.6882 (tpt) cc_final: 0.6670 (tpp) REVERT: F 74 VAL cc_start: 0.7423 (p) cc_final: 0.7109 (t) outliers start: 27 outliers final: 7 residues processed: 376 average time/residue: 0.1594 time to fit residues: 82.3379 Evaluate side-chains 212 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 343 TRP Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 11 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 390 HIS A 538 GLN ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN B 555 ASN C 265 ASN C 361 GLN ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.175157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.158598 restraints weight = 69601.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.158434 restraints weight = 66942.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.158767 restraints weight = 46504.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.158749 restraints weight = 36663.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.158898 restraints weight = 34462.415| |-----------------------------------------------------------------------------| r_work (final): 0.4599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5486 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16628 Z= 0.210 Angle : 0.814 11.238 23225 Z= 0.441 Chirality : 0.048 0.192 2526 Planarity : 0.007 0.063 2421 Dihedral : 27.505 178.416 3611 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.66 % Favored : 90.21 % Rotamer: Outliers : 2.78 % Allowed : 14.66 % Favored : 82.56 % 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: -2.93 (0.20), residues: 1542 helix: -1.23 (0.19), residues: 699 sheet: -2.30 (0.53), residues: 89 loop : -2.62 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 412 TYR 0.027 0.002 TYR A 527 PHE 0.025 0.002 PHE C 292 TRP 0.024 0.003 TRP A 343 HIS 0.022 0.002 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00469 (16628) covalent geometry : angle 0.81375 (23225) hydrogen bonds : bond 0.05319 ( 631) hydrogen bonds : angle 5.87034 ( 1685) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7478 (tm-30) REVERT: A 390 HIS cc_start: 0.6402 (OUTLIER) cc_final: 0.6140 (m170) REVERT: A 416 LYS cc_start: 0.7835 (ttpt) cc_final: 0.7569 (ttpt) REVERT: A 462 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8342 (tp) REVERT: A 464 MET cc_start: 0.8690 (ttm) cc_final: 0.8486 (tpp) REVERT: A 508 PHE cc_start: 0.6709 (t80) cc_final: 0.6494 (t80) REVERT: B 516 MET cc_start: 0.6580 (mmm) cc_final: 0.6195 (tpp) REVERT: B 538 GLN cc_start: 0.8829 (tp40) cc_final: 0.8377 (tp40) REVERT: C 358 MET cc_start: 0.7115 (pmm) cc_final: 0.6887 (pmm) REVERT: D 232 TYR cc_start: 0.4041 (t80) cc_final: 0.3615 (t80) REVERT: D 358 MET cc_start: 0.6030 (tpt) cc_final: 0.5178 (tpt) REVERT: D 465 MET cc_start: 0.2832 (ppp) cc_final: 0.2592 (ppp) REVERT: D 479 MET cc_start: 0.6177 (mmm) cc_final: 0.5539 (mtp) outliers start: 36 outliers final: 14 residues processed: 250 average time/residue: 0.1253 time to fit residues: 46.0003 Evaluate side-chains 195 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 390 HIS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 527 TYR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 163 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 555 ASN B 342 ASN B 366 HIS ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN D 301 HIS D 420 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.169009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.150693 restraints weight = 66739.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.150084 restraints weight = 59010.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.150740 restraints weight = 41871.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.150755 restraints weight = 31671.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.150882 restraints weight = 31012.000| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16628 Z= 0.222 Angle : 0.769 11.691 23225 Z= 0.419 Chirality : 0.046 0.230 2526 Planarity : 0.007 0.057 2421 Dihedral : 27.193 175.680 3595 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.79 % Favored : 90.08 % Rotamer: Outliers : 2.93 % Allowed : 19.06 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.81 (0.20), residues: 1542 helix: -0.95 (0.19), residues: 697 sheet: -2.52 (0.47), residues: 104 loop : -2.69 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 365 TYR 0.024 0.002 TYR A 527 PHE 0.017 0.002 PHE C 512 TRP 0.030 0.002 TRP A 327 HIS 0.041 0.002 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00495 (16628) covalent geometry : angle 0.76925 (23225) hydrogen bonds : bond 0.05076 ( 631) hydrogen bonds : angle 5.54539 ( 1685) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.6840 (mp10) cc_final: 0.6564 (mp10) REVERT: A 291 TRP cc_start: 0.7477 (t60) cc_final: 0.7205 (t60) REVERT: A 401 GLU cc_start: 0.7128 (pp20) cc_final: 0.6755 (pp20) REVERT: A 462 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8538 (mp) REVERT: A 464 MET cc_start: 0.9098 (ttm) cc_final: 0.7245 (tpt) REVERT: B 343 TRP cc_start: 0.6322 (t-100) cc_final: 0.5779 (t-100) REVERT: B 538 GLN cc_start: 0.8927 (tp40) cc_final: 0.8363 (tp40) REVERT: C 285 TRP cc_start: 0.7916 (m-90) cc_final: 0.7200 (m-10) REVERT: C 356 LEU cc_start: 0.5922 (tp) cc_final: 0.5648 (tp) REVERT: C 358 MET cc_start: 0.7256 (pmm) cc_final: 0.6946 (pmm) REVERT: C 389 GLN cc_start: 0.7715 (mt0) cc_final: 0.7408 (mp10) REVERT: C 391 PHE cc_start: 0.7461 (t80) cc_final: 0.6912 (m-80) REVERT: D 227 GLN cc_start: 0.4705 (tp40) cc_final: 0.3649 (mp10) REVERT: D 296 THR cc_start: 0.5733 (OUTLIER) cc_final: 0.5504 (m) REVERT: D 465 MET cc_start: 0.3242 (ppp) cc_final: 0.2691 (ppp) REVERT: D 479 MET cc_start: 0.6346 (mmm) cc_final: 0.5899 (mtp) outliers start: 38 outliers final: 23 residues processed: 229 average time/residue: 0.1203 time to fit residues: 40.6402 Evaluate side-chains 189 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 508 PHE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 42 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 130 optimal weight: 30.0000 chunk 18 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS B 451 HIS C 265 ASN C 274 HIS C 301 HIS C 310 GLN C 334 ASN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.167185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.148360 restraints weight = 65214.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.148120 restraints weight = 45877.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.148197 restraints weight = 35495.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.148294 restraints weight = 30119.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.148342 restraints weight = 28564.529| |-----------------------------------------------------------------------------| r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16628 Z= 0.197 Angle : 0.725 8.033 23225 Z= 0.396 Chirality : 0.044 0.235 2526 Planarity : 0.006 0.058 2421 Dihedral : 27.092 178.447 3595 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.53 % Favored : 90.34 % Rotamer: Outliers : 3.86 % Allowed : 20.45 % Favored : 75.69 % 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: -2.66 (0.20), residues: 1542 helix: -0.74 (0.19), residues: 695 sheet: -2.56 (0.46), residues: 109 loop : -2.69 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 514 TYR 0.022 0.002 TYR D 450 PHE 0.033 0.002 PHE A 508 TRP 0.044 0.002 TRP A 327 HIS 0.006 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00442 (16628) covalent geometry : angle 0.72511 (23225) hydrogen bonds : bond 0.04595 ( 631) hydrogen bonds : angle 5.36416 ( 1685) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.6629 (mp10) cc_final: 0.6076 (mp10) REVERT: A 327 TRP cc_start: 0.7889 (OUTLIER) cc_final: 0.7634 (m-10) REVERT: A 389 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7373 (pp30) REVERT: A 401 GLU cc_start: 0.6827 (pp20) cc_final: 0.6596 (pp20) REVERT: A 464 MET cc_start: 0.9279 (ttm) cc_final: 0.7205 (tpt) REVERT: B 343 TRP cc_start: 0.6415 (t-100) cc_final: 0.5900 (t-100) REVERT: B 403 MET cc_start: 0.3241 (tpp) cc_final: 0.2945 (tpp) REVERT: B 514 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7941 (ttm110) REVERT: B 538 GLN cc_start: 0.8930 (tp40) cc_final: 0.8333 (tp40) REVERT: C 277 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7724 (mm) REVERT: C 285 TRP cc_start: 0.7774 (m-90) cc_final: 0.7115 (m-10) REVERT: C 356 LEU cc_start: 0.5993 (tp) cc_final: 0.5745 (tp) REVERT: C 358 MET cc_start: 0.7335 (pmm) cc_final: 0.6963 (pmm) REVERT: C 479 MET cc_start: 0.5117 (ppp) cc_final: 0.4452 (tmm) REVERT: C 491 PHE cc_start: 0.6723 (m-80) cc_final: 0.6497 (m-80) REVERT: D 227 GLN cc_start: 0.4938 (tp40) cc_final: 0.4319 (mp10) REVERT: D 296 THR cc_start: 0.5934 (OUTLIER) cc_final: 0.4836 (m) REVERT: D 368 MET cc_start: 0.6253 (mtm) cc_final: 0.4086 (tpt) REVERT: D 479 MET cc_start: 0.6326 (mmm) cc_final: 0.6109 (mtp) REVERT: E 2 GLU cc_start: 0.6430 (tt0) cc_final: 0.6002 (tt0) outliers start: 50 outliers final: 27 residues processed: 215 average time/residue: 0.1268 time to fit residues: 39.9055 Evaluate side-chains 191 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 498 CYS Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 508 PHE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 39 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS B 451 HIS ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN F 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.168475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.151145 restraints weight = 65383.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.148972 restraints weight = 61910.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.148913 restraints weight = 58418.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.149544 restraints weight = 44638.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.149804 restraints weight = 37857.325| |-----------------------------------------------------------------------------| r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16628 Z= 0.159 Angle : 0.689 9.497 23225 Z= 0.374 Chirality : 0.042 0.177 2526 Planarity : 0.006 0.050 2421 Dihedral : 26.959 177.667 3595 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.56 % Favored : 91.37 % Rotamer: Outliers : 3.78 % Allowed : 22.38 % Favored : 73.84 % 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: -2.37 (0.20), residues: 1542 helix: -0.42 (0.20), residues: 694 sheet: -2.43 (0.50), residues: 95 loop : -2.63 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 505 TYR 0.026 0.002 TYR D 450 PHE 0.016 0.002 PHE C 407 TRP 0.052 0.002 TRP A 327 HIS 0.008 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00355 (16628) covalent geometry : angle 0.68910 (23225) hydrogen bonds : bond 0.03921 ( 631) hydrogen bonds : angle 5.09265 ( 1685) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.6193 (mp10) cc_final: 0.5651 (mp10) REVERT: A 288 TYR cc_start: 0.6193 (OUTLIER) cc_final: 0.5435 (t80) REVERT: A 389 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7606 (pp30) REVERT: A 464 MET cc_start: 0.9088 (ttm) cc_final: 0.7174 (tpt) REVERT: B 343 TRP cc_start: 0.6522 (t-100) cc_final: 0.5989 (t-100) REVERT: B 403 MET cc_start: 0.3120 (tpp) cc_final: 0.2894 (tpp) REVERT: B 538 GLN cc_start: 0.9015 (tp40) cc_final: 0.8401 (tp40) REVERT: C 259 GLN cc_start: 0.7127 (pp30) cc_final: 0.6837 (pp30) REVERT: C 277 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7676 (mm) REVERT: C 285 TRP cc_start: 0.7538 (m-90) cc_final: 0.7272 (m-10) REVERT: C 293 MET cc_start: 0.6611 (ptp) cc_final: 0.4546 (tpt) REVERT: C 358 MET cc_start: 0.7215 (pmm) cc_final: 0.6973 (pmm) REVERT: C 391 PHE cc_start: 0.8268 (m-80) cc_final: 0.7900 (m-80) REVERT: C 403 MET cc_start: 0.1379 (mmm) cc_final: 0.0996 (mmt) REVERT: C 479 MET cc_start: 0.5244 (ppp) cc_final: 0.4543 (tmm) REVERT: C 491 PHE cc_start: 0.6788 (m-80) cc_final: 0.6458 (m-80) REVERT: D 227 GLN cc_start: 0.5334 (tp40) cc_final: 0.4591 (mp10) REVERT: D 296 THR cc_start: 0.6284 (OUTLIER) cc_final: 0.4661 (m) REVERT: D 479 MET cc_start: 0.6510 (mmm) cc_final: 0.6017 (mtp) REVERT: E 2 GLU cc_start: 0.6501 (tt0) cc_final: 0.5921 (tt0) outliers start: 49 outliers final: 26 residues processed: 217 average time/residue: 0.1329 time to fit residues: 42.4323 Evaluate side-chains 179 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 434 TRP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 498 CYS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 117 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.158044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.137814 restraints weight = 63518.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.136768 restraints weight = 47127.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.137027 restraints weight = 41044.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.137110 restraints weight = 34091.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.137194 restraints weight = 32423.194| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.8159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 16628 Z= 0.318 Angle : 0.848 9.160 23225 Z= 0.462 Chirality : 0.049 0.236 2526 Planarity : 0.008 0.079 2421 Dihedral : 27.074 177.453 3595 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 28.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.89 % Favored : 89.04 % Rotamer: Outliers : 4.86 % Allowed : 23.84 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % 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: -2.75 (0.20), residues: 1542 helix: -0.71 (0.19), residues: 694 sheet: -3.10 (0.41), residues: 113 loop : -2.77 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C 386 TYR 0.026 0.003 TYR D 450 PHE 0.020 0.003 PHE D 407 TRP 0.059 0.004 TRP A 327 HIS 0.009 0.002 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00683 (16628) covalent geometry : angle 0.84760 (23225) hydrogen bonds : bond 0.06236 ( 631) hydrogen bonds : angle 5.61392 ( 1685) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 170 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7952 (tptt) cc_final: 0.7712 (mtmm) REVERT: A 259 GLN cc_start: 0.6338 (mp10) cc_final: 0.5786 (mp10) REVERT: A 299 THR cc_start: 0.5884 (OUTLIER) cc_final: 0.5646 (p) REVERT: A 389 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7732 (pp30) REVERT: A 464 MET cc_start: 0.9338 (ttm) cc_final: 0.7619 (tpt) REVERT: B 343 TRP cc_start: 0.6750 (t-100) cc_final: 0.5963 (t-100) REVERT: B 538 GLN cc_start: 0.9228 (tp40) cc_final: 0.8805 (tp40) REVERT: C 265 ASN cc_start: 0.7346 (m110) cc_final: 0.7114 (m110) REVERT: C 277 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7998 (mm) REVERT: C 358 MET cc_start: 0.7191 (pmm) cc_final: 0.6976 (pmm) REVERT: C 391 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: C 403 MET cc_start: 0.1597 (mmm) cc_final: 0.0577 (mtt) REVERT: C 479 MET cc_start: 0.5199 (ppp) cc_final: 0.4465 (tmm) REVERT: C 491 PHE cc_start: 0.6886 (m-80) cc_final: 0.6535 (m-80) REVERT: D 226 VAL cc_start: 0.7594 (OUTLIER) cc_final: 0.7200 (p) REVERT: D 227 GLN cc_start: 0.5472 (tp40) cc_final: 0.5058 (mp10) REVERT: D 465 MET cc_start: 0.2009 (ptm) cc_final: 0.1777 (ptm) REVERT: D 479 MET cc_start: 0.7601 (mmm) cc_final: 0.6224 (mtp) outliers start: 63 outliers final: 35 residues processed: 213 average time/residue: 0.1363 time to fit residues: 42.3086 Evaluate side-chains 190 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 556 PHE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 94 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 46 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.160831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.141842 restraints weight = 63860.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.141211 restraints weight = 49930.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.141252 restraints weight = 38234.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.141400 restraints weight = 33031.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.141453 restraints weight = 31390.765| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.8596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16628 Z= 0.195 Angle : 0.753 10.484 23225 Z= 0.407 Chirality : 0.045 0.198 2526 Planarity : 0.006 0.055 2421 Dihedral : 27.050 178.119 3595 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.40 % Favored : 90.53 % Rotamer: Outliers : 4.24 % Allowed : 25.69 % Favored : 70.06 % 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: -2.56 (0.20), residues: 1542 helix: -0.48 (0.20), residues: 687 sheet: -3.17 (0.43), residues: 99 loop : -2.71 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 246 TYR 0.017 0.002 TYR A 527 PHE 0.024 0.002 PHE A 315 TRP 0.060 0.003 TRP A 327 HIS 0.011 0.002 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00444 (16628) covalent geometry : angle 0.75309 (23225) hydrogen bonds : bond 0.04217 ( 631) hydrogen bonds : angle 5.32969 ( 1685) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8696 (p) REVERT: A 259 GLN cc_start: 0.6147 (mp10) cc_final: 0.5637 (mp10) REVERT: A 288 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.5834 (t80) REVERT: A 299 THR cc_start: 0.5545 (OUTLIER) cc_final: 0.5253 (p) REVERT: A 389 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7838 (pp30) REVERT: A 464 MET cc_start: 0.9132 (ttm) cc_final: 0.7543 (tpt) REVERT: B 325 ARG cc_start: 0.6712 (mtt180) cc_final: 0.6316 (mtm180) REVERT: B 343 TRP cc_start: 0.6709 (t-100) cc_final: 0.6233 (t-100) REVERT: B 526 LYS cc_start: 0.7950 (tptp) cc_final: 0.7701 (mmmt) REVERT: B 538 GLN cc_start: 0.9198 (tp40) cc_final: 0.8797 (tp40) REVERT: C 265 ASN cc_start: 0.7243 (m110) cc_final: 0.6988 (m110) REVERT: C 277 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8097 (mm) REVERT: C 391 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7778 (m-80) REVERT: C 403 MET cc_start: 0.0913 (mmm) cc_final: 0.0453 (mtt) REVERT: C 479 MET cc_start: 0.5177 (ppp) cc_final: 0.4314 (tmm) REVERT: C 531 TYR cc_start: 0.7649 (OUTLIER) cc_final: 0.7139 (t80) REVERT: D 226 VAL cc_start: 0.7462 (OUTLIER) cc_final: 0.7070 (p) REVERT: D 227 GLN cc_start: 0.5413 (tp40) cc_final: 0.5009 (mp10) REVERT: D 234 ARG cc_start: 0.8037 (mpp80) cc_final: 0.7609 (mpt-90) REVERT: D 235 LYS cc_start: 0.6444 (tttm) cc_final: 0.6120 (ttmt) REVERT: D 368 MET cc_start: 0.6293 (pmm) cc_final: 0.3746 (tpt) REVERT: D 479 MET cc_start: 0.7430 (mmm) cc_final: 0.6299 (mtp) REVERT: E 79 SER cc_start: 0.7669 (OUTLIER) cc_final: 0.7182 (m) outliers start: 55 outliers final: 30 residues processed: 212 average time/residue: 0.1309 time to fit residues: 40.8217 Evaluate side-chains 194 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 531 TYR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 515 ARG Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 107 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 130 optimal weight: 30.0000 chunk 126 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 ASN ** D 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.157978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.138281 restraints weight = 63938.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.137841 restraints weight = 47588.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.138121 restraints weight = 36476.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.138127 restraints weight = 32859.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.138179 restraints weight = 30533.565| |-----------------------------------------------------------------------------| r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.9254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16628 Z= 0.225 Angle : 0.778 10.486 23225 Z= 0.420 Chirality : 0.045 0.209 2526 Planarity : 0.007 0.073 2421 Dihedral : 27.047 179.744 3595 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.57 % Favored : 89.36 % Rotamer: Outliers : 3.94 % Allowed : 26.54 % Favored : 69.52 % 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: -2.57 (0.20), residues: 1542 helix: -0.58 (0.20), residues: 698 sheet: -3.07 (0.40), residues: 119 loop : -2.63 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 326 TYR 0.025 0.002 TYR D 450 PHE 0.024 0.002 PHE A 315 TRP 0.090 0.004 TRP A 327 HIS 0.022 0.002 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00507 (16628) covalent geometry : angle 0.77802 (23225) hydrogen bonds : bond 0.04836 ( 631) hydrogen bonds : angle 5.34768 ( 1685) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.6146 (mp10) cc_final: 0.5659 (mp10) REVERT: A 299 THR cc_start: 0.5565 (OUTLIER) cc_final: 0.5301 (p) REVERT: A 331 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7569 (tppt) REVERT: A 389 GLN cc_start: 0.8301 (tm-30) cc_final: 0.8010 (pp30) REVERT: A 464 MET cc_start: 0.9039 (ttm) cc_final: 0.8544 (tpt) REVERT: B 234 ARG cc_start: 0.7478 (ttp-110) cc_final: 0.6971 (tpt170) REVERT: B 325 ARG cc_start: 0.7013 (mtt180) cc_final: 0.6720 (mtm110) REVERT: B 343 TRP cc_start: 0.6638 (t-100) cc_final: 0.6201 (t-100) REVERT: B 364 MET cc_start: 0.8176 (ttm) cc_final: 0.7956 (ttp) REVERT: B 394 MET cc_start: 0.6184 (ptp) cc_final: 0.5947 (ptp) REVERT: B 538 GLN cc_start: 0.9155 (tp40) cc_final: 0.8712 (tp40) REVERT: C 265 ASN cc_start: 0.7414 (m110) cc_final: 0.7168 (m110) REVERT: C 277 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8217 (mm) REVERT: C 341 ARG cc_start: 0.6374 (ptp90) cc_final: 0.5746 (ptp-170) REVERT: C 479 MET cc_start: 0.5120 (ppp) cc_final: 0.4435 (tmm) REVERT: C 531 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.7041 (t80) REVERT: D 226 VAL cc_start: 0.7304 (OUTLIER) cc_final: 0.6927 (p) REVERT: D 227 GLN cc_start: 0.5705 (tp40) cc_final: 0.5389 (mp10) REVERT: D 234 ARG cc_start: 0.8121 (mpp80) cc_final: 0.7670 (mpt-90) REVERT: D 235 LYS cc_start: 0.6497 (tttm) cc_final: 0.6254 (ttmt) REVERT: D 429 MET cc_start: 0.4138 (ptp) cc_final: 0.3741 (ptm) REVERT: D 465 MET cc_start: 0.2069 (ptm) cc_final: 0.1355 (ptm) REVERT: D 479 MET cc_start: 0.7778 (mmm) cc_final: 0.6932 (mtp) REVERT: E 79 SER cc_start: 0.7665 (OUTLIER) cc_final: 0.7279 (m) outliers start: 51 outliers final: 30 residues processed: 205 average time/residue: 0.1356 time to fit residues: 40.3954 Evaluate side-chains 186 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 531 TYR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 140 optimal weight: 0.0870 chunk 39 optimal weight: 0.0170 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN C 295 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.160275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.141592 restraints weight = 65053.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.141457 restraints weight = 61524.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.142312 restraints weight = 42384.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.142186 restraints weight = 33061.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.142367 restraints weight = 31986.007| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.9543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 16628 Z= 0.187 Angle : 0.758 10.344 23225 Z= 0.404 Chirality : 0.045 0.257 2526 Planarity : 0.006 0.057 2421 Dihedral : 26.984 176.867 3595 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.73 % Favored : 90.21 % Rotamer: Outliers : 3.16 % Allowed : 27.62 % Favored : 69.21 % 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: -2.51 (0.20), residues: 1542 helix: -0.59 (0.20), residues: 691 sheet: -2.94 (0.43), residues: 96 loop : -2.56 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 532 TYR 0.016 0.002 TYR C 531 PHE 0.026 0.002 PHE C 468 TRP 0.076 0.004 TRP D 327 HIS 0.026 0.002 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00431 (16628) covalent geometry : angle 0.75837 (23225) hydrogen bonds : bond 0.04093 ( 631) hydrogen bonds : angle 5.34232 ( 1685) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.5907 (mp10) cc_final: 0.5520 (mp10) REVERT: A 288 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.5776 (t80) REVERT: A 299 THR cc_start: 0.5484 (OUTLIER) cc_final: 0.5190 (p) REVERT: A 358 MET cc_start: 0.7783 (tpp) cc_final: 0.7548 (mpp) REVERT: A 389 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7947 (pp30) REVERT: A 464 MET cc_start: 0.9071 (ttm) cc_final: 0.8521 (tpt) REVERT: B 234 ARG cc_start: 0.7560 (ttp-110) cc_final: 0.7103 (tpt170) REVERT: B 538 GLN cc_start: 0.9173 (tp40) cc_final: 0.8543 (tp40) REVERT: C 265 ASN cc_start: 0.7374 (m110) cc_final: 0.7128 (m110) REVERT: C 277 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8232 (mm) REVERT: C 293 MET cc_start: 0.6771 (ptp) cc_final: 0.5165 (tpt) REVERT: C 341 ARG cc_start: 0.6370 (ptp90) cc_final: 0.5793 (ptp-170) REVERT: C 391 PHE cc_start: 0.8315 (m-80) cc_final: 0.8100 (m-80) REVERT: C 479 MET cc_start: 0.5010 (ppp) cc_final: 0.4496 (tmm) REVERT: C 531 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.7103 (t80) REVERT: D 226 VAL cc_start: 0.7051 (OUTLIER) cc_final: 0.6670 (p) REVERT: D 234 ARG cc_start: 0.8142 (mpp80) cc_final: 0.7636 (mpt-90) REVERT: D 235 LYS cc_start: 0.6574 (tttm) cc_final: 0.6288 (ttmt) REVERT: D 429 MET cc_start: 0.4412 (ptp) cc_final: 0.4012 (ptm) REVERT: D 479 MET cc_start: 0.8068 (mmm) cc_final: 0.7081 (mtp) REVERT: E 1 MET cc_start: 0.5952 (tpt) cc_final: 0.5460 (tpp) REVERT: E 79 SER cc_start: 0.7547 (OUTLIER) cc_final: 0.7133 (m) outliers start: 41 outliers final: 26 residues processed: 184 average time/residue: 0.1347 time to fit residues: 36.0210 Evaluate side-chains 175 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 531 TYR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 49 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 555 ASN B 342 ASN B 361 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.154432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.135178 restraints weight = 63840.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.135088 restraints weight = 56629.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.135469 restraints weight = 38642.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.135597 restraints weight = 32031.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.135681 restraints weight = 30917.711| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 1.0321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 16628 Z= 0.276 Angle : 0.850 10.171 23225 Z= 0.455 Chirality : 0.049 0.359 2526 Planarity : 0.007 0.104 2421 Dihedral : 27.094 176.142 3595 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 27.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 2.85 % Allowed : 27.62 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.07 % 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 (0.20), residues: 1542 helix: -0.82 (0.19), residues: 702 sheet: -3.00 (0.39), residues: 117 loop : -2.71 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 393 TYR 0.021 0.002 TYR A 527 PHE 0.027 0.003 PHE A 315 TRP 0.069 0.005 TRP A 327 HIS 0.027 0.002 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00620 (16628) covalent geometry : angle 0.84967 (23225) hydrogen bonds : bond 0.05633 ( 631) hydrogen bonds : angle 5.64787 ( 1685) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.6078 (mp10) cc_final: 0.5586 (mp10) REVERT: A 299 THR cc_start: 0.6007 (OUTLIER) cc_final: 0.5791 (p) REVERT: A 389 GLN cc_start: 0.8337 (tm-30) cc_final: 0.8115 (pp30) REVERT: A 464 MET cc_start: 0.9156 (ttm) cc_final: 0.8669 (tpt) REVERT: B 234 ARG cc_start: 0.7608 (ttp-110) cc_final: 0.6904 (mtt180) REVERT: B 368 MET cc_start: 0.7387 (mpp) cc_final: 0.7001 (mpp) REVERT: B 538 GLN cc_start: 0.9026 (tp40) cc_final: 0.8586 (tp40) REVERT: C 277 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8322 (mm) REVERT: C 341 ARG cc_start: 0.7184 (ptp90) cc_final: 0.6285 (ptp-170) REVERT: C 391 PHE cc_start: 0.8349 (m-80) cc_final: 0.8074 (m-80) REVERT: C 403 MET cc_start: -0.0486 (mtt) cc_final: -0.0689 (mtt) REVERT: C 479 MET cc_start: 0.5255 (ppp) cc_final: 0.4211 (tmm) REVERT: C 531 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7173 (t80) REVERT: D 234 ARG cc_start: 0.8323 (mpp80) cc_final: 0.7838 (mpt-90) REVERT: D 235 LYS cc_start: 0.6810 (tttm) cc_final: 0.6537 (ttmt) REVERT: D 429 MET cc_start: 0.4819 (ptp) cc_final: 0.4419 (ptm) REVERT: D 479 MET cc_start: 0.8391 (mmm) cc_final: 0.7332 (mtp) REVERT: E 1 MET cc_start: 0.6121 (tpt) cc_final: 0.5559 (tpp) REVERT: E 48 MET cc_start: 0.8502 (tpt) cc_final: 0.8288 (tpt) REVERT: E 79 SER cc_start: 0.7660 (OUTLIER) cc_final: 0.7294 (m) outliers start: 37 outliers final: 28 residues processed: 182 average time/residue: 0.1326 time to fit residues: 35.3688 Evaluate side-chains 176 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 531 TYR Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 58 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 145 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 69 optimal weight: 0.0670 chunk 157 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.0070 chunk 101 optimal weight: 5.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.159992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.141092 restraints weight = 64616.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.141185 restraints weight = 46727.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.141622 restraints weight = 33822.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.141606 restraints weight = 30610.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.141628 restraints weight = 29158.752| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 1.0405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16628 Z= 0.166 Angle : 0.764 10.988 23225 Z= 0.403 Chirality : 0.044 0.216 2526 Planarity : 0.006 0.089 2421 Dihedral : 26.912 175.651 3595 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.39 % Allowed : 27.70 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.57 (0.20), residues: 1542 helix: -0.61 (0.19), residues: 689 sheet: -2.70 (0.46), residues: 98 loop : -2.67 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 325 TYR 0.028 0.002 TYR C 450 PHE 0.024 0.002 PHE C 512 TRP 0.067 0.004 TRP A 327 HIS 0.022 0.002 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00384 (16628) covalent geometry : angle 0.76410 (23225) hydrogen bonds : bond 0.03968 ( 631) hydrogen bonds : angle 5.30410 ( 1685) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2418.64 seconds wall clock time: 42 minutes 53.35 seconds (2573.35 seconds total)