Starting phenix.real_space_refine on Tue Apr 9 09:01:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi9_23843/04_2024/7mi9_23843.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi9_23843/04_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi9_23843/04_2024/7mi9_23843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi9_23843/04_2024/7mi9_23843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi9_23843/04_2024/7mi9_23843.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi9_23843/04_2024/7mi9_23843.pdb" } 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 Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A ARG 532": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 386": "NH1" <-> "NH2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 393": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B ARG 532": "NH1" <-> "NH2" Residue "B ARG 533": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C ARG 393": "NH1" <-> "NH2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C ARG 432": "NH1" <-> "NH2" Residue "C ARG 447": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C ARG 507": "NH1" <-> "NH2" Residue "C ARG 515": "NH1" <-> "NH2" Residue "C GLU 517": "OE1" <-> "OE2" Residue "C ARG 532": "NH1" <-> "NH2" Residue "C ARG 533": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 365": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 386": "NH1" <-> "NH2" Residue "D ARG 393": "NH1" <-> "NH2" Residue "D GLU 401": "OE1" <-> "OE2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D ARG 413": "NH1" <-> "NH2" Residue "D ARG 432": "NH1" <-> "NH2" Residue "D ARG 447": "NH1" <-> "NH2" Residue "D ARG 454": "NH1" <-> "NH2" Residue "D ARG 457": "NH1" <-> "NH2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D ARG 493": "NH1" <-> "NH2" Residue "D ARG 505": "NH1" <-> "NH2" Residue "D ARG 507": "NH1" <-> "NH2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D ARG 532": "NH1" <-> "NH2" Residue "D ARG 533": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "E ARG 16": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 15": "NH1" <-> "NH2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 44": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 8.80, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 7.32 Conformation dependent library (CDL) restraints added in 1.9 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: 6.51 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: 6.46 Time building geometry restraints manager: 7.76 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: 96.83 - 104.32: 793 104.32 - 111.80: 8008 111.80 - 119.29: 5695 119.29 - 126.77: 8128 126.77 - 134.26: 601 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 2.520 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 2.520 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 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.830 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 49.790 Find NCS groups from input model: 0.860 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.770 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 27 poor density : 357 time to evaluate : 1.651 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: 0.3703 time to fit residues: 189.9519 Evaluate side-chains 211 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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: 0.6980 chunk 126 optimal weight: 0.3980 chunk 70 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 40.0000 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 B 555 ASN C 265 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5089 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16628 Z= 0.261 Angle : 0.778 10.396 23225 Z= 0.421 Chirality : 0.046 0.200 2526 Planarity : 0.007 0.062 2421 Dihedral : 27.517 177.238 3611 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.66 % Favored : 90.21 % Rotamer: Outliers : 2.55 % Allowed : 13.97 % Favored : 83.49 % 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: -1.12 (0.19), residues: 694 sheet: -2.10 (0.53), residues: 94 loop : -2.65 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 343 HIS 0.024 0.002 HIS B 366 PHE 0.020 0.002 PHE C 292 TYR 0.022 0.002 TYR A 527 ARG 0.014 0.001 ARG D 515 *********************** 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 267 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 234 time to evaluate : 1.575 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 460 LEU cc_start: 0.7086 (tt) cc_final: 0.6773 (tp) REVERT: A 464 MET cc_start: 0.7664 (ttm) cc_final: 0.6490 (tpt) REVERT: A 508 PHE cc_start: 0.6232 (t80) cc_final: 0.5922 (t80) REVERT: B 538 GLN cc_start: 0.8427 (tp40) cc_final: 0.8157 (tp40) REVERT: C 358 MET cc_start: 0.7315 (pmm) cc_final: 0.7082 (pmm) REVERT: C 454 ARG cc_start: 0.5522 (tmt170) cc_final: 0.5234 (ptt90) REVERT: D 232 TYR cc_start: 0.4259 (t80) cc_final: 0.3839 (t80) REVERT: D 321 LEU cc_start: 0.4757 (OUTLIER) cc_final: 0.4523 (tp) REVERT: D 358 MET cc_start: 0.6005 (tpt) cc_final: 0.5317 (tpt) REVERT: D 368 MET cc_start: 0.6304 (ptp) cc_final: 0.5802 (mmt) REVERT: D 410 ARG cc_start: 0.3944 (mmm160) cc_final: 0.3502 (tmt170) REVERT: D 479 MET cc_start: 0.5448 (mmm) cc_final: 0.4877 (mtp) REVERT: F 24 MET cc_start: 0.7467 (tmm) cc_final: 0.7012 (tpp) REVERT: F 74 VAL cc_start: 0.7459 (p) cc_final: 0.7139 (t) outliers start: 33 outliers final: 13 residues processed: 257 average time/residue: 0.3118 time to fit residues: 115.2003 Evaluate side-chains 195 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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 518 GLN Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 424 SER 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: 3.9990 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 0.0970 chunk 103 optimal weight: 0.0020 chunk 41 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 150 optimal weight: 0.0870 chunk 51 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 overall best weight: 1.4368 ------------------------------------------------------------------------------- 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 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 538 GLN C 265 ASN C 334 ASN C 390 HIS D 334 ASN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 moved from start: 0.4860 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= 0.265 Angle : 0.738 8.450 23225 Z= 0.401 Chirality : 0.045 0.194 2526 Planarity : 0.007 0.059 2421 Dihedral : 27.176 175.357 3595 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 25.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.79 % Favored : 90.08 % Rotamer: Outliers : 3.24 % Allowed : 17.98 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.65 (0.20), residues: 1542 helix: -0.83 (0.19), residues: 691 sheet: -2.24 (0.50), residues: 99 loop : -2.63 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 327 HIS 0.015 0.002 HIS B 366 PHE 0.017 0.002 PHE C 455 TYR 0.027 0.002 TYR A 527 ARG 0.006 0.001 ARG E 90 *********************** 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 246 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 204 time to evaluate : 1.527 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 291 TRP cc_start: 0.7079 (t60) cc_final: 0.6838 (t60) REVERT: A 389 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6878 (pp30) REVERT: A 462 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8045 (tp) REVERT: A 464 MET cc_start: 0.8095 (ttm) cc_final: 0.7227 (tpt) REVERT: A 508 PHE cc_start: 0.6421 (t80) cc_final: 0.6186 (t80) REVERT: A 516 MET cc_start: 0.7206 (tpp) cc_final: 0.6802 (mmt) REVERT: C 293 MET cc_start: 0.7126 (ptp) cc_final: 0.6700 (ppp) REVERT: C 356 LEU cc_start: 0.5888 (tp) cc_final: 0.5566 (tp) REVERT: C 358 MET cc_start: 0.7275 (pmm) cc_final: 0.6975 (pmm) REVERT: C 389 GLN cc_start: 0.7286 (mt0) cc_final: 0.6885 (mp10) REVERT: C 391 PHE cc_start: 0.7980 (t80) cc_final: 0.7403 (m-80) REVERT: C 454 ARG cc_start: 0.5964 (tmt170) cc_final: 0.5633 (ptt90) REVERT: C 479 MET cc_start: 0.4992 (ppp) cc_final: 0.4575 (tmm) REVERT: C 522 HIS cc_start: 0.5074 (t-170) cc_final: 0.4581 (t-170) REVERT: D 227 GLN cc_start: 0.5064 (tp40) cc_final: 0.4154 (mp10) REVERT: D 465 MET cc_start: 0.1559 (ppp) cc_final: 0.0279 (ptm) REVERT: D 479 MET cc_start: 0.5608 (mmm) cc_final: 0.5245 (mtp) outliers start: 42 outliers final: 20 residues processed: 233 average time/residue: 0.2907 time to fit residues: 98.9758 Evaluate side-chains 182 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 102 optimal weight: 30.0000 chunk 152 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 522 HIS B 342 ASN B 390 HIS ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS D 420 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.7633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 16628 Z= 0.482 Angle : 0.937 12.173 23225 Z= 0.509 Chirality : 0.053 0.318 2526 Planarity : 0.009 0.090 2421 Dihedral : 27.330 172.824 3595 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 38.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.26 % Favored : 87.61 % Rotamer: Outliers : 4.71 % Allowed : 22.53 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % 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: -3.14 (0.19), residues: 1542 helix: -1.14 (0.18), residues: 694 sheet: -3.05 (0.41), residues: 111 loop : -2.90 (0.20), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP A 327 HIS 0.020 0.003 HIS D 301 PHE 0.036 0.003 PHE C 512 TYR 0.028 0.003 TYR A 527 ARG 0.011 0.001 ARG D 413 *********************** 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 239 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 178 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 GLN cc_start: 0.7358 (tm-30) cc_final: 0.7058 (tm-30) REVERT: A 464 MET cc_start: 0.8562 (ttm) cc_final: 0.8274 (tpt) REVERT: B 403 MET cc_start: 0.4049 (tpp) cc_final: 0.3693 (tpp) REVERT: C 224 LEU cc_start: 0.5503 (OUTLIER) cc_final: 0.5171 (mm) REVERT: C 230 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8248 (ptmm) REVERT: C 358 MET cc_start: 0.7732 (pmm) cc_final: 0.7459 (pmm) REVERT: C 429 MET cc_start: 0.8549 (tmm) cc_final: 0.8140 (tmm) REVERT: C 479 MET cc_start: 0.4766 (ppp) cc_final: 0.3873 (tmm) REVERT: C 491 PHE cc_start: 0.6811 (m-80) cc_final: 0.6603 (m-80) REVERT: D 226 VAL cc_start: 0.7840 (OUTLIER) cc_final: 0.7534 (p) REVERT: D 227 GLN cc_start: 0.5151 (tp40) cc_final: 0.4393 (mp10) REVERT: D 262 LEU cc_start: 0.7717 (mp) cc_final: 0.7315 (mt) REVERT: D 286 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7011 (mm) REVERT: D 410 ARG cc_start: 0.5597 (mmm160) cc_final: 0.3941 (tmt170) REVERT: D 465 MET cc_start: 0.2986 (ppp) cc_final: 0.2263 (ptm) REVERT: D 479 MET cc_start: 0.7219 (mmm) cc_final: 0.5845 (mtp) REVERT: E 1 MET cc_start: 0.7151 (tpp) cc_final: 0.6146 (tpt) outliers start: 61 outliers final: 35 residues processed: 221 average time/residue: 0.3095 time to fit residues: 98.2329 Evaluate side-chains 180 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 329 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 476 THR Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain B residue 296 THR 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 491 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 464 MET 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 283 VAL Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 556 PHE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 GLU 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: 0.9990 chunk 91 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 137 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 chunk 144 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN D 420 ASN D 483 ASN ** 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: 0.5694 moved from start: 0.7918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16628 Z= 0.230 Angle : 0.714 10.641 23225 Z= 0.386 Chirality : 0.044 0.185 2526 Planarity : 0.006 0.055 2421 Dihedral : 27.109 173.091 3595 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 24.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.82 % Favored : 91.05 % Rotamer: Outliers : 3.70 % Allowed : 24.61 % Favored : 71.68 % 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: -2.64 (0.20), residues: 1542 helix: -0.66 (0.20), residues: 672 sheet: -2.88 (0.42), residues: 110 loop : -2.64 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 327 HIS 0.006 0.001 HIS D 274 PHE 0.016 0.002 PHE C 556 TYR 0.020 0.001 TYR A 527 ARG 0.010 0.001 ARG C 386 *********************** 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 218 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 170 time to evaluate : 1.427 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 288 TYR cc_start: 0.6046 (OUTLIER) cc_final: 0.5445 (t80) REVERT: A 516 MET cc_start: 0.6999 (tpp) cc_final: 0.6784 (mmm) REVERT: A 531 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: C 224 LEU cc_start: 0.5146 (OUTLIER) cc_final: 0.4875 (mm) REVERT: C 265 ASN cc_start: 0.7528 (m110) cc_final: 0.6400 (m110) REVERT: C 277 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7885 (mm) REVERT: C 288 TYR cc_start: 0.7548 (t80) cc_final: 0.7214 (m-80) REVERT: C 293 MET cc_start: 0.7535 (ptp) cc_final: 0.5089 (tpt) REVERT: C 358 MET cc_start: 0.7465 (pmm) cc_final: 0.7210 (pmm) REVERT: C 391 PHE cc_start: 0.8498 (t80) cc_final: 0.7832 (m-80) REVERT: C 394 MET cc_start: 0.3578 (ppp) cc_final: 0.2603 (ppp) REVERT: C 479 MET cc_start: 0.4810 (ppp) cc_final: 0.4156 (tmm) REVERT: D 226 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7464 (p) REVERT: D 227 GLN cc_start: 0.5513 (tp40) cc_final: 0.4876 (mp10) REVERT: D 368 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.3875 (tpt) REVERT: D 410 ARG cc_start: 0.5237 (mmm160) cc_final: 0.3999 (tmt170) REVERT: D 479 MET cc_start: 0.6998 (mmm) cc_final: 0.6076 (mtp) outliers start: 48 outliers final: 22 residues processed: 202 average time/residue: 0.2923 time to fit residues: 88.1107 Evaluate side-chains 175 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 436 VAL Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 373 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 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 49 GLU 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: 9.9990 chunk 145 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 53 optimal weight: 0.0040 chunk 84 optimal weight: 6.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- 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 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 HIS ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5763 moved from start: 0.8373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16628 Z= 0.264 Angle : 0.706 8.830 23225 Z= 0.382 Chirality : 0.043 0.206 2526 Planarity : 0.006 0.050 2421 Dihedral : 26.985 172.431 3595 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 26.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.70 % Favored : 89.23 % Rotamer: Outliers : 3.94 % Allowed : 25.15 % Favored : 70.91 % 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: -2.53 (0.20), residues: 1542 helix: -0.56 (0.20), residues: 684 sheet: -2.60 (0.39), residues: 115 loop : -2.66 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 343 HIS 0.022 0.002 HIS C 295 PHE 0.013 0.002 PHE D 449 TYR 0.019 0.002 TYR A 527 ARG 0.006 0.000 ARG C 432 *********************** 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 204 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 153 time to evaluate : 1.595 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: C 224 LEU cc_start: 0.5268 (OUTLIER) cc_final: 0.5004 (mm) REVERT: C 230 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8086 (ptmm) REVERT: C 265 ASN cc_start: 0.7619 (m110) cc_final: 0.7209 (m110) REVERT: C 277 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7908 (mm) REVERT: C 358 MET cc_start: 0.7485 (pmm) cc_final: 0.7264 (pmm) REVERT: C 391 PHE cc_start: 0.8451 (t80) cc_final: 0.7757 (m-80) REVERT: C 479 MET cc_start: 0.4538 (ppp) cc_final: 0.3848 (tmm) REVERT: D 226 VAL cc_start: 0.7817 (OUTLIER) cc_final: 0.7378 (p) REVERT: D 227 GLN cc_start: 0.5497 (tp40) cc_final: 0.4926 (mp10) REVERT: D 332 ILE cc_start: 0.1465 (OUTLIER) cc_final: 0.1235 (mm) REVERT: D 368 MET cc_start: 0.6489 (OUTLIER) cc_final: 0.3687 (tpt) REVERT: D 410 ARG cc_start: 0.5456 (mmm160) cc_final: 0.4071 (tmt170) REVERT: D 450 TYR cc_start: 0.3477 (t80) cc_final: 0.2611 (t80) REVERT: D 479 MET cc_start: 0.7349 (mmm) cc_final: 0.6307 (mtp) REVERT: D 556 PHE cc_start: 0.1454 (OUTLIER) cc_final: 0.0956 (m-80) outliers start: 51 outliers final: 30 residues processed: 190 average time/residue: 0.2858 time to fit residues: 81.4686 Evaluate side-chains 176 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 140 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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 409 THR 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 373 LEU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 464 MET 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 292 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 556 PHE Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 56 VAL 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: 0.9990 chunk 92 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN C 451 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.8686 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= 0.219 Angle : 0.697 10.388 23225 Z= 0.372 Chirality : 0.042 0.176 2526 Planarity : 0.005 0.090 2421 Dihedral : 26.868 174.361 3595 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.95 % Favored : 90.99 % Rotamer: Outliers : 3.24 % Allowed : 25.69 % Favored : 71.06 % 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: -2.43 (0.20), residues: 1542 helix: -0.44 (0.20), residues: 680 sheet: -2.65 (0.42), residues: 111 loop : -2.61 (0.20), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 327 HIS 0.007 0.001 HIS A 451 PHE 0.028 0.002 PHE A 455 TYR 0.018 0.001 TYR A 527 ARG 0.006 0.000 ARG C 432 *********************** 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 209 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.5867 (OUTLIER) cc_final: 0.5221 (t80) REVERT: C 224 LEU cc_start: 0.5085 (OUTLIER) cc_final: 0.4834 (mm) REVERT: C 230 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8026 (ptmm) REVERT: C 265 ASN cc_start: 0.7531 (m110) cc_final: 0.7034 (m110) REVERT: C 277 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8011 (mm) REVERT: C 293 MET cc_start: 0.7245 (ptp) cc_final: 0.4899 (tpt) REVERT: C 391 PHE cc_start: 0.8200 (t80) cc_final: 0.7862 (m-80) REVERT: C 479 MET cc_start: 0.4626 (ppp) cc_final: 0.3970 (tmm) REVERT: C 490 ASP cc_start: 0.7362 (m-30) cc_final: 0.7134 (m-30) REVERT: C 491 PHE cc_start: 0.7361 (m-10) cc_final: 0.7116 (m-10) REVERT: D 227 GLN cc_start: 0.5402 (tp40) cc_final: 0.5144 (mp10) REVERT: D 368 MET cc_start: 0.6367 (OUTLIER) cc_final: 0.3718 (tpt) REVERT: D 410 ARG cc_start: 0.5690 (mmm160) cc_final: 0.4396 (tmt170) REVERT: D 450 TYR cc_start: 0.4428 (t80) cc_final: 0.3012 (t80) REVERT: D 479 MET cc_start: 0.7325 (mmm) cc_final: 0.6371 (mtp) REVERT: D 556 PHE cc_start: 0.1287 (OUTLIER) cc_final: 0.0709 (m-80) outliers start: 42 outliers final: 24 residues processed: 193 average time/residue: 0.3351 time to fit residues: 92.1950 Evaluate side-chains 181 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG 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 436 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 328 ILE 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 284 THR Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 556 PHE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 11 ILE 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: 2.9990 chunk 64 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 126 optimal weight: 0.0270 chunk 146 optimal weight: 0.0770 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5749 moved from start: 0.9056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16628 Z= 0.244 Angle : 0.695 8.876 23225 Z= 0.371 Chirality : 0.043 0.211 2526 Planarity : 0.005 0.054 2421 Dihedral : 26.801 175.984 3595 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.40 % Favored : 90.53 % Rotamer: Outliers : 3.47 % Allowed : 26.08 % Favored : 70.45 % 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: -2.35 (0.20), residues: 1542 helix: -0.43 (0.20), residues: 681 sheet: -2.43 (0.43), residues: 111 loop : -2.55 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP D 327 HIS 0.006 0.001 HIS A 390 PHE 0.022 0.002 PHE C 468 TYR 0.038 0.002 TYR A 450 ARG 0.007 0.000 ARG C 469 *********************** 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 199 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 154 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.7864 (tpt) cc_final: 0.7389 (tpt) REVERT: C 224 LEU cc_start: 0.5062 (OUTLIER) cc_final: 0.4833 (mm) REVERT: C 230 LYS cc_start: 0.8330 (mmmt) cc_final: 0.7986 (ptmm) REVERT: C 265 ASN cc_start: 0.7687 (m110) cc_final: 0.7206 (m110) REVERT: C 277 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8076 (mm) REVERT: C 358 MET cc_start: 0.7676 (pmm) cc_final: 0.7378 (pmm) REVERT: C 391 PHE cc_start: 0.8415 (t80) cc_final: 0.7868 (m-80) REVERT: C 452 GLN cc_start: 0.7643 (tp40) cc_final: 0.6700 (pp30) REVERT: C 479 MET cc_start: 0.4622 (ppp) cc_final: 0.3985 (tmm) REVERT: C 490 ASP cc_start: 0.7587 (m-30) cc_final: 0.7362 (m-30) REVERT: C 491 PHE cc_start: 0.7447 (m-10) cc_final: 0.7129 (m-10) REVERT: D 226 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7144 (p) REVERT: D 227 GLN cc_start: 0.5436 (tp40) cc_final: 0.5130 (mp10) REVERT: D 368 MET cc_start: 0.6259 (OUTLIER) cc_final: 0.3493 (ttm) REVERT: D 410 ARG cc_start: 0.5421 (mmm160) cc_final: 0.4377 (tmt170) REVERT: D 450 TYR cc_start: 0.4389 (t80) cc_final: 0.3632 (t80) REVERT: D 479 MET cc_start: 0.7412 (mmm) cc_final: 0.6359 (mtp) REVERT: D 556 PHE cc_start: 0.1024 (OUTLIER) cc_final: 0.0401 (m-80) REVERT: E 79 SER cc_start: 0.8161 (OUTLIER) cc_final: 0.7595 (m) outliers start: 45 outliers final: 31 residues processed: 186 average time/residue: 0.3158 time to fit residues: 84.3954 Evaluate side-chains 185 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG 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 409 THR 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 491 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 556 PHE Chi-restraints excluded: chain E residue 13 ASN 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 79 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 94 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 5.9990 chunk 140 optimal weight: 0.4980 chunk 149 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN C 555 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.9338 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= 0.238 Angle : 0.715 9.137 23225 Z= 0.380 Chirality : 0.043 0.193 2526 Planarity : 0.005 0.055 2421 Dihedral : 26.753 178.932 3595 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.69 % Favored : 91.25 % Rotamer: Outliers : 3.24 % Allowed : 26.39 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.33 (0.20), residues: 1542 helix: -0.40 (0.20), residues: 680 sheet: -2.37 (0.43), residues: 111 loop : -2.55 (0.20), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.003 TRP A 327 HIS 0.006 0.001 HIS A 390 PHE 0.017 0.002 PHE C 468 TYR 0.030 0.001 TYR A 450 ARG 0.009 0.001 ARG C 396 *********************** 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 203 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 161 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.7956 (tpt) cc_final: 0.7284 (tpt) REVERT: C 224 LEU cc_start: 0.5026 (OUTLIER) cc_final: 0.4799 (mm) REVERT: C 230 LYS cc_start: 0.8252 (mmmt) cc_final: 0.7975 (ptmm) REVERT: C 245 GLU cc_start: 0.8069 (tp30) cc_final: 0.7794 (tp30) REVERT: C 265 ASN cc_start: 0.7592 (m110) cc_final: 0.7005 (m110) REVERT: C 277 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8086 (mm) REVERT: C 293 MET cc_start: 0.7268 (ptp) cc_final: 0.4879 (tpt) REVERT: C 368 MET cc_start: 0.5884 (ptm) cc_final: 0.5317 (ppp) REVERT: C 391 PHE cc_start: 0.8454 (t80) cc_final: 0.7854 (m-80) REVERT: C 403 MET cc_start: 0.1384 (mmt) cc_final: 0.1004 (mmt) REVERT: C 452 GLN cc_start: 0.7694 (tp40) cc_final: 0.6741 (pp30) REVERT: C 479 MET cc_start: 0.4616 (ppp) cc_final: 0.4013 (tmm) REVERT: C 491 PHE cc_start: 0.7541 (m-10) cc_final: 0.7156 (m-10) REVERT: D 368 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.3513 (ttm) REVERT: D 410 ARG cc_start: 0.5447 (mmm160) cc_final: 0.4573 (tmt170) REVERT: D 450 TYR cc_start: 0.4514 (t80) cc_final: 0.3786 (t80) REVERT: D 479 MET cc_start: 0.7539 (mmm) cc_final: 0.6411 (mtp) REVERT: D 556 PHE cc_start: 0.1028 (OUTLIER) cc_final: 0.0515 (m-80) REVERT: E 79 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7565 (m) outliers start: 42 outliers final: 29 residues processed: 192 average time/residue: 0.3214 time to fit residues: 90.1228 Evaluate side-chains 181 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG 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 409 THR 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 491 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 556 PHE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN C 295 HIS C 411 ASN C 538 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 1.0339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 16628 Z= 0.432 Angle : 0.885 11.210 23225 Z= 0.471 Chirality : 0.050 0.239 2526 Planarity : 0.007 0.066 2421 Dihedral : 26.902 177.804 3595 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 34.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.61 % Favored : 88.26 % Rotamer: Outliers : 2.85 % Allowed : 27.47 % Favored : 69.68 % 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: -2.79 (0.20), residues: 1542 helix: -0.84 (0.19), residues: 687 sheet: -2.60 (0.38), residues: 128 loop : -2.75 (0.20), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.005 TRP A 327 HIS 0.008 0.002 HIS C 366 PHE 0.021 0.003 PHE C 468 TYR 0.031 0.002 TYR A 450 ARG 0.018 0.001 ARG D 234 ********************** 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 198 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 161 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.7837 (tpt) cc_final: 0.7465 (tpt) REVERT: B 394 MET cc_start: 0.6575 (ptp) cc_final: 0.6240 (ptp) REVERT: C 224 LEU cc_start: 0.5672 (OUTLIER) cc_final: 0.5381 (mm) REVERT: C 230 LYS cc_start: 0.8415 (mmmt) cc_final: 0.8050 (ptmm) REVERT: C 245 GLU cc_start: 0.8122 (tp30) cc_final: 0.7868 (tp30) REVERT: C 265 ASN cc_start: 0.7760 (m110) cc_final: 0.6694 (m110) REVERT: C 277 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8233 (mm) REVERT: C 288 TYR cc_start: 0.8251 (t80) cc_final: 0.7496 (m-80) REVERT: C 391 PHE cc_start: 0.8601 (t80) cc_final: 0.7849 (m-80) REVERT: C 452 GLN cc_start: 0.8247 (tp40) cc_final: 0.7175 (pp30) REVERT: C 479 MET cc_start: 0.4585 (ppp) cc_final: 0.4009 (tmm) REVERT: C 538 GLN cc_start: 0.6934 (tp40) cc_final: 0.6729 (tp40) REVERT: D 410 ARG cc_start: 0.5684 (mmm160) cc_final: 0.4124 (tmt170) REVERT: D 430 LEU cc_start: 0.4881 (OUTLIER) cc_final: 0.4621 (tt) REVERT: D 450 TYR cc_start: 0.5352 (t80) cc_final: 0.4234 (t80) REVERT: D 479 MET cc_start: 0.8008 (mmm) cc_final: 0.7120 (mtp) REVERT: E 79 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7800 (m) outliers start: 37 outliers final: 22 residues processed: 187 average time/residue: 0.3140 time to fit residues: 84.7370 Evaluate side-chains 172 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 136 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS B 538 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.158328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.139524 restraints weight = 63484.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.139340 restraints weight = 51346.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.139850 restraints weight = 39146.267| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 1.0453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16628 Z= 0.241 Angle : 0.766 10.697 23225 Z= 0.403 Chirality : 0.044 0.256 2526 Planarity : 0.006 0.066 2421 Dihedral : 26.834 178.119 3595 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 25.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.01 % Favored : 90.92 % Rotamer: Outliers : 2.39 % Allowed : 27.55 % 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: -2.47 (0.20), residues: 1542 helix: -0.52 (0.20), residues: 685 sheet: -2.25 (0.41), residues: 127 loop : -2.68 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP D 327 HIS 0.011 0.001 HIS C 451 PHE 0.022 0.002 PHE C 512 TYR 0.031 0.002 TYR C 450 ARG 0.015 0.001 ARG D 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3025.55 seconds wall clock time: 56 minutes 26.46 seconds (3386.46 seconds total)