Starting phenix.real_space_refine on Sat Feb 17 16:45:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/02_2024/6bob_7123.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/02_2024/6bob_7123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/02_2024/6bob_7123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/02_2024/6bob_7123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/02_2024/6bob_7123.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/02_2024/6bob_7123.pdb" } resolution = 3.9 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= 0.001 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 12524 2.51 5 N 3244 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 588": "NH1" <-> "NH2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B ARG 614": "NH1" <-> "NH2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 262": "NH1" <-> "NH2" Residue "C TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 588": "NH1" <-> "NH2" Residue "C ARG 614": "NH1" <-> "NH2" Residue "C ARG 635": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 354": "NH1" <-> "NH2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 588": "NH1" <-> "NH2" Residue "D ARG 614": "NH1" <-> "NH2" Residue "D ARG 635": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19340 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4835 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 25, 'TRANS': 577} Chain breaks: 1 Chain: "B" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4835 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 25, 'TRANS': 577} Chain breaks: 1 Chain: "C" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4835 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 25, 'TRANS': 577} Chain breaks: 1 Chain: "D" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4835 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 25, 'TRANS': 577} Chain breaks: 1 Time building chain proxies: 9.75, per 1000 atoms: 0.50 Number of scatterers: 19340 At special positions: 0 Unit cell: (132.3, 132.3, 123.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 3436 8.00 N 3244 7.00 C 12524 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: 7.93 Conformation dependent library (CDL) restraints added in 3.8 seconds 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 59.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 29 through 43 removed outlier: 3.831A pdb=" N ASP A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.574A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.902A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.682A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.530A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.730A pdb=" N GLY A 247 " --> pdb=" O PHE A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.688A pdb=" N VAL A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.597A pdb=" N ILE A 306 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 324 removed outlier: 3.654A pdb=" N GLU A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR A 323 " --> pdb=" O LYS A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 348 removed outlier: 3.599A pdb=" N TYR A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 345 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 407 removed outlier: 3.622A pdb=" N VAL A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 424 through 442 removed outlier: 3.675A pdb=" N VAL A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 3.574A pdb=" N VAL A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.525A pdb=" N ARG A 469 " --> pdb=" O TYR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 486 removed outlier: 3.592A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 482 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 removed outlier: 4.231A pdb=" N TRP A 494 " --> pdb=" O MET A 490 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 502 " --> pdb=" O VAL A 498 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 524 through 537 removed outlier: 3.545A pdb=" N ALA A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 579 removed outlier: 3.603A pdb=" N SER A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 607 removed outlier: 3.554A pdb=" N LEU A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 43 removed outlier: 3.831A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.573A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.901A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.683A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.532A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 250 removed outlier: 3.729A pdb=" N GLY B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.688A pdb=" N VAL B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.598A pdb=" N ILE B 306 " --> pdb=" O ALA B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 324 removed outlier: 3.654A pdb=" N GLU B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU B 315 " --> pdb=" O PRO B 311 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR B 323 " --> pdb=" O LYS B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 348 removed outlier: 3.598A pdb=" N TYR B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 336 " --> pdb=" O GLY B 332 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS B 345 " --> pdb=" O CYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 407 removed outlier: 3.622A pdb=" N VAL B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 424 through 442 removed outlier: 3.676A pdb=" N VAL B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 435 " --> pdb=" O TYR B 431 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 463 removed outlier: 3.574A pdb=" N VAL B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.525A pdb=" N ARG B 469 " --> pdb=" O TYR B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.593A pdb=" N THR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 482 " --> pdb=" O THR B 478 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 484 " --> pdb=" O MET B 480 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 511 removed outlier: 4.231A pdb=" N TRP B 494 " --> pdb=" O MET B 490 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY B 502 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 524 through 537 removed outlier: 3.545A pdb=" N ALA B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 579 removed outlier: 3.603A pdb=" N SER B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 563 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 570 " --> pdb=" O THR B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 607 removed outlier: 3.553A pdb=" N LEU B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.830A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.573A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.901A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 165 through 171 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.682A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 222 removed outlier: 3.532A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.730A pdb=" N GLY C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.689A pdb=" N VAL C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.597A pdb=" N ILE C 306 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 324 removed outlier: 3.654A pdb=" N GLU C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 315 " --> pdb=" O PRO C 311 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 348 removed outlier: 3.598A pdb=" N TYR C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 336 " --> pdb=" O GLY C 332 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS C 345 " --> pdb=" O CYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 407 removed outlier: 3.622A pdb=" N VAL C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 424 through 442 removed outlier: 3.676A pdb=" N VAL C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 435 " --> pdb=" O TYR C 431 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 463 removed outlier: 3.573A pdb=" N VAL C 458 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 469 removed outlier: 3.525A pdb=" N ARG C 469 " --> pdb=" O TYR C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 486 removed outlier: 3.592A pdb=" N THR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 479 " --> pdb=" O GLY C 475 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET C 480 " --> pdb=" O PRO C 476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 482 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET C 484 " --> pdb=" O MET C 480 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 511 removed outlier: 4.231A pdb=" N TRP C 494 " --> pdb=" O MET C 490 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY C 502 " --> pdb=" O VAL C 498 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 524 through 537 removed outlier: 3.546A pdb=" N ALA C 528 " --> pdb=" O ASP C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 579 removed outlier: 3.603A pdb=" N SER C 555 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 563 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU C 570 " --> pdb=" O THR C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 607 removed outlier: 3.553A pdb=" N LEU C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 43 removed outlier: 3.830A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 57 through 64 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.574A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.901A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 165 through 171 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.682A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 222 removed outlier: 3.532A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 250 removed outlier: 3.729A pdb=" N GLY D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.689A pdb=" N VAL D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.597A pdb=" N ILE D 306 " --> pdb=" O ALA D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 324 removed outlier: 3.654A pdb=" N GLU D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU D 315 " --> pdb=" O PRO D 311 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR D 323 " --> pdb=" O LYS D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 348 removed outlier: 3.598A pdb=" N TYR D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 336 " --> pdb=" O GLY D 332 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS D 345 " --> pdb=" O CYS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 407 removed outlier: 3.622A pdb=" N VAL D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 396 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Proline residue: D 404 - end of helix Processing helix chain 'D' and resid 408 through 410 No H-bonds generated for 'chain 'D' and resid 408 through 410' Processing helix chain 'D' and resid 424 through 442 removed outlier: 3.676A pdb=" N VAL D 429 " --> pdb=" O HIS D 425 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 435 " --> pdb=" O TYR D 431 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 463 removed outlier: 3.574A pdb=" N VAL D 458 " --> pdb=" O SER D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 removed outlier: 3.524A pdb=" N ARG D 469 " --> pdb=" O TYR D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 486 removed outlier: 3.593A pdb=" N THR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 479 " --> pdb=" O GLY D 475 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET D 480 " --> pdb=" O PRO D 476 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET D 484 " --> pdb=" O MET D 480 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 511 removed outlier: 4.231A pdb=" N TRP D 494 " --> pdb=" O MET D 490 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU D 495 " --> pdb=" O ARG D 491 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY D 502 " --> pdb=" O VAL D 498 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 524 through 537 removed outlier: 3.545A pdb=" N ALA D 528 " --> pdb=" O ASP D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 579 removed outlier: 3.602A pdb=" N SER D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 563 " --> pdb=" O ALA D 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU D 570 " --> pdb=" O THR D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 607 removed outlier: 3.553A pdb=" N LEU D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 263 through 269 removed outlier: 4.726A pdb=" N ILE A 265 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU A 276 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 263 through 269 removed outlier: 4.726A pdb=" N ILE B 265 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU B 276 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 263 through 269 removed outlier: 4.726A pdb=" N ILE C 265 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU C 276 " --> pdb=" O ILE C 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 263 through 269 removed outlier: 4.726A pdb=" N ILE D 265 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU D 276 " --> pdb=" O ILE D 265 " (cutoff:3.500A) 844 hydrogen bonds defined for protein. 2436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.13 Time building geometry restraints manager: 8.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6065 1.34 - 1.46: 3828 1.46 - 1.57: 9667 1.57 - 1.69: 0 1.69 - 1.81: 228 Bond restraints: 19788 Sorted by residual: bond pdb=" C ASP C 515 " pdb=" N PRO C 516 " ideal model delta sigma weight residual 1.337 1.309 0.027 1.06e-02 8.90e+03 6.68e+00 bond pdb=" C ASP D 515 " pdb=" N PRO D 516 " ideal model delta sigma weight residual 1.337 1.309 0.027 1.06e-02 8.90e+03 6.53e+00 bond pdb=" C ASP A 515 " pdb=" N PRO A 516 " ideal model delta sigma weight residual 1.337 1.310 0.027 1.06e-02 8.90e+03 6.43e+00 bond pdb=" C ASP B 515 " pdb=" N PRO B 516 " ideal model delta sigma weight residual 1.337 1.310 0.026 1.06e-02 8.90e+03 6.13e+00 bond pdb=" N ASN D 357 " pdb=" CA ASN D 357 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.70e+00 ... (remaining 19783 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.44: 420 105.44 - 112.88: 10407 112.88 - 120.33: 8382 120.33 - 127.78: 7425 127.78 - 135.23: 234 Bond angle restraints: 26868 Sorted by residual: angle pdb=" N CYS B 610 " pdb=" CA CYS B 610 " pdb=" C CYS B 610 " ideal model delta sigma weight residual 114.56 106.24 8.32 1.27e+00 6.20e-01 4.29e+01 angle pdb=" N CYS C 610 " pdb=" CA CYS C 610 " pdb=" C CYS C 610 " ideal model delta sigma weight residual 114.56 106.27 8.29 1.27e+00 6.20e-01 4.26e+01 angle pdb=" N CYS D 610 " pdb=" CA CYS D 610 " pdb=" C CYS D 610 " ideal model delta sigma weight residual 114.56 106.28 8.28 1.27e+00 6.20e-01 4.25e+01 angle pdb=" N CYS A 610 " pdb=" CA CYS A 610 " pdb=" C CYS A 610 " ideal model delta sigma weight residual 114.56 106.29 8.27 1.27e+00 6.20e-01 4.24e+01 angle pdb=" CA LEU C 228 " pdb=" CB LEU C 228 " pdb=" CG LEU C 228 " ideal model delta sigma weight residual 116.30 135.23 -18.93 3.50e+00 8.16e-02 2.93e+01 ... (remaining 26863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 10894 15.61 - 31.21: 672 31.21 - 46.82: 182 46.82 - 62.42: 20 62.42 - 78.03: 12 Dihedral angle restraints: 11780 sinusoidal: 4732 harmonic: 7048 Sorted by residual: dihedral pdb=" CA ARG B 354 " pdb=" C ARG B 354 " pdb=" N ILE B 355 " pdb=" CA ILE B 355 " ideal model delta harmonic sigma weight residual 180.00 -132.20 -47.80 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CA ARG C 354 " pdb=" C ARG C 354 " pdb=" N ILE C 355 " pdb=" CA ILE C 355 " ideal model delta harmonic sigma weight residual -180.00 -132.25 -47.75 0 5.00e+00 4.00e-02 9.12e+01 dihedral pdb=" CA ARG D 354 " pdb=" C ARG D 354 " pdb=" N ILE D 355 " pdb=" CA ILE D 355 " ideal model delta harmonic sigma weight residual -180.00 -132.25 -47.75 0 5.00e+00 4.00e-02 9.12e+01 ... (remaining 11777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2089 0.054 - 0.107: 739 0.107 - 0.161: 182 0.161 - 0.215: 30 0.215 - 0.268: 16 Chirality restraints: 3056 Sorted by residual: chirality pdb=" CA THR D 310 " pdb=" N THR D 310 " pdb=" C THR D 310 " pdb=" CB THR D 310 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA THR A 310 " pdb=" N THR A 310 " pdb=" C THR A 310 " pdb=" CB THR A 310 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA THR C 310 " pdb=" N THR C 310 " pdb=" C THR C 310 " pdb=" CB THR C 310 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 3053 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 354 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ARG D 354 " -0.062 2.00e-02 2.50e+03 pdb=" O ARG D 354 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE D 355 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 354 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ARG C 354 " -0.061 2.00e-02 2.50e+03 pdb=" O ARG C 354 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE C 355 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 354 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C ARG B 354 " -0.061 2.00e-02 2.50e+03 pdb=" O ARG B 354 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE B 355 " 0.021 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5012 2.79 - 3.32: 18582 3.32 - 3.84: 32030 3.84 - 4.37: 37973 4.37 - 4.90: 61282 Nonbonded interactions: 154879 Sorted by model distance: nonbonded pdb=" OH TYR C 323 " pdb=" O PRO C 613 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR D 323 " pdb=" O PRO D 613 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR A 323 " pdb=" O PRO A 613 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR B 323 " pdb=" O PRO B 613 " model vdw 2.260 2.440 nonbonded pdb=" OH TYR C 338 " pdb=" O SER C 391 " model vdw 2.274 2.440 ... (remaining 154874 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.840 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 49.850 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.100 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 19788 Z= 0.431 Angle : 1.198 18.931 26868 Z= 0.634 Chirality : 0.060 0.268 3056 Planarity : 0.007 0.067 3396 Dihedral : 11.836 78.026 7236 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.14 % Favored : 88.52 % Rotamer: Outliers : 0.76 % Allowed : 8.03 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -4.96 (0.13), residues: 2396 helix: -3.23 (0.09), residues: 1292 sheet: -0.70 (0.59), residues: 76 loop : -3.48 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 29 HIS 0.006 0.002 HIS D 425 PHE 0.019 0.003 PHE D 530 TYR 0.022 0.003 TYR D 62 ARG 0.009 0.001 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 714 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7146 (t60) cc_final: 0.6603 (t60) REVERT: A 40 GLN cc_start: 0.8477 (tt0) cc_final: 0.8216 (mt0) REVERT: A 51 LEU cc_start: 0.7720 (tt) cc_final: 0.7314 (mt) REVERT: A 96 GLN cc_start: 0.8134 (tt0) cc_final: 0.7899 (mt0) REVERT: A 195 LEU cc_start: 0.7870 (mm) cc_final: 0.7137 (mt) REVERT: A 218 LEU cc_start: 0.8566 (tp) cc_final: 0.8133 (tt) REVERT: A 222 TYR cc_start: 0.7850 (m-80) cc_final: 0.6990 (m-80) REVERT: A 252 ILE cc_start: 0.7742 (mt) cc_final: 0.7426 (tp) REVERT: A 267 TRP cc_start: 0.7013 (p-90) cc_final: 0.6810 (p-90) REVERT: A 305 GLN cc_start: 0.8018 (mt0) cc_final: 0.7605 (tm-30) REVERT: A 480 MET cc_start: 0.7175 (mtm) cc_final: 0.6659 (mmt) REVERT: B 29 TRP cc_start: 0.7059 (t60) cc_final: 0.6565 (t60) REVERT: B 51 LEU cc_start: 0.7672 (tt) cc_final: 0.7176 (mt) REVERT: B 61 LEU cc_start: 0.8174 (mt) cc_final: 0.7972 (mt) REVERT: B 80 GLU cc_start: 0.6115 (pm20) cc_final: 0.5914 (pm20) REVERT: B 218 LEU cc_start: 0.8592 (tp) cc_final: 0.8053 (mt) REVERT: B 222 TYR cc_start: 0.8106 (m-80) cc_final: 0.7396 (m-80) REVERT: B 252 ILE cc_start: 0.7616 (mt) cc_final: 0.7193 (tp) REVERT: B 276 LEU cc_start: 0.7362 (tp) cc_final: 0.7027 (tp) REVERT: B 305 GLN cc_start: 0.7946 (mt0) cc_final: 0.7462 (tm-30) REVERT: B 329 CYS cc_start: 0.7409 (m) cc_final: 0.7034 (t) REVERT: B 458 VAL cc_start: 0.7589 (m) cc_final: 0.7354 (p) REVERT: B 490 MET cc_start: 0.7147 (tpt) cc_final: 0.6168 (mtt) REVERT: B 515 ASP cc_start: 0.7686 (t0) cc_final: 0.7087 (t0) REVERT: B 595 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7673 (mt0) REVERT: C 29 TRP cc_start: 0.6997 (t60) cc_final: 0.6315 (t60) REVERT: C 40 GLN cc_start: 0.8414 (tt0) cc_final: 0.8203 (mt0) REVERT: C 51 LEU cc_start: 0.7712 (tt) cc_final: 0.7316 (mt) REVERT: C 74 GLN cc_start: 0.7087 (tp-100) cc_final: 0.6875 (mp10) REVERT: C 96 GLN cc_start: 0.8300 (tt0) cc_final: 0.8078 (mt0) REVERT: C 116 GLU cc_start: 0.6612 (tt0) cc_final: 0.6285 (tt0) REVERT: C 218 LEU cc_start: 0.8584 (tp) cc_final: 0.8003 (mt) REVERT: C 222 TYR cc_start: 0.8232 (m-80) cc_final: 0.7593 (m-80) REVERT: C 449 GLU cc_start: 0.7248 (pp20) cc_final: 0.6878 (pt0) REVERT: C 490 MET cc_start: 0.6945 (tpt) cc_final: 0.5915 (mtt) REVERT: C 595 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7762 (mt0) REVERT: D 40 GLN cc_start: 0.8540 (tt0) cc_final: 0.8315 (mt0) REVERT: D 51 LEU cc_start: 0.7831 (tt) cc_final: 0.7407 (mt) REVERT: D 195 LEU cc_start: 0.7997 (mm) cc_final: 0.7600 (tp) REVERT: D 218 LEU cc_start: 0.8555 (tp) cc_final: 0.8253 (mt) REVERT: D 273 THR cc_start: 0.7036 (p) cc_final: 0.6509 (p) REVERT: D 305 GLN cc_start: 0.7896 (mt0) cc_final: 0.7357 (tm-30) REVERT: D 449 GLU cc_start: 0.7190 (pp20) cc_final: 0.6907 (pt0) REVERT: D 454 SER cc_start: 0.7867 (t) cc_final: 0.7626 (t) REVERT: D 462 CYS cc_start: 0.8268 (m) cc_final: 0.8068 (m) REVERT: D 480 MET cc_start: 0.7051 (mtm) cc_final: 0.6748 (mmt) REVERT: D 490 MET cc_start: 0.6758 (tpt) cc_final: 0.6069 (mtt) REVERT: D 508 TYR cc_start: 0.6994 (t80) cc_final: 0.6397 (t80) outliers start: 16 outliers final: 7 residues processed: 724 average time/residue: 0.3341 time to fit residues: 361.0148 Evaluate side-chains 432 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 425 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN A 217 ASN A 227 HIS A 257 HIS A 309 GLN A 357 ASN A 360 ASN A 463 ASN B 40 GLN B 118 GLN ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN B 217 ASN B 227 HIS B 251 ASN B 257 HIS B 309 GLN B 360 ASN B 445 ASN B 463 ASN B 571 ASN C 118 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 HIS ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN C 217 ASN C 227 HIS C 251 ASN C 257 HIS C 360 ASN C 463 ASN D 96 GLN D 118 GLN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 HIS D 208 ASN D 217 ASN D 227 HIS D 251 ASN D 257 HIS ** D 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN D 463 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19788 Z= 0.201 Angle : 0.732 12.099 26868 Z= 0.363 Chirality : 0.044 0.174 3056 Planarity : 0.005 0.045 3396 Dihedral : 5.965 46.881 2649 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.14 % Favored : 92.70 % Rotamer: Outliers : 4.59 % Allowed : 14.87 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.88 (0.15), residues: 2396 helix: -1.09 (0.12), residues: 1392 sheet: -0.25 (0.57), residues: 84 loop : -3.35 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 612 HIS 0.010 0.001 HIS C 257 PHE 0.026 0.001 PHE A 342 TYR 0.026 0.002 TYR C 62 ARG 0.005 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 470 time to evaluate : 2.157 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 40 GLN cc_start: 0.8408 (tt0) cc_final: 0.8113 (tt0) REVERT: A 144 SER cc_start: 0.8924 (p) cc_final: 0.8471 (t) REVERT: A 214 GLN cc_start: 0.7971 (tt0) cc_final: 0.7504 (tm-30) REVERT: A 215 MET cc_start: 0.7350 (ttm) cc_final: 0.6964 (mtp) REVERT: A 222 TYR cc_start: 0.7485 (m-80) cc_final: 0.7196 (m-80) REVERT: A 259 MET cc_start: 0.8672 (tpp) cc_final: 0.8416 (mpp) REVERT: A 329 CYS cc_start: 0.7997 (m) cc_final: 0.7661 (t) REVERT: A 358 ARG cc_start: 0.6719 (mpt180) cc_final: 0.6208 (ptp-110) REVERT: A 366 LEU cc_start: 0.6718 (mp) cc_final: 0.6171 (tp) REVERT: A 433 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.7098 (m-10) REVERT: A 480 MET cc_start: 0.7267 (mtm) cc_final: 0.6816 (mmt) REVERT: A 492 PHE cc_start: 0.7050 (t80) cc_final: 0.6724 (t80) REVERT: B 99 MET cc_start: 0.8666 (mmp) cc_final: 0.8226 (tmm) REVERT: B 100 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7247 (pp20) REVERT: B 144 SER cc_start: 0.9002 (p) cc_final: 0.8543 (t) REVERT: B 214 GLN cc_start: 0.7682 (tt0) cc_final: 0.7271 (tm-30) REVERT: B 222 TYR cc_start: 0.7643 (m-80) cc_final: 0.7393 (m-80) REVERT: B 305 GLN cc_start: 0.7971 (mt0) cc_final: 0.7584 (tm-30) REVERT: B 329 CYS cc_start: 0.7296 (m) cc_final: 0.7031 (t) REVERT: B 490 MET cc_start: 0.7082 (tpt) cc_final: 0.6141 (mtt) REVERT: B 515 ASP cc_start: 0.7755 (t0) cc_final: 0.7392 (t0) REVERT: B 521 HIS cc_start: 0.7104 (OUTLIER) cc_final: 0.6296 (t-90) REVERT: B 620 ARG cc_start: 0.7919 (mmt90) cc_final: 0.7643 (mmt180) REVERT: C 40 GLN cc_start: 0.8414 (tt0) cc_final: 0.8143 (tt0) REVERT: C 100 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7478 (pp20) REVERT: C 116 GLU cc_start: 0.6795 (tt0) cc_final: 0.6438 (tt0) REVERT: C 144 SER cc_start: 0.9067 (p) cc_final: 0.8666 (t) REVERT: C 214 GLN cc_start: 0.7629 (tt0) cc_final: 0.7198 (tm-30) REVERT: C 222 TYR cc_start: 0.7818 (m-80) cc_final: 0.7596 (m-80) REVERT: C 305 GLN cc_start: 0.7580 (mp10) cc_final: 0.7268 (tm-30) REVERT: C 308 ASP cc_start: 0.8117 (t70) cc_final: 0.7708 (t0) REVERT: C 490 MET cc_start: 0.6632 (tpt) cc_final: 0.5637 (mtt) REVERT: C 576 MET cc_start: 0.7566 (mmt) cc_final: 0.7319 (mmm) REVERT: C 620 ARG cc_start: 0.7939 (mmt90) cc_final: 0.7731 (mmt180) REVERT: D 116 GLU cc_start: 0.7404 (tt0) cc_final: 0.7023 (tm-30) REVERT: D 215 MET cc_start: 0.7011 (ttm) cc_final: 0.6777 (ttm) REVERT: D 305 GLN cc_start: 0.8021 (mt0) cc_final: 0.7749 (tm-30) REVERT: D 480 MET cc_start: 0.7411 (mtm) cc_final: 0.6916 (mmt) REVERT: D 513 THR cc_start: 0.7144 (OUTLIER) cc_final: 0.6873 (t) REVERT: D 521 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.6179 (t-90) REVERT: D 553 MET cc_start: 0.8375 (mmm) cc_final: 0.7735 (tpt) REVERT: D 620 ARG cc_start: 0.7739 (mpt90) cc_final: 0.7535 (mmt180) REVERT: D 632 VAL cc_start: 0.7391 (t) cc_final: 0.7171 (p) outliers start: 96 outliers final: 39 residues processed: 533 average time/residue: 0.2785 time to fit residues: 232.1971 Evaluate side-chains 437 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 394 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 523 TYR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 634 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 148 optimal weight: 0.0970 chunk 60 optimal weight: 0.0980 chunk 218 optimal weight: 0.2980 chunk 235 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN A 445 ASN A 463 ASN B 40 GLN ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN B 425 HIS B 463 ASN B 571 ASN C 96 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN C 425 HIS C 463 ASN D 40 GLN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN D 425 HIS D 463 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19788 Z= 0.159 Angle : 0.671 11.540 26868 Z= 0.330 Chirality : 0.042 0.164 3056 Planarity : 0.004 0.056 3396 Dihedral : 5.415 46.518 2641 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.35 % Favored : 92.49 % Rotamer: Outliers : 3.87 % Allowed : 18.02 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.07 (0.16), residues: 2396 helix: -0.26 (0.14), residues: 1388 sheet: -0.10 (0.57), residues: 84 loop : -3.30 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 612 HIS 0.004 0.001 HIS A 227 PHE 0.034 0.001 PHE B 492 TYR 0.016 0.001 TYR C 62 ARG 0.003 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 455 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8230 (tt0) cc_final: 0.7913 (tt0) REVERT: A 144 SER cc_start: 0.9001 (p) cc_final: 0.8556 (t) REVERT: A 161 TYR cc_start: 0.8517 (t80) cc_final: 0.7998 (t80) REVERT: A 177 GLU cc_start: 0.8602 (mp0) cc_final: 0.8299 (mp0) REVERT: A 214 GLN cc_start: 0.7765 (tt0) cc_final: 0.7417 (tm-30) REVERT: A 222 TYR cc_start: 0.7633 (m-80) cc_final: 0.7407 (m-80) REVERT: A 329 CYS cc_start: 0.7981 (m) cc_final: 0.7617 (t) REVERT: A 358 ARG cc_start: 0.6655 (mpt180) cc_final: 0.6064 (ptp-110) REVERT: A 480 MET cc_start: 0.7425 (mtm) cc_final: 0.6936 (mmt) REVERT: A 492 PHE cc_start: 0.6974 (t80) cc_final: 0.6636 (t80) REVERT: A 496 MET cc_start: 0.6802 (ttp) cc_final: 0.6463 (tpp) REVERT: A 595 GLN cc_start: 0.8107 (mm-40) cc_final: 0.7423 (mm-40) REVERT: B 99 MET cc_start: 0.8529 (mmp) cc_final: 0.8100 (tmm) REVERT: B 144 SER cc_start: 0.9053 (p) cc_final: 0.8649 (t) REVERT: B 214 GLN cc_start: 0.7764 (tt0) cc_final: 0.7342 (tm-30) REVERT: B 305 GLN cc_start: 0.7888 (mt0) cc_final: 0.7539 (tm-30) REVERT: B 308 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7475 (m-30) REVERT: B 329 CYS cc_start: 0.7277 (m) cc_final: 0.7026 (t) REVERT: B 490 MET cc_start: 0.6990 (tpt) cc_final: 0.5984 (mtt) REVERT: B 576 MET cc_start: 0.7441 (mmt) cc_final: 0.7180 (mmt) REVERT: B 622 TYR cc_start: 0.5448 (m-80) cc_final: 0.5227 (m-80) REVERT: C 40 GLN cc_start: 0.8282 (tt0) cc_final: 0.7980 (tt0) REVERT: C 144 SER cc_start: 0.9088 (p) cc_final: 0.8691 (t) REVERT: C 214 GLN cc_start: 0.7676 (tt0) cc_final: 0.7307 (tm-30) REVERT: C 219 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8430 (mm) REVERT: C 305 GLN cc_start: 0.7676 (mp10) cc_final: 0.7431 (tm-30) REVERT: C 465 MET cc_start: 0.8318 (mmm) cc_final: 0.8091 (mmm) REVERT: C 490 MET cc_start: 0.6431 (tpt) cc_final: 0.5554 (mtt) REVERT: C 521 HIS cc_start: 0.6710 (OUTLIER) cc_final: 0.5428 (t-90) REVERT: D 144 SER cc_start: 0.9198 (p) cc_final: 0.8711 (t) REVERT: D 219 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8388 (mm) REVERT: D 281 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6671 (tp30) REVERT: D 305 GLN cc_start: 0.7950 (mt0) cc_final: 0.7693 (tm-30) REVERT: D 480 MET cc_start: 0.7429 (mtm) cc_final: 0.6986 (mmt) REVERT: D 521 HIS cc_start: 0.7163 (OUTLIER) cc_final: 0.5570 (t-90) REVERT: D 553 MET cc_start: 0.8242 (mmm) cc_final: 0.7698 (tpt) outliers start: 81 outliers final: 35 residues processed: 514 average time/residue: 0.2885 time to fit residues: 229.5685 Evaluate side-chains 436 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 396 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 523 TYR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 521 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 231 optimal weight: 0.0970 chunk 114 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 463 ASN B 40 GLN B 122 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN B 571 ASN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 571 ASN D 309 GLN D 463 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19788 Z= 0.187 Angle : 0.688 10.410 26868 Z= 0.331 Chirality : 0.043 0.275 3056 Planarity : 0.003 0.045 3396 Dihedral : 5.107 46.065 2641 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.43 % Favored : 92.49 % Rotamer: Outliers : 4.30 % Allowed : 19.46 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.71 (0.17), residues: 2396 helix: 0.09 (0.14), residues: 1392 sheet: -0.44 (0.54), residues: 84 loop : -3.21 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 29 HIS 0.003 0.001 HIS A 201 PHE 0.025 0.001 PHE B 492 TYR 0.015 0.001 TYR C 62 ARG 0.005 0.000 ARG B 384 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 419 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8214 (tt0) cc_final: 0.7878 (tt0) REVERT: A 144 SER cc_start: 0.9078 (p) cc_final: 0.8642 (t) REVERT: A 161 TYR cc_start: 0.8481 (t80) cc_final: 0.8036 (t80) REVERT: A 214 GLN cc_start: 0.8064 (tt0) cc_final: 0.7655 (tm-30) REVERT: A 245 LEU cc_start: 0.8141 (tp) cc_final: 0.7849 (tp) REVERT: A 305 GLN cc_start: 0.8034 (tt0) cc_final: 0.7522 (tm-30) REVERT: A 358 ARG cc_start: 0.6693 (mpt180) cc_final: 0.6114 (ptp-110) REVERT: A 465 MET cc_start: 0.8761 (mmm) cc_final: 0.8521 (mmm) REVERT: A 480 MET cc_start: 0.7453 (mtm) cc_final: 0.7023 (mmt) REVERT: A 492 PHE cc_start: 0.6927 (t80) cc_final: 0.6667 (t80) REVERT: A 496 MET cc_start: 0.6774 (ttp) cc_final: 0.6377 (tpp) REVERT: A 515 ASP cc_start: 0.8158 (t0) cc_final: 0.7924 (t0) REVERT: A 595 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7420 (mm-40) REVERT: B 99 MET cc_start: 0.8371 (mmp) cc_final: 0.8051 (tmm) REVERT: B 144 SER cc_start: 0.9123 (p) cc_final: 0.8748 (t) REVERT: B 214 GLN cc_start: 0.7734 (tt0) cc_final: 0.7328 (tm-30) REVERT: B 219 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8428 (mm) REVERT: B 293 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 305 GLN cc_start: 0.7750 (mt0) cc_final: 0.7453 (tm-30) REVERT: B 308 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: B 329 CYS cc_start: 0.7434 (m) cc_final: 0.7217 (t) REVERT: B 480 MET cc_start: 0.6921 (mmt) cc_final: 0.6563 (mtp) REVERT: B 490 MET cc_start: 0.7190 (tpt) cc_final: 0.6212 (mtt) REVERT: B 492 PHE cc_start: 0.6975 (t80) cc_final: 0.6694 (t80) REVERT: B 521 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.6155 (t-90) REVERT: B 622 TYR cc_start: 0.5530 (m-80) cc_final: 0.5265 (m-80) REVERT: C 40 GLN cc_start: 0.8278 (tt0) cc_final: 0.7971 (tt0) REVERT: C 144 SER cc_start: 0.9129 (p) cc_final: 0.8742 (t) REVERT: C 214 GLN cc_start: 0.7938 (tt0) cc_final: 0.7500 (tm-30) REVERT: C 281 GLU cc_start: 0.7489 (tp30) cc_final: 0.7251 (tp30) REVERT: C 363 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8141 (p0) REVERT: C 465 MET cc_start: 0.8474 (mmm) cc_final: 0.8193 (mmm) REVERT: C 490 MET cc_start: 0.6385 (tpt) cc_final: 0.5467 (mtt) REVERT: C 521 HIS cc_start: 0.7136 (OUTLIER) cc_final: 0.5495 (t-90) REVERT: C 581 HIS cc_start: 0.5653 (t70) cc_final: 0.5409 (t70) REVERT: D 116 GLU cc_start: 0.7598 (tt0) cc_final: 0.7085 (tm-30) REVERT: D 144 SER cc_start: 0.9215 (p) cc_final: 0.8826 (t) REVERT: D 305 GLN cc_start: 0.7923 (mt0) cc_final: 0.7694 (tm-30) REVERT: D 308 ASP cc_start: 0.7962 (t70) cc_final: 0.7643 (t70) REVERT: D 465 MET cc_start: 0.8271 (mmm) cc_final: 0.8038 (mmm) REVERT: D 480 MET cc_start: 0.7480 (mtm) cc_final: 0.6972 (mmt) REVERT: D 513 THR cc_start: 0.7293 (OUTLIER) cc_final: 0.7060 (t) REVERT: D 521 HIS cc_start: 0.7549 (OUTLIER) cc_final: 0.5906 (t-90) REVERT: D 530 PHE cc_start: 0.7917 (t80) cc_final: 0.7692 (t80) REVERT: D 553 MET cc_start: 0.8109 (mmm) cc_final: 0.7579 (tpp) REVERT: D 581 HIS cc_start: 0.5006 (t70) cc_final: 0.4774 (t70) REVERT: D 593 ARG cc_start: 0.8018 (mpt-90) cc_final: 0.7788 (tpp80) REVERT: D 595 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7391 (mm-40) outliers start: 90 outliers final: 53 residues processed: 474 average time/residue: 0.2715 time to fit residues: 202.5907 Evaluate side-chains 441 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 381 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 523 TYR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 634 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.3980 chunk 131 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 463 ASN B 40 GLN B 206 GLN B 463 ASN ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 309 GLN C 425 HIS C 463 ASN D 425 HIS D 463 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19788 Z= 0.172 Angle : 0.675 10.596 26868 Z= 0.324 Chirality : 0.042 0.240 3056 Planarity : 0.003 0.038 3396 Dihedral : 4.904 46.219 2641 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.40 % Allowed : 21.08 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.50 (0.17), residues: 2396 helix: 0.26 (0.14), residues: 1400 sheet: -0.60 (0.53), residues: 84 loop : -3.12 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 29 HIS 0.003 0.001 HIS A 201 PHE 0.015 0.001 PHE B 492 TYR 0.015 0.001 TYR C 62 ARG 0.004 0.000 ARG C 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 406 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8285 (tt0) cc_final: 0.7928 (tt0) REVERT: A 127 ASN cc_start: 0.8796 (m110) cc_final: 0.8461 (m110) REVERT: A 144 SER cc_start: 0.9093 (p) cc_final: 0.8666 (t) REVERT: A 161 TYR cc_start: 0.8484 (t80) cc_final: 0.8033 (t80) REVERT: A 214 GLN cc_start: 0.8067 (tt0) cc_final: 0.7665 (tm-30) REVERT: A 305 GLN cc_start: 0.8039 (tt0) cc_final: 0.7502 (tm-30) REVERT: A 358 ARG cc_start: 0.7014 (mpt180) cc_final: 0.6383 (ptp-110) REVERT: A 465 MET cc_start: 0.8693 (mmm) cc_final: 0.8356 (mmm) REVERT: A 480 MET cc_start: 0.7457 (mtm) cc_final: 0.6997 (mmt) REVERT: A 492 PHE cc_start: 0.7003 (t80) cc_final: 0.6725 (t80) REVERT: A 496 MET cc_start: 0.6752 (ttp) cc_final: 0.6357 (tpp) REVERT: A 595 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7383 (mm-40) REVERT: B 99 MET cc_start: 0.8395 (mmp) cc_final: 0.8037 (tmm) REVERT: B 144 SER cc_start: 0.9088 (p) cc_final: 0.8687 (t) REVERT: B 214 GLN cc_start: 0.7815 (tt0) cc_final: 0.7375 (tm-30) REVERT: B 305 GLN cc_start: 0.7841 (mt0) cc_final: 0.7559 (tm-30) REVERT: B 480 MET cc_start: 0.6845 (mmt) cc_final: 0.6613 (mtp) REVERT: B 490 MET cc_start: 0.7113 (tpt) cc_final: 0.6244 (mtt) REVERT: B 492 PHE cc_start: 0.7016 (t80) cc_final: 0.6676 (t80) REVERT: B 521 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.6018 (t-90) REVERT: B 553 MET cc_start: 0.8292 (mmm) cc_final: 0.7677 (mmm) REVERT: C 40 GLN cc_start: 0.8330 (tt0) cc_final: 0.7974 (tt0) REVERT: C 127 ASN cc_start: 0.8769 (m110) cc_final: 0.8508 (m110) REVERT: C 144 SER cc_start: 0.9162 (p) cc_final: 0.8771 (t) REVERT: C 214 GLN cc_start: 0.7850 (tt0) cc_final: 0.7440 (tm-30) REVERT: C 363 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8051 (p0) REVERT: C 449 GLU cc_start: 0.7120 (pp20) cc_final: 0.6819 (pt0) REVERT: C 465 MET cc_start: 0.8560 (mmm) cc_final: 0.8249 (mmm) REVERT: C 480 MET cc_start: 0.7006 (mmt) cc_final: 0.6647 (mtp) REVERT: C 490 MET cc_start: 0.6428 (tpt) cc_final: 0.5606 (mtt) REVERT: C 496 MET cc_start: 0.5740 (ttp) cc_final: 0.5510 (tpp) REVERT: C 553 MET cc_start: 0.8092 (mmm) cc_final: 0.7653 (tpp) REVERT: C 571 ASN cc_start: 0.6650 (m110) cc_final: 0.6405 (m-40) REVERT: D 144 SER cc_start: 0.9219 (p) cc_final: 0.8902 (t) REVERT: D 164 GLU cc_start: 0.7405 (mp0) cc_final: 0.7177 (pm20) REVERT: D 305 GLN cc_start: 0.7924 (mt0) cc_final: 0.7693 (tm-30) REVERT: D 480 MET cc_start: 0.7493 (mtm) cc_final: 0.7027 (mmt) REVERT: D 490 MET cc_start: 0.5977 (tpt) cc_final: 0.5009 (mtt) REVERT: D 513 THR cc_start: 0.7060 (OUTLIER) cc_final: 0.6857 (t) REVERT: D 521 HIS cc_start: 0.7426 (OUTLIER) cc_final: 0.5674 (t-90) REVERT: D 553 MET cc_start: 0.8085 (mmm) cc_final: 0.7630 (tpp) REVERT: D 593 ARG cc_start: 0.8042 (mpt-90) cc_final: 0.7809 (tpp80) REVERT: D 595 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7935 (mm-40) outliers start: 92 outliers final: 52 residues processed: 468 average time/residue: 0.2838 time to fit residues: 206.9226 Evaluate side-chains 438 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 382 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 634 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.3980 chunk 208 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 57 optimal weight: 0.0980 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 0.0670 chunk 121 optimal weight: 5.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 463 ASN C 96 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 581 HIS D 463 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19788 Z= 0.157 Angle : 0.678 11.156 26868 Z= 0.320 Chirality : 0.043 0.276 3056 Planarity : 0.003 0.038 3396 Dihedral : 4.680 46.465 2639 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.25 % Allowed : 22.42 % Favored : 73.33 % 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: -1.35 (0.17), residues: 2396 helix: 0.41 (0.14), residues: 1396 sheet: -0.71 (0.53), residues: 84 loop : -3.08 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 29 HIS 0.004 0.001 HIS A 201 PHE 0.021 0.001 PHE D 492 TYR 0.014 0.001 TYR C 62 ARG 0.003 0.000 ARG C 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 414 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6544 (mmt) cc_final: 0.5444 (mpp) REVERT: A 127 ASN cc_start: 0.8760 (m110) cc_final: 0.8418 (m110) REVERT: A 144 SER cc_start: 0.9134 (p) cc_final: 0.8727 (t) REVERT: A 164 GLU cc_start: 0.7727 (mp0) cc_final: 0.7249 (pm20) REVERT: A 214 GLN cc_start: 0.8086 (tt0) cc_final: 0.7672 (tm-30) REVERT: A 215 MET cc_start: 0.7792 (tpp) cc_final: 0.7495 (tpp) REVERT: A 245 LEU cc_start: 0.8105 (tp) cc_final: 0.7800 (tp) REVERT: A 305 GLN cc_start: 0.8039 (tt0) cc_final: 0.7498 (tm-30) REVERT: A 358 ARG cc_start: 0.6955 (mpt180) cc_final: 0.6434 (ptp-110) REVERT: A 465 MET cc_start: 0.8669 (mmm) cc_final: 0.8365 (mmm) REVERT: A 480 MET cc_start: 0.7362 (mtm) cc_final: 0.6902 (mmt) REVERT: A 492 PHE cc_start: 0.6999 (t80) cc_final: 0.6684 (t80) REVERT: A 496 MET cc_start: 0.6752 (ttp) cc_final: 0.6368 (tpp) REVERT: A 595 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7371 (mm-40) REVERT: A 602 MET cc_start: 0.8619 (ttp) cc_final: 0.8394 (ttp) REVERT: B 99 MET cc_start: 0.8406 (mmp) cc_final: 0.8017 (tmm) REVERT: B 144 SER cc_start: 0.9137 (p) cc_final: 0.8753 (t) REVERT: B 164 GLU cc_start: 0.7589 (mp0) cc_final: 0.7161 (pm20) REVERT: B 214 GLN cc_start: 0.7880 (tt0) cc_final: 0.7414 (tm-30) REVERT: B 215 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6823 (mtp) REVERT: B 293 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8252 (tm-30) REVERT: B 305 GLN cc_start: 0.7918 (mt0) cc_final: 0.7662 (tm-30) REVERT: B 480 MET cc_start: 0.6832 (mmt) cc_final: 0.6616 (mtp) REVERT: B 490 MET cc_start: 0.7178 (tpt) cc_final: 0.6229 (mtt) REVERT: B 521 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.6025 (t-90) REVERT: B 553 MET cc_start: 0.8149 (mmm) cc_final: 0.7604 (mmm) REVERT: B 622 TYR cc_start: 0.5051 (m-80) cc_final: 0.4586 (m-10) REVERT: C 38 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6103 (mm) REVERT: C 40 GLN cc_start: 0.8257 (tt0) cc_final: 0.7914 (tt0) REVERT: C 144 SER cc_start: 0.9202 (p) cc_final: 0.8833 (t) REVERT: C 214 GLN cc_start: 0.7915 (tt0) cc_final: 0.7477 (tm-30) REVERT: C 289 GLN cc_start: 0.7119 (mp10) cc_final: 0.6842 (mp10) REVERT: C 305 GLN cc_start: 0.7713 (tt0) cc_final: 0.7076 (tm-30) REVERT: C 363 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7969 (p0) REVERT: C 446 SER cc_start: 0.6697 (t) cc_final: 0.6235 (p) REVERT: C 449 GLU cc_start: 0.7049 (pp20) cc_final: 0.6678 (pt0) REVERT: C 465 MET cc_start: 0.8428 (mmm) cc_final: 0.8091 (mmm) REVERT: C 480 MET cc_start: 0.7004 (mmt) cc_final: 0.6567 (mtp) REVERT: C 490 MET cc_start: 0.6365 (tpt) cc_final: 0.5559 (mtt) REVERT: C 496 MET cc_start: 0.5818 (ttp) cc_final: 0.5594 (tpp) REVERT: C 553 MET cc_start: 0.7980 (mmm) cc_final: 0.7593 (tpp) REVERT: C 571 ASN cc_start: 0.6702 (m110) cc_final: 0.6440 (m-40) REVERT: D 116 GLU cc_start: 0.7696 (tt0) cc_final: 0.7167 (tm-30) REVERT: D 144 SER cc_start: 0.9255 (p) cc_final: 0.8948 (t) REVERT: D 222 TYR cc_start: 0.7121 (m-80) cc_final: 0.6862 (m-10) REVERT: D 305 GLN cc_start: 0.7969 (mt0) cc_final: 0.7730 (tm-30) REVERT: D 308 ASP cc_start: 0.8212 (t0) cc_final: 0.7720 (t0) REVERT: D 480 MET cc_start: 0.7515 (mtm) cc_final: 0.7055 (mmt) REVERT: D 521 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.5629 (t-90) REVERT: D 553 MET cc_start: 0.8042 (mmm) cc_final: 0.7623 (tpp) REVERT: D 593 ARG cc_start: 0.8028 (mpt-90) cc_final: 0.7785 (tpp80) REVERT: D 595 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7354 (mm-40) outliers start: 89 outliers final: 51 residues processed: 471 average time/residue: 0.2872 time to fit residues: 210.3739 Evaluate side-chains 450 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 394 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 612 TRP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 523 TYR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 626 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 169 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 309 GLN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 HIS B 40 GLN B 74 GLN B 309 GLN B 463 ASN B 571 ASN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN D 118 GLN D 463 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19788 Z= 0.218 Angle : 0.735 14.088 26868 Z= 0.345 Chirality : 0.045 0.321 3056 Planarity : 0.003 0.035 3396 Dihedral : 4.758 45.868 2639 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.54 % Allowed : 22.71 % Favored : 72.75 % 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: -1.29 (0.17), residues: 2396 helix: 0.38 (0.14), residues: 1404 sheet: 0.28 (0.53), residues: 64 loop : -2.98 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 612 HIS 0.003 0.001 HIS A 201 PHE 0.036 0.002 PHE D 492 TYR 0.014 0.002 TYR C 62 ARG 0.003 0.000 ARG C 384 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 426 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6585 (mmt) cc_final: 0.5554 (mpp) REVERT: A 108 GLU cc_start: 0.7850 (pt0) cc_final: 0.7449 (pm20) REVERT: A 127 ASN cc_start: 0.8780 (m110) cc_final: 0.8360 (m110) REVERT: A 144 SER cc_start: 0.9157 (p) cc_final: 0.8767 (t) REVERT: A 164 GLU cc_start: 0.8061 (mp0) cc_final: 0.7501 (pm20) REVERT: A 214 GLN cc_start: 0.8201 (tt0) cc_final: 0.7817 (tm-30) REVERT: A 215 MET cc_start: 0.7857 (tpp) cc_final: 0.7474 (tpp) REVERT: A 222 TYR cc_start: 0.7303 (m-80) cc_final: 0.7070 (m-10) REVERT: A 305 GLN cc_start: 0.8076 (tt0) cc_final: 0.7549 (tm-30) REVERT: A 358 ARG cc_start: 0.6930 (mpt180) cc_final: 0.6410 (ptp-110) REVERT: A 480 MET cc_start: 0.7499 (mtm) cc_final: 0.7072 (mmt) REVERT: A 492 PHE cc_start: 0.7088 (t80) cc_final: 0.6695 (t80) REVERT: A 496 MET cc_start: 0.6731 (ttp) cc_final: 0.6332 (tpp) REVERT: A 522 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.5350 (p90) REVERT: A 595 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7373 (mm-40) REVERT: A 602 MET cc_start: 0.8665 (ttp) cc_final: 0.8429 (ttp) REVERT: B 99 MET cc_start: 0.8398 (mmp) cc_final: 0.8034 (tmm) REVERT: B 116 GLU cc_start: 0.7310 (tp30) cc_final: 0.6903 (tt0) REVERT: B 144 SER cc_start: 0.9188 (p) cc_final: 0.8769 (t) REVERT: B 164 GLU cc_start: 0.8015 (mp0) cc_final: 0.7429 (pm20) REVERT: B 214 GLN cc_start: 0.7867 (tt0) cc_final: 0.7480 (tm-30) REVERT: B 222 TYR cc_start: 0.7381 (m-80) cc_final: 0.7152 (m-10) REVERT: B 305 GLN cc_start: 0.7989 (mt0) cc_final: 0.7663 (tm-30) REVERT: B 362 ARG cc_start: 0.8847 (ppt170) cc_final: 0.8464 (ptt-90) REVERT: B 465 MET cc_start: 0.8968 (mmm) cc_final: 0.8757 (mmm) REVERT: B 490 MET cc_start: 0.7097 (tpt) cc_final: 0.6213 (mtt) REVERT: B 521 HIS cc_start: 0.8022 (OUTLIER) cc_final: 0.6439 (t-90) REVERT: B 593 ARG cc_start: 0.7959 (mpt-90) cc_final: 0.7688 (tpp80) REVERT: C 40 GLN cc_start: 0.8290 (tt0) cc_final: 0.8016 (tt0) REVERT: C 144 SER cc_start: 0.9116 (p) cc_final: 0.8708 (t) REVERT: C 214 GLN cc_start: 0.7811 (tt0) cc_final: 0.7358 (tm-30) REVERT: C 222 TYR cc_start: 0.7356 (m-80) cc_final: 0.7070 (m-10) REVERT: C 289 GLN cc_start: 0.6906 (mp10) cc_final: 0.6662 (mp10) REVERT: C 305 GLN cc_start: 0.7802 (tt0) cc_final: 0.7181 (tm-30) REVERT: C 449 GLU cc_start: 0.7336 (pp20) cc_final: 0.7083 (pt0) REVERT: C 480 MET cc_start: 0.6993 (mmt) cc_final: 0.6550 (mtp) REVERT: C 490 MET cc_start: 0.6756 (tpt) cc_final: 0.5956 (mtt) REVERT: C 521 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.6277 (t-90) REVERT: C 540 ILE cc_start: 0.8306 (pt) cc_final: 0.7997 (mt) REVERT: C 553 MET cc_start: 0.8056 (mmm) cc_final: 0.7726 (tpp) REVERT: C 593 ARG cc_start: 0.8101 (mpt-90) cc_final: 0.7820 (tpp80) REVERT: D 144 SER cc_start: 0.9239 (p) cc_final: 0.8928 (t) REVERT: D 222 TYR cc_start: 0.7056 (m-80) cc_final: 0.6846 (m-10) REVERT: D 305 GLN cc_start: 0.7999 (mt0) cc_final: 0.7786 (tm-30) REVERT: D 480 MET cc_start: 0.7584 (mtm) cc_final: 0.7147 (mmt) REVERT: D 553 MET cc_start: 0.8102 (mmm) cc_final: 0.7706 (tpp) REVERT: D 593 ARG cc_start: 0.8058 (mpt-90) cc_final: 0.7848 (tpp80) REVERT: D 605 ARG cc_start: 0.7297 (tmm-80) cc_final: 0.6993 (tpm170) outliers start: 95 outliers final: 59 residues processed: 490 average time/residue: 0.2899 time to fit residues: 219.8431 Evaluate side-chains 453 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 391 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 634 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 HIS ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 HIS ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 521 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19788 Z= 0.290 Angle : 0.787 13.140 26868 Z= 0.373 Chirality : 0.048 0.330 3056 Planarity : 0.004 0.034 3396 Dihedral : 5.065 45.616 2637 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 4.30 % Allowed : 23.57 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.37 (0.17), residues: 2396 helix: 0.24 (0.14), residues: 1400 sheet: -0.18 (0.50), residues: 64 loop : -2.83 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 612 HIS 0.003 0.001 HIS D 185 PHE 0.042 0.002 PHE D 492 TYR 0.014 0.002 TYR D 466 ARG 0.004 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 402 time to evaluate : 2.167 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6593 (mmt) cc_final: 0.5754 (mpp) REVERT: A 108 GLU cc_start: 0.8047 (pt0) cc_final: 0.7381 (pm20) REVERT: A 127 ASN cc_start: 0.8697 (m110) cc_final: 0.8231 (m110) REVERT: A 144 SER cc_start: 0.9168 (p) cc_final: 0.8742 (t) REVERT: A 164 GLU cc_start: 0.8125 (mp0) cc_final: 0.7634 (pm20) REVERT: A 214 GLN cc_start: 0.8177 (tt0) cc_final: 0.7619 (tm-30) REVERT: A 305 GLN cc_start: 0.7925 (tt0) cc_final: 0.7384 (tm-30) REVERT: A 358 ARG cc_start: 0.6855 (mpt180) cc_final: 0.6020 (ptp90) REVERT: A 362 ARG cc_start: 0.8742 (ppt170) cc_final: 0.8445 (ptt-90) REVERT: A 480 MET cc_start: 0.7397 (mtm) cc_final: 0.7010 (mmt) REVERT: A 492 PHE cc_start: 0.7136 (t80) cc_final: 0.6806 (t80) REVERT: A 496 MET cc_start: 0.6687 (ttp) cc_final: 0.6425 (ttp) REVERT: A 522 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.8003 (p90) REVERT: A 602 MET cc_start: 0.8641 (ttp) cc_final: 0.8424 (ttp) REVERT: B 99 MET cc_start: 0.8421 (mmp) cc_final: 0.7972 (tmm) REVERT: B 144 SER cc_start: 0.9146 (p) cc_final: 0.8650 (t) REVERT: B 164 GLU cc_start: 0.8122 (mp0) cc_final: 0.7622 (pm20) REVERT: B 175 SER cc_start: 0.7918 (t) cc_final: 0.7595 (t) REVERT: B 305 GLN cc_start: 0.7999 (mt0) cc_final: 0.7669 (tm-30) REVERT: B 362 ARG cc_start: 0.8931 (ppt170) cc_final: 0.8625 (ptt-90) REVERT: B 490 MET cc_start: 0.7201 (tpt) cc_final: 0.6354 (mtt) REVERT: B 492 PHE cc_start: 0.7055 (t80) cc_final: 0.6650 (t80) REVERT: B 553 MET cc_start: 0.8348 (mmm) cc_final: 0.7896 (tpp) REVERT: B 581 HIS cc_start: 0.5562 (t70) cc_final: 0.5360 (t70) REVERT: B 593 ARG cc_start: 0.7993 (mpt-90) cc_final: 0.7763 (tpp80) REVERT: B 595 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7504 (mm-40) REVERT: C 40 GLN cc_start: 0.8358 (tt0) cc_final: 0.8086 (tt0) REVERT: C 144 SER cc_start: 0.9140 (p) cc_final: 0.8656 (t) REVERT: C 161 TYR cc_start: 0.8433 (t80) cc_final: 0.8069 (t80) REVERT: C 214 GLN cc_start: 0.7887 (tt0) cc_final: 0.7441 (tm-30) REVERT: C 305 GLN cc_start: 0.7982 (tt0) cc_final: 0.7394 (tm-30) REVERT: C 490 MET cc_start: 0.7047 (tpt) cc_final: 0.6144 (mtt) REVERT: C 553 MET cc_start: 0.7978 (mmm) cc_final: 0.7653 (tpp) REVERT: C 581 HIS cc_start: 0.5344 (t-90) cc_final: 0.5075 (t70) REVERT: C 593 ARG cc_start: 0.8042 (mpt-90) cc_final: 0.7806 (tpp80) REVERT: D 144 SER cc_start: 0.9318 (p) cc_final: 0.8878 (t) REVERT: D 222 TYR cc_start: 0.7396 (m-80) cc_final: 0.7041 (m-10) REVERT: D 305 GLN cc_start: 0.8082 (mt0) cc_final: 0.7699 (tm-30) REVERT: D 308 ASP cc_start: 0.8616 (t0) cc_final: 0.7989 (m-30) REVERT: D 446 SER cc_start: 0.6762 (OUTLIER) cc_final: 0.6025 (p) REVERT: D 465 MET cc_start: 0.8526 (mmm) cc_final: 0.8296 (mmt) REVERT: D 480 MET cc_start: 0.7516 (mtm) cc_final: 0.7102 (mmt) REVERT: D 553 MET cc_start: 0.8078 (mmm) cc_final: 0.7675 (tpp) outliers start: 90 outliers final: 62 residues processed: 464 average time/residue: 0.2910 time to fit residues: 209.0927 Evaluate side-chains 442 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 378 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 634 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.7980 chunk 221 optimal weight: 0.3980 chunk 202 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 169 optimal weight: 0.0470 chunk 66 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 214 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 84 HIS C 96 GLN C 118 GLN C 122 HIS C 463 ASN C 571 ASN D 214 GLN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.6690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19788 Z= 0.179 Angle : 0.757 15.670 26868 Z= 0.348 Chirality : 0.045 0.458 3056 Planarity : 0.003 0.034 3396 Dihedral : 4.769 46.170 2637 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 2.87 % Allowed : 25.86 % Favored : 71.27 % 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: -1.20 (0.17), residues: 2396 helix: 0.41 (0.14), residues: 1412 sheet: -0.26 (0.50), residues: 64 loop : -2.85 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 29 HIS 0.004 0.001 HIS A 201 PHE 0.040 0.001 PHE D 492 TYR 0.015 0.001 TYR A 554 ARG 0.003 0.000 ARG C 605 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 410 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6570 (OUTLIER) cc_final: 0.5713 (mpp) REVERT: A 108 GLU cc_start: 0.7936 (pt0) cc_final: 0.7392 (pm20) REVERT: A 144 SER cc_start: 0.9179 (p) cc_final: 0.8750 (t) REVERT: A 164 GLU cc_start: 0.7829 (mp0) cc_final: 0.7618 (pm20) REVERT: A 214 GLN cc_start: 0.8078 (tt0) cc_final: 0.7509 (tm-30) REVERT: A 222 TYR cc_start: 0.7258 (m-80) cc_final: 0.6952 (m-10) REVERT: A 305 GLN cc_start: 0.7877 (tt0) cc_final: 0.7342 (tm-30) REVERT: A 358 ARG cc_start: 0.7094 (mpt180) cc_final: 0.6550 (ptp-110) REVERT: A 362 ARG cc_start: 0.8771 (ppt170) cc_final: 0.8475 (ptt-90) REVERT: A 480 MET cc_start: 0.7570 (mtm) cc_final: 0.7215 (mmt) REVERT: A 492 PHE cc_start: 0.7191 (t80) cc_final: 0.6868 (t80) REVERT: A 496 MET cc_start: 0.6631 (ttp) cc_final: 0.6165 (tpp) REVERT: A 571 ASN cc_start: 0.6953 (m-40) cc_final: 0.6741 (m-40) REVERT: A 602 MET cc_start: 0.8568 (ttp) cc_final: 0.8303 (ttp) REVERT: B 99 MET cc_start: 0.8409 (mmp) cc_final: 0.7982 (tmm) REVERT: B 144 SER cc_start: 0.9142 (p) cc_final: 0.8652 (t) REVERT: B 164 GLU cc_start: 0.7830 (mp0) cc_final: 0.7582 (pm20) REVERT: B 175 SER cc_start: 0.7945 (t) cc_final: 0.7629 (t) REVERT: B 214 GLN cc_start: 0.7876 (tt0) cc_final: 0.7499 (tm-30) REVERT: B 305 GLN cc_start: 0.7967 (mt0) cc_final: 0.7620 (tm-30) REVERT: B 362 ARG cc_start: 0.8939 (ppt170) cc_final: 0.8618 (ptt-90) REVERT: B 446 SER cc_start: 0.6928 (t) cc_final: 0.6372 (p) REVERT: B 490 MET cc_start: 0.7189 (tpt) cc_final: 0.6176 (mtt) REVERT: B 496 MET cc_start: 0.6476 (ttp) cc_final: 0.6185 (tpp) REVERT: B 521 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.6447 (t-90) REVERT: B 553 MET cc_start: 0.8206 (mmm) cc_final: 0.7754 (tpp) REVERT: B 593 ARG cc_start: 0.7907 (mpt-90) cc_final: 0.7680 (tpp80) REVERT: B 595 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7556 (mm-40) REVERT: C 40 GLN cc_start: 0.8320 (tt0) cc_final: 0.8050 (tt0) REVERT: C 144 SER cc_start: 0.9163 (p) cc_final: 0.8691 (t) REVERT: C 175 SER cc_start: 0.7873 (t) cc_final: 0.7432 (p) REVERT: C 214 GLN cc_start: 0.7783 (tt0) cc_final: 0.7331 (tm-30) REVERT: C 222 TYR cc_start: 0.7300 (m-80) cc_final: 0.6973 (m-10) REVERT: C 305 GLN cc_start: 0.7886 (tt0) cc_final: 0.7267 (tm-30) REVERT: C 449 GLU cc_start: 0.7454 (pp20) cc_final: 0.6594 (pp20) REVERT: C 490 MET cc_start: 0.6955 (tpt) cc_final: 0.6269 (mtt) REVERT: C 494 TRP cc_start: 0.7530 (m100) cc_final: 0.7237 (m100) REVERT: C 496 MET cc_start: 0.6404 (ttp) cc_final: 0.6176 (tpp) REVERT: C 553 MET cc_start: 0.7785 (mmm) cc_final: 0.7457 (tpp) REVERT: C 593 ARG cc_start: 0.8018 (mpt-90) cc_final: 0.7778 (tpp80) REVERT: D 144 SER cc_start: 0.9276 (p) cc_final: 0.8875 (t) REVERT: D 189 ILE cc_start: 0.8443 (mm) cc_final: 0.8223 (mm) REVERT: D 222 TYR cc_start: 0.7400 (m-80) cc_final: 0.6933 (m-10) REVERT: D 305 GLN cc_start: 0.8024 (mt0) cc_final: 0.7745 (tm-30) REVERT: D 308 ASP cc_start: 0.8449 (t0) cc_final: 0.7862 (m-30) REVERT: D 446 SER cc_start: 0.6628 (OUTLIER) cc_final: 0.5995 (p) REVERT: D 480 MET cc_start: 0.7543 (mtm) cc_final: 0.7142 (mmt) REVERT: D 553 MET cc_start: 0.7959 (mmm) cc_final: 0.7635 (tpp) outliers start: 60 outliers final: 45 residues processed: 452 average time/residue: 0.2965 time to fit residues: 206.7815 Evaluate side-chains 437 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 389 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 634 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN A 445 ASN A 463 ASN B 40 GLN B 463 ASN B 581 HIS ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19788 Z= 0.257 Angle : 0.790 17.418 26868 Z= 0.367 Chirality : 0.047 0.478 3056 Planarity : 0.003 0.038 3396 Dihedral : 4.849 45.620 2637 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 3.01 % Allowed : 25.91 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.23 (0.17), residues: 2396 helix: 0.38 (0.14), residues: 1408 sheet: -0.49 (0.48), residues: 64 loop : -2.81 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 612 HIS 0.003 0.001 HIS A 201 PHE 0.045 0.002 PHE D 492 TYR 0.014 0.002 TYR B 622 ARG 0.008 0.000 ARG B 605 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 396 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6573 (mmt) cc_final: 0.5799 (mpp) REVERT: A 108 GLU cc_start: 0.8092 (pt0) cc_final: 0.7409 (pm20) REVERT: A 144 SER cc_start: 0.9076 (p) cc_final: 0.8592 (t) REVERT: A 164 GLU cc_start: 0.8133 (mp0) cc_final: 0.7792 (pm20) REVERT: A 214 GLN cc_start: 0.8162 (tt0) cc_final: 0.7589 (tm-30) REVERT: A 222 TYR cc_start: 0.7240 (m-80) cc_final: 0.6986 (m-10) REVERT: A 305 GLN cc_start: 0.7937 (tt0) cc_final: 0.7382 (tm-30) REVERT: A 358 ARG cc_start: 0.7039 (mpt180) cc_final: 0.6490 (ptp-110) REVERT: A 362 ARG cc_start: 0.8739 (ppt170) cc_final: 0.8458 (ptt-90) REVERT: A 480 MET cc_start: 0.7520 (mtm) cc_final: 0.7188 (mmt) REVERT: A 492 PHE cc_start: 0.7176 (t80) cc_final: 0.6828 (t80) REVERT: A 496 MET cc_start: 0.6608 (ttp) cc_final: 0.6361 (ttp) REVERT: A 522 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7946 (p90) REVERT: A 602 MET cc_start: 0.8578 (ttp) cc_final: 0.8326 (ttp) REVERT: B 99 MET cc_start: 0.8418 (mmp) cc_final: 0.7947 (tmm) REVERT: B 127 ASN cc_start: 0.8737 (m110) cc_final: 0.8438 (m110) REVERT: B 144 SER cc_start: 0.9136 (p) cc_final: 0.8646 (t) REVERT: B 164 GLU cc_start: 0.8088 (mp0) cc_final: 0.7726 (pm20) REVERT: B 175 SER cc_start: 0.8064 (t) cc_final: 0.7711 (t) REVERT: B 222 TYR cc_start: 0.7118 (m-80) cc_final: 0.6904 (m-10) REVERT: B 305 GLN cc_start: 0.8057 (mt0) cc_final: 0.7697 (tm-30) REVERT: B 362 ARG cc_start: 0.8882 (ppt170) cc_final: 0.8480 (ptt-90) REVERT: B 446 SER cc_start: 0.6705 (t) cc_final: 0.6144 (p) REVERT: B 463 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7692 (t0) REVERT: B 490 MET cc_start: 0.7196 (tpt) cc_final: 0.6225 (mtt) REVERT: B 496 MET cc_start: 0.6442 (ttp) cc_final: 0.6167 (tpp) REVERT: B 521 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.6632 (t-90) REVERT: B 553 MET cc_start: 0.8303 (mmm) cc_final: 0.7848 (tpp) REVERT: B 593 ARG cc_start: 0.8002 (mpt-90) cc_final: 0.7774 (tpp80) REVERT: B 595 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7503 (mm-40) REVERT: C 40 GLN cc_start: 0.8333 (tt0) cc_final: 0.8045 (tt0) REVERT: C 144 SER cc_start: 0.9200 (p) cc_final: 0.8742 (t) REVERT: C 175 SER cc_start: 0.7833 (t) cc_final: 0.7505 (p) REVERT: C 214 GLN cc_start: 0.7663 (tt0) cc_final: 0.7432 (tm-30) REVERT: C 215 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6613 (ttt) REVERT: C 222 TYR cc_start: 0.7175 (m-80) cc_final: 0.6887 (m-10) REVERT: C 305 GLN cc_start: 0.7917 (tt0) cc_final: 0.7299 (tm-30) REVERT: C 490 MET cc_start: 0.6973 (tpt) cc_final: 0.6146 (mtt) REVERT: C 496 MET cc_start: 0.6434 (ttp) cc_final: 0.6181 (tpp) REVERT: C 553 MET cc_start: 0.7900 (mmm) cc_final: 0.7589 (tpp) REVERT: C 571 ASN cc_start: 0.6927 (m-40) cc_final: 0.6701 (m-40) REVERT: C 576 MET cc_start: 0.7474 (mmt) cc_final: 0.7226 (mmm) REVERT: C 593 ARG cc_start: 0.8042 (mpt-90) cc_final: 0.7795 (tpp80) REVERT: D 144 SER cc_start: 0.9295 (p) cc_final: 0.8853 (t) REVERT: D 189 ILE cc_start: 0.8440 (mm) cc_final: 0.8207 (mm) REVERT: D 222 TYR cc_start: 0.7335 (m-80) cc_final: 0.6896 (m-10) REVERT: D 305 GLN cc_start: 0.8032 (mt0) cc_final: 0.7685 (tm-30) REVERT: D 308 ASP cc_start: 0.8512 (t0) cc_final: 0.7889 (m-30) REVERT: D 446 SER cc_start: 0.6518 (OUTLIER) cc_final: 0.5866 (p) REVERT: D 465 MET cc_start: 0.8511 (mmm) cc_final: 0.8205 (mmt) REVERT: D 480 MET cc_start: 0.7562 (mtm) cc_final: 0.7171 (mmt) REVERT: D 553 MET cc_start: 0.7988 (mmm) cc_final: 0.7771 (mmm) outliers start: 63 outliers final: 48 residues processed: 441 average time/residue: 0.2872 time to fit residues: 195.9016 Evaluate side-chains 443 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 390 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 634 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 79 optimal weight: 0.0010 chunk 195 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 463 ASN B 581 HIS ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120271 restraints weight = 32648.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.122358 restraints weight = 22788.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123545 restraints weight = 18040.790| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.6907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19788 Z= 0.194 Angle : 0.781 17.742 26868 Z= 0.358 Chirality : 0.046 0.489 3056 Planarity : 0.003 0.033 3396 Dihedral : 4.775 45.780 2637 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.15 % Allowed : 26.39 % Favored : 70.46 % 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: -1.12 (0.17), residues: 2396 helix: 0.44 (0.14), residues: 1404 sheet: -0.52 (0.48), residues: 64 loop : -2.69 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 29 HIS 0.003 0.001 HIS A 201 PHE 0.044 0.001 PHE D 492 TYR 0.016 0.001 TYR A 554 ARG 0.003 0.000 ARG D 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4349.93 seconds wall clock time: 79 minutes 39.70 seconds (4779.70 seconds total)