Starting phenix.real_space_refine on Tue Dec 31 13:38:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mi9_23843/12_2024/7mi9_23843.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mi9_23843/12_2024/7mi9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mi9_23843/12_2024/7mi9_23843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mi9_23843/12_2024/7mi9_23843.map" model { file = "/net/cci-nas-00/data/ceres_data/7mi9_23843/12_2024/7mi9_23843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mi9_23843/12_2024/7mi9_23843.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLU:plan': 1, 'ARG: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: 9.80, per 1000 atoms: 0.62 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: 4.69 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 6.50 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: 6.39 Time building geometry restraints manager: 4.98 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: 1.780 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: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 41.720 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.110 ------------------------------------------------------------------------------- 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= 0.385 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 : 38.70 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.033 0.003 TRP B 434 HIS 0.009 0.002 HIS A 295 PHE 0.018 0.002 PHE B 556 TYR 0.037 0.003 TYR B 387 ARG 0.024 0.001 ARG C 514 *********************** 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 : 1.562 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: A 464 MET cc_start: 0.7780 (ttm) cc_final: 0.6769 (tpt) REVERT: A 508 PHE cc_start: 0.6403 (t80) cc_final: 0.6123 (t80) REVERT: B 293 MET cc_start: 0.6330 (mmt) cc_final: 0.6094 (mmm) REVERT: B 343 TRP cc_start: 0.5166 (OUTLIER) cc_final: 0.4937 (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: 0.8318 (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: 0.5625 (tp) REVERT: C 454 ARG cc_start: 0.5319 (tmt170) cc_final: 0.5050 (tpt-90) REVERT: C 472 ILE cc_start: 0.5861 (mp) cc_final: 0.5585 (mm) REVERT: D 236 ASP cc_start: 0.6354 (p0) cc_final: 0.6025 (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: 0.5782 (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: 0.3095 (tmt170) REVERT: D 479 MET cc_start: 0.5382 (mmm) cc_final: 0.4808 (mtp) REVERT: E 1 MET cc_start: 0.6882 (tpt) cc_final: 0.6675 (tpp) REVERT: F 74 VAL cc_start: 0.7423 (p) cc_final: 0.7115 (t) outliers start: 27 outliers final: 7 residues processed: 376 average time/residue: 0.3776 time to fit residues: 193.5830 Evaluate side-chains 211 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 141 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 40.0000 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 97 optimal weight: 0.0070 chunk 151 optimal weight: 4.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 B 420 ASN B 555 ASN C 265 ASN ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5114 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16628 Z= 0.265 Angle : 0.793 10.222 23225 Z= 0.431 Chirality : 0.047 0.193 2526 Planarity : 0.007 0.065 2421 Dihedral : 27.519 178.352 3611 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.27 % Favored : 90.60 % Rotamer: Outliers : 2.70 % Allowed : 13.89 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.20), residues: 1542 helix: -1.17 (0.19), residues: 697 sheet: -2.21 (0.52), residues: 89 loop : -2.60 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 343 HIS 0.022 0.002 HIS B 366 PHE 0.021 0.002 PHE C 292 TYR 0.023 0.002 TYR A 527 ARG 0.008 0.001 ARG C 340 *********************** 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 273 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 1.550 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: A 389 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: A 460 LEU cc_start: 0.7112 (tt) cc_final: 0.6807 (tp) REVERT: A 464 MET cc_start: 0.7707 (ttm) cc_final: 0.6523 (tpt) REVERT: A 508 PHE cc_start: 0.6284 (t80) cc_final: 0.5944 (t80) REVERT: B 341 ARG cc_start: 0.0816 (OUTLIER) cc_final: 0.0104 (ptp90) REVERT: B 516 MET cc_start: 0.4888 (mmm) cc_final: 0.4668 (tpp) REVERT: C 358 MET cc_start: 0.7235 (pmm) cc_final: 0.6994 (pmm) REVERT: C 454 ARG cc_start: 0.5570 (tmt170) cc_final: 0.5258 (ptt90) REVERT: C 479 MET cc_start: 0.4974 (ppp) cc_final: 0.4767 (ppp) REVERT: D 232 TYR cc_start: 0.4181 (t80) cc_final: 0.3729 (t80) REVERT: D 321 LEU cc_start: 0.4693 (OUTLIER) cc_final: 0.4455 (tp) REVERT: D 358 MET cc_start: 0.6066 (tpt) cc_final: 0.5363 (tpt) REVERT: D 368 MET cc_start: 0.6301 (ptp) cc_final: 0.5803 (mmt) REVERT: D 410 ARG cc_start: 0.3593 (mmm160) cc_final: 0.3316 (tmt170) REVERT: D 479 MET cc_start: 0.5684 (mmm) cc_final: 0.5138 (mtp) REVERT: F 24 MET cc_start: 0.7492 (tmm) cc_final: 0.7085 (tpp) outliers start: 35 outliers final: 13 residues processed: 262 average time/residue: 0.3371 time to fit residues: 125.9726 Evaluate side-chains 194 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 409 THR Chi-restraints excluded: chain A residue 518 GLN 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 341 ARG 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 49 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 150 optimal weight: 0.1980 chunk 51 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- 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 B 366 HIS ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 390 HIS ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS D 420 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 16628 Z= 0.435 Angle : 0.899 13.060 23225 Z= 0.493 Chirality : 0.051 0.220 2526 Planarity : 0.009 0.083 2421 Dihedral : 27.278 175.621 3595 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 30.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.22 % Favored : 88.65 % Rotamer: Outliers : 4.24 % Allowed : 18.90 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.19), residues: 1542 helix: -1.19 (0.19), residues: 697 sheet: -2.27 (0.54), residues: 73 loop : -2.83 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 327 HIS 0.012 0.002 HIS B 366 PHE 0.031 0.003 PHE C 512 TYR 0.031 0.003 TYR A 527 ARG 0.019 0.001 ARG C 344 *********************** 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 243 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 1.636 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: A 259 GLN cc_start: 0.7312 (mp10) cc_final: 0.7104 (mp10) REVERT: A 375 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8288 (t) REVERT: A 464 MET cc_start: 0.8392 (ttm) cc_final: 0.7297 (tpt) REVERT: B 343 TRP cc_start: 0.6257 (t-100) cc_final: 0.6003 (t-100) REVERT: B 538 GLN cc_start: 0.8199 (tp40) cc_final: 0.7814 (tp40) REVERT: C 224 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5373 (mm) REVERT: C 230 LYS cc_start: 0.8568 (mmmt) cc_final: 0.7935 (ptmm) REVERT: C 285 TRP cc_start: 0.8007 (m-90) cc_final: 0.7051 (m-10) REVERT: C 295 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.6277 (t70) REVERT: C 356 LEU cc_start: 0.6135 (tp) cc_final: 0.5804 (tp) REVERT: C 358 MET cc_start: 0.7362 (pmm) cc_final: 0.7026 (pmm) REVERT: C 389 GLN cc_start: 0.7651 (mt0) cc_final: 0.7351 (mp10) REVERT: C 454 ARG cc_start: 0.6621 (tmt170) cc_final: 0.6398 (ptt90) REVERT: C 522 HIS cc_start: 0.5526 (t-170) cc_final: 0.5224 (t70) REVERT: D 296 THR cc_start: 0.6139 (OUTLIER) cc_final: 0.5891 (m) REVERT: D 410 ARG cc_start: 0.4950 (mmm160) cc_final: 0.3550 (tmt170) REVERT: D 465 MET cc_start: 0.2046 (ppp) cc_final: 0.1776 (ppp) outliers start: 55 outliers final: 29 residues processed: 228 average time/residue: 0.3061 time to fit residues: 102.1230 Evaluate side-chains 184 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 357 LEU Chi-restraints excluded: chain A residue 375 VAL 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 518 GLN Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 423 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 283 VAL 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 407 PHE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 508 PHE Chi-restraints excluded: chain E residue 31 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 A 522 HIS B 342 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5682 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 16628 Z= 0.307 Angle : 0.744 8.077 23225 Z= 0.409 Chirality : 0.045 0.194 2526 Planarity : 0.007 0.061 2421 Dihedral : 27.192 179.837 3595 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 22.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.95 % Favored : 90.92 % Rotamer: Outliers : 4.32 % Allowed : 21.53 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.19), residues: 1542 helix: -0.88 (0.19), residues: 693 sheet: -2.48 (0.44), residues: 106 loop : -2.78 (0.19), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 327 HIS 0.005 0.001 HIS D 274 PHE 0.025 0.002 PHE A 508 TYR 0.022 0.002 TYR A 527 ARG 0.008 0.001 ARG C 302 *********************** 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 235 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 1.566 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: 0.6738 (mp10) cc_final: 0.6364 (mp10) REVERT: A 288 TYR cc_start: 0.5944 (OUTLIER) cc_final: 0.5404 (t80) REVERT: A 299 THR cc_start: 0.5624 (OUTLIER) cc_final: 0.5335 (p) REVERT: A 375 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8388 (t) REVERT: A 464 MET cc_start: 0.8329 (ttm) cc_final: 0.7396 (tpt) REVERT: A 476 THR cc_start: 0.8229 (t) cc_final: 0.8018 (m) REVERT: B 343 TRP cc_start: 0.6323 (t-100) cc_final: 0.5958 (t-100) REVERT: B 463 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7848 (t0) REVERT: C 230 LYS cc_start: 0.8568 (mmmt) cc_final: 0.7987 (ptmm) REVERT: C 277 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7861 (mm) REVERT: C 285 TRP cc_start: 0.7807 (m-90) cc_final: 0.7348 (m-90) REVERT: C 356 LEU cc_start: 0.6115 (tp) cc_final: 0.5880 (tp) REVERT: C 358 MET cc_start: 0.7280 (pmm) cc_final: 0.7033 (pmm) REVERT: C 389 GLN cc_start: 0.7854 (mt0) cc_final: 0.7603 (mp10) REVERT: C 429 MET cc_start: 0.8452 (tmm) cc_final: 0.7827 (tmm) REVERT: C 432 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7460 (ttp80) REVERT: C 479 MET cc_start: 0.4868 (ppp) cc_final: 0.4122 (tmm) REVERT: C 491 PHE cc_start: 0.6787 (m-80) cc_final: 0.6278 (m-80) REVERT: D 227 GLN cc_start: 0.5388 (tm-30) cc_final: 0.4798 (mp10) REVERT: D 296 THR cc_start: 0.6844 (OUTLIER) cc_final: 0.6032 (m) REVERT: D 410 ARG cc_start: 0.4406 (mmm160) cc_final: 0.3294 (tmt170) outliers start: 56 outliers final: 25 residues processed: 218 average time/residue: 0.3120 time to fit residues: 99.4211 Evaluate side-chains 177 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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 299 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 276 CYS 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 407 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 E residue 95 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 134 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** B 555 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5669 moved from start: 0.7607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16628 Z= 0.242 Angle : 0.710 10.724 23225 Z= 0.384 Chirality : 0.043 0.177 2526 Planarity : 0.006 0.049 2421 Dihedral : 27.008 178.413 3595 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.60 % Favored : 90.34 % Rotamer: Outliers : 3.78 % Allowed : 22.30 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.20), residues: 1542 helix: -0.51 (0.20), residues: 688 sheet: -2.32 (0.50), residues: 92 loop : -2.68 (0.19), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A 327 HIS 0.005 0.001 HIS C 295 PHE 0.030 0.002 PHE A 508 TYR 0.019 0.002 TYR A 527 ARG 0.008 0.001 ARG B 514 *********************** 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 214 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 165 time to evaluate : 1.723 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: 0.6446 (mp10) cc_final: 0.6019 (mp10) REVERT: A 299 THR cc_start: 0.5750 (OUTLIER) cc_final: 0.5382 (p) REVERT: A 375 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8349 (t) REVERT: A 464 MET cc_start: 0.8279 (ttm) cc_final: 0.7500 (tpt) REVERT: A 476 THR cc_start: 0.8299 (t) cc_final: 0.8086 (m) REVERT: B 463 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7769 (t0) REVERT: C 224 LEU cc_start: 0.5246 (OUTLIER) cc_final: 0.5012 (mm) REVERT: C 230 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8073 (ptmm) REVERT: C 277 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7864 (mm) REVERT: C 285 TRP cc_start: 0.7815 (m-90) cc_final: 0.7453 (m-10) REVERT: C 358 MET cc_start: 0.7420 (pmm) cc_final: 0.7191 (pmm) REVERT: C 368 MET cc_start: 0.5897 (mtm) cc_final: 0.5641 (ppp) REVERT: C 391 PHE cc_start: 0.8382 (m-80) cc_final: 0.8037 (m-80) REVERT: C 429 MET cc_start: 0.8407 (tmm) cc_final: 0.8167 (tmm) REVERT: C 479 MET cc_start: 0.4861 (ppp) cc_final: 0.4328 (tmm) REVERT: C 491 PHE cc_start: 0.6661 (m-80) cc_final: 0.6105 (m-80) REVERT: D 226 VAL cc_start: 0.7496 (OUTLIER) cc_final: 0.7056 (p) REVERT: D 227 GLN cc_start: 0.5398 (tm-30) cc_final: 0.4940 (mp10) REVERT: D 234 ARG cc_start: 0.8494 (mpp80) cc_final: 0.7950 (mpt-90) REVERT: D 286 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7399 (mm) REVERT: D 410 ARG cc_start: 0.4745 (mmm160) cc_final: 0.3753 (tmt170) REVERT: D 465 MET cc_start: 0.1344 (ptm) cc_final: 0.0954 (ptm) REVERT: D 556 PHE cc_start: 0.0874 (OUTLIER) cc_final: -0.2318 (p90) REVERT: E 95 VAL cc_start: 0.5934 (OUTLIER) cc_final: 0.5600 (p) outliers start: 49 outliers final: 24 residues processed: 199 average time/residue: 0.3146 time to fit residues: 92.8030 Evaluate side-chains 177 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 2.153 ------------------------------------------------------------------------------- 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 375 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 492 VAL 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 276 CYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 556 PHE Chi-restraints excluded: chain E residue 1 MET 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 95 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 94 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 0.0770 overall best weight: 1.3742 ------------------------------------------------------------------------------- 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** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS ** C 555 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 0.8133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16628 Z= 0.252 Angle : 0.703 10.158 23225 Z= 0.380 Chirality : 0.043 0.188 2526 Planarity : 0.006 0.058 2421 Dihedral : 26.927 179.831 3595 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.01 % Favored : 90.92 % Rotamer: Outliers : 4.24 % Allowed : 24.23 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.20), residues: 1542 helix: -0.42 (0.20), residues: 683 sheet: -2.80 (0.48), residues: 87 loop : -2.64 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP A 327 HIS 0.007 0.001 HIS A 390 PHE 0.031 0.002 PHE A 508 TYR 0.035 0.002 TYR D 450 ARG 0.010 0.001 ARG B 369 *********************** 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 227 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 1.621 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: A 259 GLN cc_start: 0.6328 (mp10) cc_final: 0.5922 (mp10) REVERT: A 299 THR cc_start: 0.5838 (OUTLIER) cc_final: 0.5493 (p) REVERT: A 476 THR cc_start: 0.8134 (t) cc_final: 0.7882 (m) REVERT: B 463 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7824 (t0) REVERT: C 230 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8073 (ptmm) REVERT: C 277 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7871 (mm) REVERT: C 358 MET cc_start: 0.7372 (pmm) cc_final: 0.7139 (pmm) REVERT: C 368 MET cc_start: 0.5510 (mtm) cc_final: 0.5257 (ppp) REVERT: C 391 PHE cc_start: 0.8339 (m-80) cc_final: 0.8051 (m-80) REVERT: C 403 MET cc_start: 0.1102 (mmm) cc_final: 0.0533 (mtt) REVERT: C 429 MET cc_start: 0.8554 (tmm) cc_final: 0.8228 (tmm) REVERT: C 474 ASP cc_start: 0.8070 (m-30) cc_final: 0.7608 (t0) REVERT: C 479 MET cc_start: 0.5052 (ppp) cc_final: 0.4474 (tmm) REVERT: C 491 PHE cc_start: 0.6605 (m-80) cc_final: 0.6029 (m-80) REVERT: D 226 VAL cc_start: 0.7535 (OUTLIER) cc_final: 0.7052 (p) REVERT: D 227 GLN cc_start: 0.5435 (tm-30) cc_final: 0.5070 (mp10) REVERT: D 234 ARG cc_start: 0.8443 (mpp80) cc_final: 0.7865 (mpt-90) REVERT: D 368 MET cc_start: 0.6742 (mtt) cc_final: 0.6449 (pmm) REVERT: D 410 ARG cc_start: 0.4677 (mmm160) cc_final: 0.3633 (tmt170) outliers start: 55 outliers final: 30 residues processed: 206 average time/residue: 0.3629 time to fit residues: 107.2807 Evaluate side-chains 192 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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 299 THR Chi-restraints excluded: chain A residue 395 LEU 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 328 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 349 GLU 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 D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 6 ILE 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 95 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 155 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 117 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 555 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5761 moved from start: 0.8698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16628 Z= 0.270 Angle : 0.721 10.619 23225 Z= 0.388 Chirality : 0.043 0.187 2526 Planarity : 0.006 0.049 2421 Dihedral : 26.872 178.304 3595 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.53 % Favored : 90.40 % Rotamer: Outliers : 4.32 % Allowed : 24.85 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.20), residues: 1542 helix: -0.37 (0.20), residues: 688 sheet: -2.95 (0.43), residues: 104 loop : -2.62 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP A 327 HIS 0.009 0.001 HIS C 274 PHE 0.027 0.002 PHE A 455 TYR 0.019 0.002 TYR F 5 ARG 0.006 0.001 ARG C 469 *********************** 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 227 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 1.896 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: 0.6155 (mp10) cc_final: 0.5781 (mp10) REVERT: A 299 THR cc_start: 0.5836 (OUTLIER) cc_final: 0.5492 (p) REVERT: A 476 THR cc_start: 0.8120 (t) cc_final: 0.7883 (m) REVERT: A 555 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7490 (t0) REVERT: B 463 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7924 (t0) REVERT: B 517 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6726 (mm-30) REVERT: C 277 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8008 (mm) REVERT: C 391 PHE cc_start: 0.8313 (m-80) cc_final: 0.7850 (m-80) REVERT: C 403 MET cc_start: 0.0561 (mmm) cc_final: 0.0101 (mtt) REVERT: C 429 MET cc_start: 0.8441 (tmm) cc_final: 0.8084 (tmm) REVERT: C 479 MET cc_start: 0.5027 (ppp) cc_final: 0.4461 (tmm) REVERT: C 491 PHE cc_start: 0.6574 (m-80) cc_final: 0.6140 (m-10) REVERT: D 226 VAL cc_start: 0.7773 (OUTLIER) cc_final: 0.7311 (p) REVERT: D 234 ARG cc_start: 0.8447 (mpp80) cc_final: 0.8089 (mpt-90) REVERT: D 410 ARG cc_start: 0.4701 (mmm160) cc_final: 0.4232 (tmt170) REVERT: D 429 MET cc_start: 0.4142 (ptp) cc_final: 0.3931 (ptm) REVERT: D 515 ARG cc_start: 0.8752 (tpp-160) cc_final: 0.8255 (ttp80) REVERT: E 79 SER cc_start: 0.8263 (OUTLIER) cc_final: 0.7892 (m) REVERT: E 95 VAL cc_start: 0.5787 (OUTLIER) cc_final: 0.5508 (p) outliers start: 56 outliers final: 33 residues processed: 209 average time/residue: 0.3344 time to fit residues: 99.7509 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 : 1.572 ------------------------------------------------------------------------------- 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 335 CYS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 492 VAL 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 276 CYS Chi-restraints excluded: chain D residue 283 VAL 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 E residue 1 MET Chi-restraints excluded: chain E residue 6 ILE 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 E residue 79 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 94 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 0.7980 chunk 64 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 0.0570 chunk 102 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- 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 555 ASN ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.9278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16628 Z= 0.299 Angle : 0.754 10.623 23225 Z= 0.404 Chirality : 0.044 0.203 2526 Planarity : 0.006 0.050 2421 Dihedral : 26.838 177.089 3595 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.92 % Favored : 90.01 % Rotamer: Outliers : 3.47 % Allowed : 26.00 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.20), residues: 1542 helix: -0.50 (0.20), residues: 696 sheet: -2.94 (0.44), residues: 99 loop : -2.63 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP A 327 HIS 0.010 0.002 HIS A 390 PHE 0.022 0.002 PHE A 508 TYR 0.019 0.002 TYR D 450 ARG 0.010 0.001 ARG D 365 *********************** 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 201 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 1.728 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: 0.5759 (mp10) REVERT: A 299 THR cc_start: 0.6068 (OUTLIER) cc_final: 0.5761 (p) REVERT: A 476 THR cc_start: 0.8132 (t) cc_final: 0.7916 (m) REVERT: B 327 TRP cc_start: 0.7932 (m100) cc_final: 0.7652 (m100) REVERT: B 343 TRP cc_start: 0.4990 (t-100) cc_final: 0.4532 (t-100) REVERT: B 450 TYR cc_start: 0.7436 (t80) cc_final: 0.6802 (t80) REVERT: C 277 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8146 (mm) REVERT: C 293 MET cc_start: 0.6707 (ptp) cc_final: 0.4661 (tpt) REVERT: C 341 ARG cc_start: 0.6523 (ptp90) cc_final: 0.5775 (ptp-170) REVERT: C 391 PHE cc_start: 0.8383 (m-80) cc_final: 0.8054 (m-80) REVERT: C 403 MET cc_start: 0.0649 (mmm) cc_final: 0.0190 (mtt) REVERT: C 429 MET cc_start: 0.8262 (tmm) cc_final: 0.7974 (tmm) REVERT: C 452 GLN cc_start: 0.7587 (tp40) cc_final: 0.6629 (pp30) REVERT: C 474 ASP cc_start: 0.8028 (m-30) cc_final: 0.7663 (t0) REVERT: C 479 MET cc_start: 0.4920 (ppp) cc_final: 0.4287 (tmm) REVERT: C 491 PHE cc_start: 0.7159 (m-80) cc_final: 0.6731 (m-10) REVERT: D 234 ARG cc_start: 0.8307 (mpp80) cc_final: 0.7920 (mpt-90) REVERT: D 235 LYS cc_start: 0.6862 (tttm) cc_final: 0.6511 (ttmt) REVERT: D 368 MET cc_start: 0.6252 (pmm) cc_final: 0.3896 (tpt) REVERT: D 410 ARG cc_start: 0.4709 (mmm160) cc_final: 0.4180 (tmt170) REVERT: D 429 MET cc_start: 0.4012 (ptp) cc_final: 0.3737 (ptm) REVERT: E 79 SER cc_start: 0.8151 (OUTLIER) cc_final: 0.7704 (m) outliers start: 45 outliers final: 33 residues processed: 185 average time/residue: 0.3244 time to fit residues: 87.2070 Evaluate side-chains 184 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 335 CYS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 349 GLU 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 531 TYR Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 283 VAL 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 E residue 6 ILE 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 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 154 optimal weight: 7.9990 chunk 140 optimal weight: 0.0870 chunk 149 optimal weight: 0.3980 chunk 90 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 141 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5735 moved from start: 0.9496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16628 Z= 0.226 Angle : 0.733 11.039 23225 Z= 0.390 Chirality : 0.043 0.186 2526 Planarity : 0.006 0.048 2421 Dihedral : 26.752 176.927 3595 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.69 % Favored : 91.25 % Rotamer: Outliers : 2.70 % Allowed : 27.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.20), residues: 1542 helix: -0.46 (0.20), residues: 698 sheet: -2.71 (0.45), residues: 103 loop : -2.66 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.004 TRP D 327 HIS 0.010 0.001 HIS C 274 PHE 0.032 0.002 PHE A 455 TYR 0.033 0.001 TYR D 450 ARG 0.005 0.000 ARG B 325 *********************** 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 205 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.5943 (OUTLIER) cc_final: 0.5222 (t80) REVERT: B 450 TYR cc_start: 0.7170 (t80) cc_final: 0.6803 (t80) REVERT: C 262 LEU cc_start: 0.7559 (mp) cc_final: 0.7219 (pp) REVERT: C 277 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8083 (mm) REVERT: C 327 TRP cc_start: 0.5622 (m100) cc_final: 0.5271 (m100) REVERT: C 341 ARG cc_start: 0.6478 (ptp90) cc_final: 0.5740 (ptp-170) REVERT: C 386 ARG cc_start: 0.7950 (ptt180) cc_final: 0.7447 (pmt170) REVERT: C 391 PHE cc_start: 0.8447 (m-80) cc_final: 0.8114 (m-80) REVERT: C 452 GLN cc_start: 0.7579 (tp40) cc_final: 0.6662 (pp30) REVERT: C 474 ASP cc_start: 0.7973 (m-30) cc_final: 0.7627 (t0) REVERT: C 479 MET cc_start: 0.5024 (ppp) cc_final: 0.4361 (tmm) REVERT: C 491 PHE cc_start: 0.6837 (m-80) cc_final: 0.6402 (m-10) REVERT: C 536 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7704 (mm-30) REVERT: D 234 ARG cc_start: 0.8241 (mpp80) cc_final: 0.7763 (mpt-90) REVERT: D 235 LYS cc_start: 0.6828 (tttm) cc_final: 0.6499 (ttmt) REVERT: D 332 ILE cc_start: 0.1450 (OUTLIER) cc_final: 0.1212 (mm) REVERT: D 368 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.3907 (tpt) REVERT: D 410 ARG cc_start: 0.4472 (mmm160) cc_final: 0.4119 (tmt170) REVERT: D 429 MET cc_start: 0.4466 (ptp) cc_final: 0.4166 (ptm) REVERT: F 48 MET cc_start: 0.9026 (mmm) cc_final: 0.8807 (tpp) outliers start: 35 outliers final: 25 residues processed: 191 average time/residue: 0.3206 time to fit residues: 88.3916 Evaluate side-chains 176 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 335 CYS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 349 GLU 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 236 ASP Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 285 TRP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 416 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 166 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 141 optimal weight: 0.3980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN C 274 HIS ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.9838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16628 Z= 0.268 Angle : 0.755 11.619 23225 Z= 0.401 Chirality : 0.044 0.211 2526 Planarity : 0.006 0.048 2421 Dihedral : 26.730 176.299 3595 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.34 % Favored : 90.60 % Rotamer: Outliers : 2.85 % Allowed : 27.08 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.20), residues: 1542 helix: -0.45 (0.20), residues: 695 sheet: -2.53 (0.40), residues: 123 loop : -2.64 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.004 TRP D 327 HIS 0.010 0.001 HIS A 390 PHE 0.022 0.002 PHE A 508 TYR 0.024 0.002 TYR D 450 ARG 0.015 0.001 ARG B 393 ********************** 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 186 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 THR cc_start: 0.5888 (OUTLIER) cc_final: 0.5574 (p) REVERT: A 555 ASN cc_start: 0.7635 (OUTLIER) cc_final: 0.7403 (t0) REVERT: B 450 TYR cc_start: 0.7358 (t80) cc_final: 0.6982 (t80) REVERT: C 277 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8147 (mm) REVERT: C 327 TRP cc_start: 0.5743 (m100) cc_final: 0.5387 (m100) REVERT: C 386 ARG cc_start: 0.7778 (ptt180) cc_final: 0.7209 (pmt170) REVERT: C 391 PHE cc_start: 0.8458 (m-80) cc_final: 0.8087 (m-80) REVERT: C 452 GLN cc_start: 0.7806 (tp40) cc_final: 0.6747 (pp30) REVERT: C 474 ASP cc_start: 0.8041 (m-30) cc_final: 0.7665 (t0) REVERT: C 479 MET cc_start: 0.4872 (ppp) cc_final: 0.4317 (tmm) REVERT: C 491 PHE cc_start: 0.7148 (m-80) cc_final: 0.6677 (m-10) REVERT: C 536 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7775 (mm-30) REVERT: D 234 ARG cc_start: 0.8279 (mpp80) cc_final: 0.7806 (mpt-90) REVERT: D 235 LYS cc_start: 0.6818 (tttm) cc_final: 0.6555 (ttmt) REVERT: D 332 ILE cc_start: 0.1635 (OUTLIER) cc_final: 0.1405 (mm) REVERT: D 368 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.3611 (ttp) REVERT: D 410 ARG cc_start: 0.4836 (mmm160) cc_final: 0.3799 (tmt170) REVERT: D 429 MET cc_start: 0.4592 (ptp) cc_final: 0.4353 (ptm) REVERT: F 24 MET cc_start: 0.7970 (ttp) cc_final: 0.7640 (ttp) outliers start: 37 outliers final: 26 residues processed: 174 average time/residue: 0.3107 time to fit residues: 79.2093 Evaluate side-chains 174 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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 335 CYS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 349 GLU 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 236 ASP Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 416 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN ** C 555 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.160048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.141166 restraints weight = 65507.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.141000 restraints weight = 49904.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.141249 restraints weight = 41046.001| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.9847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 16628 Z= 0.314 Angle : 0.926 59.200 23225 Z= 0.533 Chirality : 0.044 0.388 2526 Planarity : 0.006 0.049 2421 Dihedral : 26.732 176.318 3595 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.27 % Favored : 90.66 % Rotamer: Outliers : 3.01 % Allowed : 27.08 % Favored : 69.91 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.20), residues: 1542 helix: -0.43 (0.20), residues: 689 sheet: -2.42 (0.41), residues: 123 loop : -2.61 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.004 TRP D 327 HIS 0.009 0.001 HIS A 390 PHE 0.020 0.002 PHE A 508 TYR 0.024 0.002 TYR D 450 ARG 0.012 0.001 ARG B 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3061.58 seconds wall clock time: 57 minutes 26.80 seconds (3446.80 seconds total)